Starting phenix.real_space_refine on Mon Jul 6 02:08:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pkf_13470/07_2026/7pkf_13470.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pkf_13470/07_2026/7pkf_13470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pkf_13470/07_2026/7pkf_13470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pkf_13470/07_2026/7pkf_13470.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7pkf_13470/07_2026/7pkf_13470.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pkf_13470/07_2026/7pkf_13470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pkf_13470/07_2026/7pkf_13470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pkf_13470/07_2026/7pkf_13470.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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: 6 Type Number sf(0) Gaussians Ca 20 9.91 5 S 40 5.16 5 C 10580 2.51 5 N 2610 2.21 5 O 3100 1.98 5 H 15960 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32310 Number of models: 1 Model: "" Number of chains: 30 Chain: "J" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "F" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "G" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "H" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "I" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "E" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "D" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "B" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3226 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 5.44, per 1000 atoms: 0.17 Number of scatterers: 32310 At special positions: 0 Unit cell: (140.448, 131.252, 111.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 20 19.99 S 40 16.00 O 3100 8.00 N 2610 7.00 C 10580 6.00 H 15960 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS J 36 " - pdb=" SG CYS J 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 36 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 36 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 36 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 36 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.04 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " distance=2.03 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: 2.36 Conformation dependent library (CDL) restraints added in 850.1 milliseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 31 sheets defined 12.4% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'J' and resid 42 through 46 removed outlier: 4.051A pdb=" N SER J 45 " --> pdb=" O GLU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 151 Processing helix chain 'J' and resid 167 through 177 Processing helix chain 'J' and resid 186 through 190 removed outlier: 4.045A pdb=" N LEU J 190 " --> pdb=" O TRP J 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.821A pdb=" N SER F 45 " --> pdb=" O GLU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 151 Processing helix chain 'F' and resid 167 through 177 Processing helix chain 'F' and resid 186 through 190 removed outlier: 3.847A pdb=" N LEU F 190 " --> pdb=" O TRP F 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 46 removed outlier: 3.800A pdb=" N SER G 45 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 177 Processing helix chain 'G' and resid 186 through 190 removed outlier: 3.986A pdb=" N LEU G 190 " --> pdb=" O TRP G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 46 removed outlier: 3.583A pdb=" N SER H 45 " --> pdb=" O GLU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 151 Processing helix chain 'H' and resid 167 through 177 Processing helix chain 'H' and resid 186 through 190 removed outlier: 3.809A pdb=" N LEU H 190 " --> pdb=" O TRP H 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.682A pdb=" N SER I 45 " --> pdb=" O GLU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 176 Processing helix chain 'I' and resid 186 through 190 removed outlier: 3.803A pdb=" N LEU I 190 " --> pdb=" O TRP I 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 46 Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 177 Processing helix chain 'E' and resid 186 through 190 removed outlier: 3.776A pdb=" N LEU E 190 " --> pdb=" O TRP E 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.995A pdb=" N SER D 45 " --> pdb=" O GLU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 176 Processing helix chain 'D' and resid 186 through 190 removed outlier: 3.946A pdb=" N LEU D 190 " --> pdb=" O TRP D 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.854A pdb=" N SER C 45 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.624A pdb=" N LEU C 190 " --> pdb=" O TRP C 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.757A pdb=" N SER B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.825A pdb=" N LEU B 190 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.770A pdb=" N SER A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.936A pdb=" N LEU A 190 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 114 through 115 Processing sheet with id=AA2, first strand: chain 'J' and resid 114 through 115 removed outlier: 3.508A pdb=" N ILE J 106 " --> pdb=" O GLU J 101 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR