Starting phenix.real_space_refine on Sun Jun 29 04:29:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bk9_16093/06_2025/8bk9_16093.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bk9_16093/06_2025/8bk9_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/cci-nas-00/data/ceres_data/8bk9_16093/06_2025/8bk9_16093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bk9_16093/06_2025/8bk9_16093.map" model { file = "/net/cci-nas-00/data/ceres_data/8bk9_16093/06_2025/8bk9_16093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bk9_16093/06_2025/8bk9_16093.cif" } 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. Time to flip 85 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 21.84, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.03 Conformation dependent library (CDL) restraints added in 4.3 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: 2.85 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: 11.63 Time building geometry restraints manager: 10.62 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: 0.00 - 1.67: 45594 1.67 - 3.34: 597 3.34 - 5.01: 147 5.01 - 6.68: 54 6.68 - 8.36: 24 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 3.040 nonbonded pdb=" O ALA I 163 " pdb=" O HOH I 201 " model vdw 2.222 3.040 nonbonded pdb=" O ALA D 163 " pdb=" O HOH D 301 " model vdw 2.222 3.040 nonbonded pdb=" O ALA C 163 " pdb=" O HOH C 301 " model vdw 2.222 3.040 nonbonded pdb=" O ALA J 163 " pdb=" O HOH J 201 " model vdw 2.222 3.040 ... (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 Time spend for trying shortcut: 0.07 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: 3.430 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: 1.450 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 76.180 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.250 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:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.260 ------------------------------------------------------------------------------- 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= 0.155 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 Details of bonding type rmsd hydrogen bonds : bond 0.08042 ( 2616) hydrogen bonds : angle 3.75047 ( 7848) covalent geometry : bond 0.00326 (34512) covalent geometry : angle 0.60609 (46416) *********************** 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 to be fit. rotamer outliers: 18 poor density : 746 time to evaluate : 5.778 Fit side-chains outliers start: 18 outliers final: 0 residues processed: 758 average time/residue: 2.5217 time to fit residues: 2146.7271 Evaluate side-chains 725 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 725 time to evaluate : 5.821 ------------------------------------------------------------------------------- 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: 8.9990 chunk 309 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 238 optimal weight: 8.9990 chunk 370 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.135817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.129203 restraints weight = 29065.027| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 0.50 r_work: 0.3327 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work: 0.2979 rms_B_bonded: 4.66 restraints_weight: 0.1250 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 34512 Z= 0.113 Angle : 0.482 5.776 46416 Z= 0.260 Chirality : 0.034 0.112 4848 Planarity : 0.003 0.021 6096 Dihedral : 3.834 20.174 4512 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.96 % Allowed : 8.44 % 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: 5.45 (0.13), residues: 4080 helix: 4.18 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : 1.10 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 93 HIS 0.002 0.001 HIS A 128 PHE 0.013 0.002 PHE C 41 TYR 0.012 0.001 TYR V 137 ARG 0.001 0.000 ARG G 63 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 2616) hydrogen bonds : angle 3.27719 ( 7848) covalent geometry : bond 0.00237 (34512) covalent geometry : angle 0.48206 (46416) *********************** 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 795 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 760 time to evaluate : 4.019 Fit side-chains outliers start: 35 outliers final: 0 residues processed: 768 average time/residue: 2.3796 time to fit residues: 2054.8073 Evaluate side-chains 711 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 711 time to evaluate : 6.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 195 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 355 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 344 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 319 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 chunk 295 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 60 HIS E 83 GLN F 60 HIS F 83 GLN G 60 HIS 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: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127461 restraints weight = 28895.723| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 0.51 r_work: 0.3301 rms_B_bonded: 0.83 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work: 0.2951 rms_B_bonded: 4.65 restraints_weight: 0.1250 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0577 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= 0.135 Angle : 0.519 5.824 46416 Z= 0.282 Chirality : 0.035 0.115 4848 Planarity : 0.003 0.020 6096 Dihedral : 3.882 20.181 4512 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: 5.46 (0.13), residues: 4080 helix: 4.19 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : 1.07 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP N 93 HIS 0.003 0.001 HIS R 128 PHE 