J 34 " --> pdb=" O MET J 161 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET J 161 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS J 36 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL J 159 " --> pdb=" O CYS J 36 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN J 158 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N LYS J 7 " --> pdb=" O ASN J 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 80 through 85 removed outlier: 6.518A pdb=" N TRP J 67 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N SER J 50 " --> pdb=" O TRP J 67 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE J 133 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'F' and resid 114 through 115 removed outlier: 6.541A pdb=" N THR F 34 " --> pdb=" O MET F 161 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET F 161 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYS F 36 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL F 159 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN F 158 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N LYS F 7 " --> pdb=" O ASN F 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 85 removed outlier: 3.507A pdb=" N TYR F 73 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN F 61 " --> pdb=" O THR F 56 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR F 56 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP F 67 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER F 50 " --> pdb=" O TRP F 67 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE F 133 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 139 through 141 removed outlier: 7.462A pdb=" N GLN F 139 " --> pdb=" O PHE F 146 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE F 146 " --> pdb=" O GLN F 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 114 through 115 Processing sheet with id=AA9, first strand: chain 'G' and resid 114 through 115 removed outlier: 3.766A pdb=" N ILE G 106 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR G 34 " --> pdb=" O MET G 161 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET G 161 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS G 36 " --> pdb=" O VAL G 159 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL G 159 " --> pdb=" O CYS G 36 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN G 158 " --> pdb=" O LYS G 7 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N LYS G 7 " --> pdb=" O ASN G 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 80 through 85 removed outlier: 3.680A pdb=" N TYR G 73 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASN G 61 " --> pdb=" O THR G 56 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR G 56 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP G 67 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N SER G 50 " --> pdb=" O TRP G 67 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE G 133 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 114 through 115 Processing sheet with id=AB3, first strand: chain 'H' and resid 114 through 115 removed outlier: 3.631A pdb=" N ILE H 106 " --> pdb=" O GLU H 101 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR H 34 " --> pdb=" O MET H 161 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET H 161 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS H 36 " --> pdb=" O VAL H 159 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL H 159 " --> pdb=" O CYS H 36 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN H 158 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N LYS H 7 " --> pdb=" O ASN H 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 80 through 85 removed outlier: 3.556A pdb=" N TYR H 73 " --> pdb=" O PHE H 84 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASN H 61 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR H 56 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 67 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N SER H 50 " --> pdb=" O TRP H 67 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE H 133 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 114 through 115 Processing sheet with id=AB6, first strand: chain 'I' and resid 114 through 115 removed outlier: 3.602A pdb=" N ILE I 106 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N HIS I 38 " --> pdb=" O ASN I 158 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN I 158 " --> pdb=" O HIS I 38 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR I 40 " --> pdb=" O ILE I 156 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE I 156 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASN I 158 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LYS I 7 " --> pdb=" O ASN I 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 80 through 85 removed outlier: 6.511A pdb=" N TRP I 67 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N SER I 50 " --> pdb=" O TRP I 67 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE I 133 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AB9, first strand: chain 'E' and resid 114 through 115 removed outlier: 3.605A pdb=" N ILE E 106 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR E 34 " --> pdb=" O MET E 161 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N MET E 161 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS E 36 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL E 159 " --> pdb=" O CYS E 36 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN E 158 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N LYS E 7 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 80 through 85 removed outlier: 3.552A pdb=" N TYR E 73 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN E 61 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR E 56 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP E 67 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER E 50 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AC3, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.646A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR D 34 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET D 161 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS D 36 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL D 159 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 80 through 85 removed outlier: 6.036A pdb=" N ASN D 61 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR D 56 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP D 67 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N SER D 50 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS D 191 " --> pdb=" O LYS D 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AC6, first strand: chain 'C' and resid 114 through 115 removed outlier: 3.594A pdb=" N ILE C 106 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR C 34 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET C 161 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N CYS C 36 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL C 159 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN C 158 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N LYS C 7 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.125A pdb=" N ASN C 61 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR C 56 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP C 67 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER C 50 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AC9, first strand: chain 'B' and resid 114 through 115 removed outlier: 3.569A pdb=" N ILE B 106 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR B 34 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N MET B 161 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS B 36 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL B 159 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 80 through 85 removed outlier: 3.562A pdb=" N TYR B 73 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN B 61 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR B 54 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE B 63 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE B 52 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE B 65 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER B 50 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AD3, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.627A pdb=" N ILE A 106 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR A 34 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 161 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N CYS A 36 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 159 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 10.160A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 80 through 85 removed outlier: 6.497A pdb=" N TRP A 67 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER A 50 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.22 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15960 1.03 - 1.22: 2 1.22 - 1.42: 7288 1.42 - 1.62: 9430 1.62 - 1.81: 60 Bond restraints: 32740 Sorted by residual: bond pdb=" CB PHE F 109 " pdb=" CG PHE F 109 " ideal model delta sigma weight residual 1.502 1.437 0.065 2.30e-02 1.89e+03 7.88e+00 bond pdb=" CD1 PHE F 109 " pdb=" CE1 PHE F 109 " ideal model delta sigma weight residual 1.382 1.328 0.054 3.00e-02 1.11e+03 3.27e+00 bond pdb=" CE1 PHE F 109 " pdb=" CZ PHE F 109 " ideal model delta sigma weight residual 1.382 1.330 0.052 3.00e-02 1.11e+03 2.99e+00 bond pdb=" CG PHE F 109 " pdb=" CD2 PHE F 109 " ideal model delta sigma weight residual 1.384 1.352 0.032 2.10e-02 2.27e+03 2.39e+00 bond pdb=" CB PRO E 25 " pdb=" CG PRO E 25 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.84e+00 ... (remaining 32735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 58961 5.95 - 11.91: 62 11.91 - 17.86: 4 17.86 - 23.81: 15 23.81 - 29.77: 68 Bond angle restraints: 59110 Sorted by residual: angle pdb=" CG GLU J 147 " pdb=" CB GLU J 147 " pdb=" HB3 GLU J 147 " ideal model delta sigma weight residual 108.00 78.23 29.77 3.00e+00 1.11e-01 9.85e+01 angle pdb=" CG GLU J 147 " pdb=" CB GLU J 147 " pdb=" HB2 GLU J 147 " ideal model delta sigma weight residual 108.00 78.26 29.74 3.00e+00 1.11e-01 9.82e+01 angle pdb=" CG2 THR A 46 " pdb=" CB THR A 46 " pdb=" HB THR A 46 " ideal model delta sigma weight residual 108.00 79.19 28.81 3.00e+00 1.11e-01 9.22e+01 angle pdb=" OG1 THR A 46 " pdb=" CB THR A 46 " pdb=" HB THR A 46 " ideal model delta sigma weight residual 109.00 81.16 27.84 3.00e+00 1.11e-01 8.61e+01 angle pdb=" CA GLU J 147 " pdb=" CB GLU J 147 " pdb=" HB3 GLU J 147 " ideal model delta sigma weight residual 109.00 81.35 27.65 3.00e+00 1.11e-01 8.50e+01 ... (remaining 59105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14102 17.89 - 35.79: 924 35.79 - 53.68: 290 53.68 - 71.57: 228 71.57 - 89.46: 26 Dihedral angle restraints: 15570 sinusoidal: 8200 harmonic: 7370 Sorted by residual: dihedral pdb=" CA ASP I 140 " pdb=" C ASP I 140 " pdb=" N SER I 141 " pdb=" CA SER I 141 " ideal model delta harmonic sigma weight residual 180.00 152.41 27.59 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA ASP H 140 " pdb=" C ASP H 140 " pdb=" N SER H 141 " pdb=" CA SER H 141 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLU E 62 " pdb=" C GLU E 62 " pdb=" N ILE E 63 " pdb=" CA ILE E 63 " ideal model delta harmonic sigma weight residual 180.00 152.93 27.07 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 15567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.412: 2444 0.412 - 0.825: 0 0.825 - 1.237: 2 1.237 - 1.650: 19 1.650 - 2.062: 5 Chirality restraints: 2470 Sorted by residual: chirality pdb=" CG LEU D 83 " pdb=" CB LEU D 83 " pdb=" CD1 LEU D 83 " pdb=" CD2 LEU D 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.53 -2.06 2.00e-01 2.50e+01 1.06e+02 chirality pdb=" CG LEU A 83 " pdb=" CB LEU A 83 " pdb=" CD1 LEU A 83 " pdb=" CD2 LEU A 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.52e+01 chirality pdb=" CG LEU I 83 " pdb=" CB LEU I 83 " pdb=" CD1 LEU I 83 " pdb=" CD2 LEU I 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.37e+01 ... (remaining 2467 not shown) Planarity restraints: 4840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G 38 " -0.011 2.00e-02 2.50e+03 4.06e-02 4.12e+01 pdb=" CG HIS G 38 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS G 38 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 HIS G 38 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 HIS G 38 " 0.027 2.00e-02 2.50e+03 pdb=" NE2 HIS G 38 " 0.025 2.00e-02 2.50e+03 pdb=" HD1 HIS G 38 " -0.072 2.00e-02 2.50e+03 pdb=" HD2 HIS G 38 " -0.054 2.00e-02 2.50e+03 pdb=" HE1 HIS G 38 " -0.022 2.00e-02 2.50e+03 pdb=" HE2 HIS G 38 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 38 " 0.010 2.00e-02 2.50e+03 3.88e-02 3.76e+01 pdb=" CG HIS F 38 " -0.035 2.00e-02 2.50e+03 pdb=" ND1 HIS F 38 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 HIS F 38 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 HIS F 38 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS F 38 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS F 38 " 0.068 2.00e-02 2.50e+03 pdb=" HD2 HIS F 38 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 HIS F 38 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 HIS F 38 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 38 " -0.011 2.00e-02 2.50e+03 3.76e-02 3.53e+01 pdb=" CG HIS D 38 " 0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS D 38 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 HIS D 38 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS D 38 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS D 38 " 0.022 2.00e-02 2.50e+03 pdb=" HD1 HIS D 38 " -0.067 2.00e-02 2.50e+03 pdb=" HD2 HIS D 38 " -0.049 2.00e-02 2.50e+03 pdb=" HE1 HIS D 38 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 HIS D 38 " -0.020 2.00e-02 2.50e+03 ... (remaining 4837 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1261 2.13 - 2.75: 58974 2.75 - 3.37: 92737 3.37 - 3.98: 128567 3.98 - 4.60: 197830 Nonbonded interactions: 479369 Sorted by model distance: nonbonded pdb=" OD1 ASP F 3 " pdb=" HG SER F 5 " model vdw 1.513 2.450 nonbonded pdb=" OD1 ASP E 3 " pdb=" HG SER E 5 " model vdw 1.533 2.450 nonbonded pdb=" OD1 ASP A 3 " pdb=" HG SER A 5 " model vdw 1.536 2.450 nonbonded pdb=" H SER D 167 " pdb=" OE1 GLU D 170 " model vdw 1.548 2.450 nonbonded pdb=" HG SER F 74 " pdb=" OE2 GLU F 81 " model vdw 1.562 2.450 ... (remaining 479364 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 3.780 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: 0.230 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.710 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 : 0.004 0.068 16790 Z= 0.167 Angle : 0.903 14.670 22830 Z= 0.496 Chirality : 0.160 2.062 2470 Planarity : 0.006 0.124 2900 Dihedral : 13.325 89.463 5980 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.18), residues: 2040 helix: -0.96 (0.40), residues: 100 sheet: -0.13 (0.17), residues: 830 loop : -0.57 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.009 ARG A 118 TYR 0.026 0.005 TYR E 54 PHE 0.048 0.003 PHE F 84 TRP 0.032 0.006 TRP E 205 HIS 0.042 0.006 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (16780) covalent geometry : angle 0.90092 / 0.50 (22810) SS BOND : bond 0.00302 / 0.15 ( 10) SS BOND : angle 2.02198 / 1.29 ( 20) hydrogen bonds : bond 0.19371 / 12.73 ( 664) hydrogen bonds : angle 8.07814 / 5.51 ( 1638) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: H 193 GLU cc_start: 0.7342 (tt0) cc_final: 0.7123 (tt0) REVERT: I 88 GLU cc_start: 0.7100 (pp20) cc_final: 0.6846 (pm20) REVERT: D 