0.015 0.002 PHE C 41 TYR 0.013 0.002 TYR T 137 ARG 0.002 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.05110 ( 2616) hydrogen bonds : angle 3.37779 ( 7848) covalent geometry : bond 0.00290 (34512) covalent geometry : angle 0.51893 (46416) *********************** 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 758 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 740 time to evaluate : 4.095 Fit side-chains REVERT: A 62 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: C 62 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8424 (mp0) REVERT: D 62 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8433 (mp0) REVERT: F 62 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: H 62 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: I 62 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8419 (mp0) REVERT: J 62 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: K 62 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8458 (mp0) REVERT: L 62 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: M 62 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8435 (mp0) REVERT: Q 62 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8363 (mp0) outliers start: 18 outliers final: 0 residues processed: 744 average time/residue: 2.5924 time to fit residues: 2167.8510 Evaluate side-chains 737 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 726 time to evaluate : 4.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain Q residue 62 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 97 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 311 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 354 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.136219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.129632 restraints weight = 29138.101| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 0.50 r_work: 0.3332 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work: 0.2987 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0632 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= 0.109 Angle : 0.471 5.366 46416 Z= 0.255 Chirality : 0.033 0.113 4848 Planarity : 0.003 0.018 6096 Dihedral : 3.762 20.076 4512 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.25 % Allowed : 9.87 % Favored : 89.88 % 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: 5.69 (0.13), residues: 4080 helix: 4.35 (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 N 93 HIS 0.002 0.001 HIS H 128 PHE 0.013 0.002 PHE M 41 TYR 0.011 0.001 TYR B 137 ARG 0.002 0.000 ARG J 63 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 2616) hydrogen bonds : angle 3.21066 ( 7848) covalent geometry : bond 0.00229 (34512) covalent geometry : angle 0.47150 (46416) *********************** 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 756 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 747 time to evaluate : 3.928 Fit side-chains REVERT: A 62 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: D 62 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8453 (mp0) REVERT: F 62 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: H 62 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: J 62 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8441 (mp0) REVERT: K 62 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: M 62 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8456 (mp0) outliers start: 9 outliers final: 0 residues processed: 747 average time/residue: 2.5733 time to fit residues: 2174.0750 Evaluate side-chains 697 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 690 time to evaluate : 3.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain M residue 62 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 63 optimal weight: 0.0870 chunk 114 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 402 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 228 optimal weight: 1.9990 chunk 335 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 369 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 overall best weight: 3.2166 ------------------------------------------------------------------------------- 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 60 HIS D 83 GLN E 60 HIS E 83 GLN F 60 HIS F 83 GLN G 60 HIS 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: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126888 restraints weight = 28973.605| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 0.50 r_work: 0.3295 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work: 0.2942 rms_B_bonded: 4.65 restraints_weight: 0.1250 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34512 Z= 0.152 Angle : 0.545 5.941 46416 Z= 0.296 Chirality : 0.036 0.116 4848 Planarity : 0.004 0.023 6096 Dihedral : 3.906 19.918 4512 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.01 % Allowed : 9.13 % Favored : 89.86 % 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: 5.38 (0.13), residues: 4080 helix: 4.11 (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 0.004 0.001 HIS J 128 PHE 0.018 0.003 PHE C 41 TYR 0.014 0.002 TYR H 137 ARG 0.002 0.000 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.05384 ( 2616) hydrogen bonds : angle 3.44069 ( 7848) covalent geometry : bond 0.00331 (34512) covalent geometry : angle 0.54479 (46416) *********************** 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 760 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 723 time to evaluate : 3.873 Fit side-chains REVERT: A 62 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: C 62 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: D 62 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: F 62 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: H 62 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: I 62 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8436 (mp0) REVERT: J 62 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8437 (mp0) REVERT: K 62 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: L 62 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: M 62 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8448 (mp0) outliers start: 37 outliers final: 0 residues processed: 723 average time/residue: 2.5133 time to fit residues: 2038.7831 Evaluate side-chains 703 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 693 time to evaluate : 4.