4 MET cc_start: 0.8484 (mmm) cc_final: 0.8220 (mmm) REVERT: C 81 GLU cc_start: 0.7828 (tt0) cc_final: 0.7565 (tt0) REVERT: C 91 VAL cc_start: 0.8276 (t) cc_final: 0.8010 (m) outliers start: 0 outliers final: 1 residues processed: 223 average time/residue: 1.3306 time to fit residues: 327.7400 Evaluate side-chains 148 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 172 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 95 HIS E 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.097682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.078260 restraints weight = 65090.071| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.85 r_work: 0.2691 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 16790 Z= 0.285 Angle : 0.838 15.952 22830 Z= 0.442 Chirality : 0.162 1.774 2470 Planarity : 0.005 0.074 2900 Dihedral : 6.752 41.909 2202 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.06 % Allowed : 5.94 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.17), residues: 2040 helix: 1.02 (0.40), residues: 110 sheet: 0.18 (0.16), residues: 890 loop : -0.81 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 58 TYR 0.027 0.002 TYR A 54 PHE 0.019 0.002 PHE E 52 TRP 0.014 0.002 TRP E 110 HIS 0.012 0.003 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.28 (16780) covalent geometry : angle 0.83777 / 0.44 (22810) SS BOND : bond 0.00449 / 0.23 ( 10) SS BOND : angle 0.65762 / 0.41 ( 20) hydrogen bonds : bond 0.05613 / 3.68 ( 664) hydrogen bonds : angle 6.35944 / 4.32 ( 1638) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.905 Fit side-chains REVERT: J 193 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: F 81 GLU cc_start: 0.8560 (tt0) cc_final: 0.8315 (tt0) REVERT: G 193 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: H 193 GLU cc_start: 0.7969 (tt0) cc_final: 0.7674 (tt0) REVERT: I 88 GLU cc_start: 0.7303 (pp20) cc_final: 0.6900 (pm20) REVERT: I 155 ASP cc_start: 0.8777 (m-30) cc_final: 0.8459 (m-30) REVERT: I 197 GLU cc_start: 0.7628 (tt0) cc_final: 0.7113 (tt0) REVERT: E 138 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: E 163 ASP cc_start: 0.8730 (p0) cc_final: 0.8441 (p0) REVERT: D 4 MET cc_start: 0.8792 (mmm) cc_final: 0.8502 (mmm) REVERT: C 91 VAL cc_start: 0.8448 (t) cc_final: 0.8224 (p) outliers start: 19 outliers final: 9 residues processed: 172 average time/residue: 1.3611 time to fit residues: 258.4341 Evaluate side-chains 157 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 82 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 149 optimal weight: 0.3980 chunk 173 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 128 optimal weight: 0.0770 chunk 93 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.100287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.082201 restraints weight = 64837.246| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.68 r_work: 0.2761 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16790 Z= 0.141 Angle : 0.752 15.726 22830 Z= 0.389 Chirality : 0.161 1.733 2470 Planarity : 0.004 0.069 2900 Dihedral : 5.942 41.687 2202 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.22 % Allowed : 6.89 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.18), residues: 2040 helix: 2.07 (0.44), residues: 110 sheet: 0.18 (0.16), residues: 890 loop : -0.71 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 58 TYR 0.020 0.001 TYR J 54 PHE 0.012 0.001 PHE E 52 TRP 0.010 0.001 TRP E 110 HIS 0.008 0.002 HIS I 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (16780) covalent geometry : angle 0.75226 / 0.39 (22810) SS BOND : bond 0.00080 / 0.04 ( 10) SS BOND : angle 0.40125 / 0.24 ( 20) hydrogen bonds : bond 0.04389 / 2.87 ( 664) hydrogen bonds : angle 5.79763 / 3.94 ( 1638) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: J 193 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7437 (tp30) REVERT: F 88 GLU cc_start: 0.8065 (pp20) cc_final: 0.7271 (mm-30) REVERT: F 197 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: H 193 GLU cc_start: 0.7915 (tt0) cc_final: 0.7666 (tt0) REVERT: I 13 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8211 (mtmm) REVERT: I 88 GLU cc_start: 0.7302 (pp20) cc_final: 0.6865 (pm20) REVERT: I 155 ASP cc_start: 0.8643 (m-30) cc_final: 0.8299 (m-30) REVERT: I 197 GLU cc_start: 0.7624 (tt0) cc_final: 0.7192 (tt0) REVERT: E 138 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: C 91 VAL cc_start: 0.8508 (t) cc_final: 0.8290 (p) REVERT: B 108 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8108 (mt-10) outliers start: 22 outliers final: 11 residues processed: 175 average time/residue: 1.2982 time to fit residues: 251.3862 Evaluate side-chains 159 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain A residue 46 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.097594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.078160 restraints weight = 64590.963| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.86 r_work: 0.2697 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16790 Z= 0.182 Angle : 0.754 15.755 22830 Z= 0.390 Chirality : 0.161 1.726 2470 Planarity : 0.004 0.076 2900 Dihedral : 5.794 40.843 2202 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.22 % Allowed : 8.50 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.18), residues: 2040 helix: 2.24 (0.46), residues: 110 sheet: 0.16 (0.16), residues: 890 loop : -0.79 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 58 TYR 0.023 0.002 TYR J 54 PHE 0.014 0.001 PHE E 52 TRP 0.008 0.001 TRP E 110 HIS 0.009 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (16780) covalent geometry : angle 0.75425 / 0.39 (22810) SS BOND : bond 0.00161 / 0.08 ( 10) SS BOND : angle 0.47873 / 0.30 ( 20) hydrogen bonds : bond 0.04256 / 2.78 ( 664) hydrogen bonds : angle 5.69152 / 3.87 ( 1638) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.941 Fit side-chains REVERT: F 197 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: G 147 GLU cc_start: 0.7579 (mt-10) cc_final: 0.6979 (mt-10) REVERT: H 193 GLU cc_start: 0.7931 (tt0) cc_final: 0.7642 (tt0) REVERT: I 13 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8215 (mtmm) REVERT: I 88 GLU cc_start: 0.7472 (pp20) cc_final: 0.6985 (pm20) REVERT: I 155 ASP cc_start: 0.8729 (m-30) cc_final: 0.8376 (m-30) REVERT: E 138 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: E 163 ASP cc_start: 0.8741 (p0) cc_final: 0.8473 (p0) REVERT: C 91 VAL cc_start: 0.8518 (t) cc_final: 0.8285 (p) REVERT: B 108 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8200 (mt-10) outliers start: 22 outliers final: 14 residues processed: 167 average time/residue: 1.2879 time to fit residues: 237.8848 Evaluate side-chains 161 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain A residue 46 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.077541 restraints weight = 64820.964| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.89 r_work: 0.2685 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16790 Z= 0.193 Angle : 0.755 15.731 22830 Z= 0.390 Chirality : 0.161 1.733 2470 Planarity : 0.004 0.077 2900 Dihedral : 5.726 41.122 2202 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.44 % Allowed : 8.94 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.18), residues: 2040 helix: 2.24 (0.47), residues: 110 sheet: 0.13 (0.16), residues: 890 loop : -0.86 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 58 TYR 0.023 0.002 TYR J 54 PHE 0.014 0.001 PHE E 52 TRP 0.008 0.001 TRP E 162 HIS 0.008 0.002 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (16780) covalent geometry : angle 0.75545 / 0.39 (22810) SS BOND : bond 0.00172 / 0.08 ( 10) SS BOND : angle 0.47500 / 0.30 ( 20) hydrogen bonds : bond 0.04189 / 2.74 ( 664) hydrogen bonds : angle 5.67621 / 3.86 ( 1638) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.770 Fit side-chains REVERT: J 193 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7408 (tp30) REVERT: F 88 GLU cc_start: 0.8068 (pp20) cc_final: 0.7199 (mm-30) REVERT: G 147 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6946 (mt-10) REVERT: H 193 GLU cc_start: 0.7965 (tt0) cc_final: 0.7635 (tt0) REVERT: I 13 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8211 (mtmm) REVERT: I 88 GLU cc_start: 0.7567 (pp20) cc_final: 0.7020 (pm20) REVERT: I 155 ASP cc_start: 0.8743 (m-30) cc_final: 0.8394 (m-30) REVERT: I 197 GLU cc_start: 0.7658 (tt0) cc_final: 0.7276 (tt0) REVERT: E 138 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: E 163 ASP cc_start: 0.8754 (p0) cc_final: 0.8502 (p0) REVERT: C 91 VAL cc_start: 0.8474 (t) cc_final: 0.8256 (p) REVERT: B 108 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8245 (mt-10) outliers start: 26 outliers final: 13 residues processed: 176 average time/residue: 1.2343 time to fit residues: 241.4368 Evaluate side-chains 161 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain A residue 46 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 121 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 70 optimal weight: 0.0570 chunk 143 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.098182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.078686 restraints weight = 64620.885| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.87 r_work: 0.2705 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16790 Z= 0.143 Angle : 0.730 15.686 22830 Z= 0.375 Chirality : 0.161 1.734 2470 Planarity : 0.004 0.082 2900 Dihedral : 5.477 40.328 2202 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.22 % Allowed : 9.56 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.18), residues: 2040 helix: 2.43 (0.47), residues: 110 sheet: 0.15 (0.16), residues: 890 loop : -0.83 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 58 TYR 0.021 0.001 TYR J 54 PHE 0.012 0.001 PHE E 52 TRP 0.007 0.001 TRP I 162 HIS 0.008 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (16780) covalent geometry : angle 0.72977 / 0.38 (22810) SS BOND : bond 0.00075 / 0.04 ( 10) SS BOND : angle 0.32041 / 0.20 ( 20) hydrogen bonds : bond 0.03808 / 2.49 ( 664) hydrogen bonds : angle 5.53032 / 3.74 ( 1638) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.831 Fit side-chains REVERT: J 193 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7379 (tp30) REVERT: G 147 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6961 (mt-10) REVERT: H 193 GLU cc_start: 0.7909 (tt0) cc_final: 0.7579 (tt0) REVERT: I 13 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8184 (mtmm) REVERT: I 88 GLU cc_start: 0.7604 (pp20) cc_final: 0.7383 (pp20) REVERT: E 138 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: E 163 ASP cc_start: 0.8672 (p0) cc_final: 0.8419 (p0) REVERT: D 14 GLU cc_start: 0.8278 (tt0) cc_final: 0.7964 (tm-30) REVERT: C 91 VAL cc_start: 0.8457 (t) cc_final: 0.8237 (p) outliers start: 22 outliers final: 12 residues processed: 175 average time/residue: 1.2343 time to fit residues: 240.0303 Evaluate side-chains 161 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain A residue 46 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 31 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 169 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.078017 restraints weight = 64910.511| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.88 r_work: 0.2692 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16790 Z= 0.170 Angle : 0.739 15.704 22830 Z= 0.381 Chirality : 0.161 1.763 2470 Planarity : 0.004 0.085 2900 Dihedral : 5.476 40.138 2202 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.39 % Allowed : 10.33 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.18), residues: 2040 helix: 2.32 (0.47), residues: 110 sheet: 0.15 (0.17), residues: 890 loop : -0.86 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 188 TYR 0.022 0.001 TYR J 54 PHE 0.013 0.001 PHE G 52 TRP 0.008 0.001 TRP I 162 HIS 0.007 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (16780) covalent geometry : angle 0.73972 / 0.38 (22810) SS BOND : bond 0.00123 / 0.06 ( 10) SS BOND : angle 0.41051 / 0.26 ( 20) hydrogen bonds : bond 0.03910 / 2.55 ( 664) hydrogen bonds : angle 5.54997 / 3.76 ( 1638) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.730 Fit side-chains REVERT: J 193 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7398 (tp30) REVERT: F 88 GLU cc_start: 0.8091 (pp20) cc_final: 0.7210 (mm-30) REVERT: G 147 GLU cc_start: 0.7528 (mt-10) cc_final: 0.6961 (mt-10) REVERT: H 193 GLU cc_start: 0.7952 (tt0) cc_final: 0.7601 (tt0) REVERT: I 88 GLU cc_start: 0.7634 (pp20) cc_final: 0.7411 (pp20) REVERT: E 138 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7314 (tm-30) REVERT: E 163 ASP cc_start: 0.8690 (p0) cc_final: 0.8440 (p0) REVERT: C 91 VAL cc_start: 0.8473 (t) cc_final: 0.8252 (p) REVERT: B 138 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7402 (tm-30) outliers start: 25 outliers final: 15 residues processed: 168 average time/residue: 1.3117 time to fit residues: 245.2981 Evaluate side-chains 159 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 126 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 181 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.097170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.077481 restraints weight = 64814.341| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 1.89 r_work: 0.2684 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16790 Z= 0.185 Angle : 0.748 15.644 22830 Z= 0.386 Chirality : 0.161 1.805 2470 Planarity : 0.005 0.101 2900 Dihedral : 5.521 40.096 2202 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.33 % Allowed : 10.56 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.18), residues: 2040 helix: 2.24 (0.46), residues: 110 sheet: 0.16 (0.17), residues: 890 loop : -0.89 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 58 TYR 0.023 0.001 TYR J 54 PHE 0.014 0.001 PHE E 52 TRP 0.008 0.001 TRP I 162 HIS 0.008 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (16780) covalent geometry : angle 0.74831 / 0.39 (22810) SS BOND : bond 0.00150 / 0.07 ( 10) SS BOND : angle 0.43578 / 0.28 ( 20) hydrogen bonds : bond 0.03967 / 2.59 ( 664) hydrogen bonds : angle 5.57197 / 3.78 ( 1638) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.881 Fit side-chains REVERT: J 193 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7400 (tp30) REVERT: F 88 GLU cc_start: 0.8104 (pp20) cc_final: 0.7205 (mm-30) REVERT: G 147 GLU cc_start: 0.7552 (mt-10) cc_final: 0.6996 (mt-10) REVERT: H 193 GLU cc_start: 0.7993 (tt0) cc_final: 0.7641 (tt0) REVERT: I 88 GLU cc_start: 0.7621 (pp20) cc_final: 0.7397 (pp20) REVERT: I 141 SER cc_start: 0.6829 (p) cc_final: 0.6578 (m) REVERT: E 138 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: E 163 ASP cc_start: 0.8713 (p0) cc_final: 0.8465 (p0) REVERT: C 91 VAL cc_start: 0.8485 (t) cc_final: 0.8265 (p) REVERT: B 88 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: B 138 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7440 (tm-30) outliers start: 24 outliers final: 16 residues processed: 163 average time/residue: 1.3453 time to fit residues: 243.5560 Evaluate side-chains 160 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.097164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.077543 restraints weight = 64664.510| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.89 r_work: 0.2684 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16790 Z= 0.184 Angle : 0.748 15.678 22830 Z= 0.385 Chirality : 0.161 1.774 2470 Planarity : 0.005 0.093 2900 Dihedral : 5.517 40.061 2202 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.28 % Allowed : 10.89 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 2040 helix: 2.23 (0.47), residues: 110 