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain M residue 62 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 57 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 260 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 396 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126877 restraints weight = 28922.924| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 0.51 r_work: 0.3294 rms_B_bonded: 0.83 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 1.55 restraints_weight: 0.2500 r_work: 0.2943 rms_B_bonded: 4.66 restraints_weight: 0.1250 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.0644 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= 0.146 Angle : 0.538 5.971 46416 Z= 0.292 Chirality : 0.035 0.116 4848 Planarity : 0.003 0.025 6096 Dihedral : 3.909 19.973 4512 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.36 % Allowed : 9.13 % Favored : 90.52 % 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: 5.33 (0.13), residues: 4080 helix: 4.07 (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 0.009 0.002 TRP X 93 HIS 0.004 0.001 HIS A 128 PHE 0.019 0.003 PHE O 41 TYR 0.014 0.002 TYR L 137 ARG 0.002 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.05248 ( 2616) hydrogen bonds : angle 3.41099 ( 7848) covalent geometry : bond 0.00317 (34512) covalent geometry : angle 0.53763 (46416) *********************** 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 726 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 713 time to evaluate : 3.939 Fit side-chains REVERT: A 62 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8429 (mp0) REVERT: C 62 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: D 62 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8437 (mp0) REVERT: F 62 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: H 62 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8435 (mp0) REVERT: I 62 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: J 62 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: K 62 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8428 (mp0) REVERT: L 62 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8419 (mp0) REVERT: M 62 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8434 (mp0) outliers start: 13 outliers final: 0 residues processed: 713 average time/residue: 2.4929 time to fit residues: 1992.6424 Evaluate side-chains 713 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 703 time to evaluate : 4.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain M residue 62 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 223 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 305 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.132219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125681 restraints weight = 29003.741| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 0.49 r_work: 0.3281 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work: 0.2931 rms_B_bonded: 4.59 restraints_weight: 0.1250 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0686 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= 0.183 Angle : 0.593 6.245 46416 Z= 0.322 Chirality : 0.037 0.123 4848 Planarity : 0.004 0.027 6096 Dihedral : 3.991 19.701 4512 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.01 % Allowed : 9.13 % Favored : 89.86 % 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: 5.00 (0.13), residues: 4080 helix: 3.84 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.07 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 93 HIS 0.004 0.001 HIS A 128 PHE 0.022 0.003 PHE Y 41 TYR 0.015 0.002 TYR B 137 ARG 0.002 0.000 ARG G 63 Details of bonding type rmsd hydrogen bonds : bond 0.05786 ( 2616) hydrogen bonds : angle 3.53514 ( 7848) covalent geometry : bond 0.00404 (34512) covalent geometry : angle 0.59346 (46416) *********************** 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 756 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 719 time to evaluate : 4.448 Fit side-chains outliers start: 37 outliers final: 0 residues processed: 719 average time/residue: 2.4390 time to fit residues: 1968.7573 Evaluate side-chains 698 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 698 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 247 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 395 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 328 optimal weight: 1.9990 chunk 320 optimal weight: 6.9990 chunk 240 optimal weight: 9.9990 chunk 197 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128812 restraints weight = 29213.581| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 0.50 r_work: 0.3321 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work: 0.2975 rms_B_bonded: 4.64 restraints_weight: 0.1250 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34512 Z= 0.116 Angle : 0.502 5.566 46416 Z= 0.272 Chirality : 0.034 0.113 4848 Planarity : 0.003 0.017 6096 Dihedral : 3.827 20.313 4512 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.22 % Allowed : 9.38 % Favored : 90.41 % 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: 5.56 (0.13), residues: 4080 helix: 4.25 (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 0.010 0.002 TRP P 93 HIS 0.002 0.001 HIS T 128 PHE 0.014 0.002 PHE M 41 TYR 0.012 0.001 TYR V 137 ARG 0.001 0.000 ARG M 90 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 2616) hydrogen bonds : angle 3.26714 ( 7848) covalent geometry : bond 0.00249 (34512) covalent geometry : angle 0.50236 (46416) *********************** 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 718 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 710 time to evaluate : 3.995 Fit side-chains REVERT: E 62 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8426 (mm-30) REVERT: G 62 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8416 (mm-30) outliers start: 8 outliers final: 0 residues processed: 710 average time/residue: 2.4536 time to fit residues: 1960.5593 Evaluate side-chains 674 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 674 time to evaluate : 4.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 107 optimal weight: 1.9990 chunk 302 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 399 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 219 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.129604 restraints weight = 29453.877| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 0.50 r_work: 0.3331 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 1.54 restraints_weight: 0.2500 r_work: 0.2982 rms_B_bonded: 4.68 restraints_weight: 0.1250 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34512 Z= 0.112 Angle : 0.492 5.386 46416 Z= 0.267 Chirality : 0.034 0.113 4848 Planarity : 0.003 0.017 6096 Dihedral : 3.764 20.075 4512 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % 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: 5.58 (0.13), residues: 4080 helix: 4.26 (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 0.010 0.002 TRP P 93 HIS 0.002 0.001 HIS A 128 PHE 0.013 0.002 PHE D 41 TYR 0.011 0.001 TYR V 137 ARG 0.003 0.000 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 2616) hydrogen bonds : angle 3.24177 ( 7848) covalent geometry : bond 0.00239 (34512) covalent geometry : angle 0.49192 (46416) *********************** 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 698 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 698 time to evaluate : 5.184 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 698 average time/residue: 2.7060 time to fit residues: 2124.8484 Evaluate side-chains 673 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 673 time to evaluate : 4.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 281 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 312 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 342 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 329 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.127605 restraints weight = 29084.390| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 0.50 r_work: 0.3304 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work: 0.2953 rms_B_bonded: 4.65 restraints_weight: 0.1250 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34512 Z= 0.137 Angle : 0.536 5.790 46416 Z= 0.291 Chirality : 0.035 0.114 4848 Planarity : 0.003 0.020 6096 Dihedral : 3.881 20.434 4512 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % 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: 5.39 (0.13), residues: 4080 helix: 4.12 (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 H 93 HIS 0.004 0.001 HIS O 128 PHE 0.016 0.002 PHE Y 41 TYR 0.013 0.002 TYR I 137 ARG 0.003 0.000 ARG H 63 Details of bonding type rmsd hydrogen bonds : bond 0.05121 ( 2616) hydrogen bonds : angle 3.37366 ( 7848) covalent geometry : bond 0.00295 (34512) covalent geometry : angle 0.53630 (46416) ********************** 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 697 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 697 time to evaluate : 5.015 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 697 average time/residue: 2.5582 time to fit residues: 2004.0865 Evaluate side-chains 675 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 675 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 324 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 321 optimal weight: 3.9990 chunk 269 optimal weight: 8.9990 chunk 252 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 366 optimal weight: 8.9990 chunk 242 optimal weight: 0.9990 chunk 401 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.136432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.129857 restraints weight = 29376.593| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 0.50 r_work: 0.3335 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work: 0.2991 rms_B_bonded: 4.61 restraints_weight: 0.1250 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34512 Z= 0.111 Angle : 0.493 5.343 46416 Z= 0.267 Chirality : 0.034 0.113 4848 Planarity : 0.003 0.016 6096 Dihedral : 3.758 20.070 4512 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % 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: 5.56 (0.13), residues: 4080 helix: 4.24 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.22 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 93 HIS 0.002 0.001 HIS L 128 PHE 0.013 0.002 PHE K 41 TYR 0.011 0.001 TYR V 137 ARG 0.003 0.000 ARG H 63 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 2616) hydrogen bonds : angle 3.21416 ( 7848) covalent geometry : bond 0.00236 (34512) covalent geometry : angle 0.49296 (46416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 48102.41 seconds wall clock time: 837 minutes 51.37 seconds (50271.37 seconds total)