sheet: 0.16 (0.17), residues: 890 loop : -0.92 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 58 TYR 0.022 0.001 TYR J 54 PHE 0.014 0.001 PHE E 52 TRP 0.008 0.001 TRP I 162 HIS 0.008 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (16780) covalent geometry : angle 0.74783 / 0.39 (22810) SS BOND : bond 0.00148 / 0.07 ( 10) SS BOND : angle 0.42354 / 0.28 ( 20) hydrogen bonds : bond 0.03956 / 2.59 ( 664) hydrogen bonds : angle 5.56625 / 3.77 ( 1638) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.727 Fit side-chains REVERT: J 58 ARG cc_start: 0.7986 (ttp-110) cc_final: 0.7731 (ttp80) REVERT: J 193 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7386 (tp30) REVERT: F 88 GLU cc_start: 0.8119 (pp20) cc_final: 0.7205 (mm-30) REVERT: G 147 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6987 (mt-10) REVERT: H 193 GLU cc_start: 0.7995 (tt0) cc_final: 0.7641 (tt0) REVERT: I 88 GLU cc_start: 0.7656 (pp20) cc_final: 0.7416 (pp20) REVERT: I 141 SER cc_start: 0.6791 (OUTLIER) cc_final: 0.6571 (m) REVERT: E 138 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: E 163 ASP cc_start: 0.8697 (p0) cc_final: 0.8448 (p0) REVERT: C 91 VAL cc_start: 0.8491 (t) cc_final: 0.8270 (p) REVERT: B 88 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: B 138 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7457 (tm-30) outliers start: 23 outliers final: 15 residues processed: 165 average time/residue: 1.3189 time to fit residues: 242.6799 Evaluate side-chains 163 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.098426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.078875 restraints weight = 64721.280| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.89 r_work: 0.2706 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16790 Z= 0.133 Angle : 0.729 15.664 22830 Z= 0.374 Chirality : 0.161 1.744 2470 Planarity : 0.005 0.097 2900 Dihedral : 5.308 38.851 2202 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.17 % Allowed : 11.11 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.18), residues: 2040 helix: 2.45 (0.47), residues: 110 sheet: 0.17 (0.17), residues: 890 loop : -0.84 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 58 TYR 0.019 0.001 TYR J 54 PHE 0.011 0.001 PHE E 52 TRP 0.008 0.001 TRP C 162 HIS 0.007 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (16780) covalent geometry : angle 0.72909 / 0.37 (22810) SS BOND : bond 0.00064 / 0.03 ( 10) SS BOND : angle 0.29046 / 0.18 ( 20) hydrogen bonds : bond 0.03648 / 2.38 ( 664) hydrogen bonds : angle 5.43249 / 3.67 ( 1638) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.751 Fit side-chains REVERT: J 58 ARG cc_start: 0.8025 (ttp-110) cc_final: 0.7745 (ttp80) REVERT: J 193 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: F 88 GLU cc_start: 0.8101 (pp20) cc_final: 0.7249 (mm-30) REVERT: G 147 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6986 (mt-10) REVERT: H 193 GLU cc_start: 0.7929 (tt0) cc_final: 0.7562 (tt0) REVERT: I 58 ARG cc_start: 0.6442 (mtp-110) cc_final: 0.6124 (mtm-85) REVERT: I 88 GLU cc_start: 0.7682 (pp20) cc_final: 0.7452 (pp20) REVERT: I 141 SER cc_start: 0.6825 (OUTLIER) cc_final: 0.6616 (m) REVERT: E 138 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: E 163 ASP cc_start: 0.8629 (p0) cc_final: 0.8394 (p0) REVERT: D 14 GLU cc_start: 0.8289 (tt0) cc_final: 0.7977 (tm-30) REVERT: C 91 VAL cc_start: 0.8457 (t) cc_final: 0.8235 (p) REVERT: B 13 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8280 (mtmm) REVERT: B 88 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: B 138 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7353 (tm-30) outliers start: 21 outliers final: 13 residues processed: 166 average time/residue: 1.3068 time to fit residues: 241.8134 Evaluate side-chains 161 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 193 GLU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 47 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 196 optimal weight: 0.0870 chunk 136 optimal weight: 0.4980 chunk 189 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.098975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.079260 restraints weight = 64776.526| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.91 r_work: 0.2717 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16790 Z= 0.122 Angle : 0.722 15.671 22830 Z= 0.370 Chirality : 0.161 1.737 2470 Planarity : 0.004 0.082 2900 Dihedral : 5.088 30.949 2200 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.06 % Allowed : 11.44 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.18), residues: 2040 helix: 2.56 (0.47), residues: 110 sheet: 0.19 (0.17), residues: 890 loop : -0.78 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 188 TYR 0.020 0.001 TYR H 54 PHE 0.010 0.001 PHE E 52 TRP 0.009 0.001 TRP C 162 HIS 0.007 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (16780) covalent geometry : angle 0.72254 / 0.37 (22810) SS BOND : bond 0.00062 / 0.03 ( 10) SS BOND : angle 0.31742 / 0.19 ( 20) hydrogen bonds : bond 0.03527 / 2.30 ( 664) hydrogen bonds : angle 5.35343 / 3.61 ( 1638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9104.11 seconds wall clock time: 154 minutes 43.87 seconds (9283.87 seconds total)