Starting phenix.real_space_refine on Fri Mar 6 15:16:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pkf_13470/03_2026/7pkf_13470.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pkf_13470/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pkf_13470/03_2026/7pkf_13470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pkf_13470/03_2026/7pkf_13470.map" model { file = "/net/cci-nas-00/data/ceres_data/7pkf_13470/03_2026/7pkf_13470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pkf_13470/03_2026/7pkf_13470.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 6.11, per 1000 atoms: 0.19 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: 2.92 Conformation dependent library (CDL) restraints added in 978.7 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: 0.90 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: 8.44 Time building geometry restraints manager: 4.08 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: 2.850 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: 0.210 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 31.780 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 covalent geometry : bond 0.00385 (16780) covalent geometry : angle 0.90092 (22810) SS BOND : bond 0.00302 ( 10) SS BOND : angle 2.02198 ( 20) hydrogen bonds : bond 0.19371 ( 664) hydrogen bonds : angle 8.07814 ( 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 : 0.828 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: 1.6865 time to fit residues: 409.7316 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 : 0.996 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.097621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.078226 restraints weight = 65077.653| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 1.84 r_work: 0.2698 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 16790 Z= 0.286 Angle : 0.835 15.909 22830 Z= 0.440 Chirality : 0.162 1.771 2470 Planarity : 0.005 0.076 2900 Dihedral : 6.749 42.010 2202 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.11 % Allowed : 5.89 % 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 G 6 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 covalent geometry : bond 0.00678 (16780) covalent geometry : angle 0.83560 (22810) SS BOND : bond 0.00447 ( 10) SS BOND : angle 0.70396 ( 20) hydrogen bonds : bond 0.05680 ( 664) hydrogen bonds : angle 6.34586 ( 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 180 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.946 Fit side-chains REVERT: J 193 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7426 (tp30) REVERT: F 81 GLU cc_start: 0.8553 (tt0) cc_final: 0.8298 (tt0) REVERT: H 193 GLU cc_start: 0.7972 (tt0) cc_final: 0.7680 (tt0) REVERT: I 88 GLU cc_start: 0.7299 (pp20) cc_final: 0.6894 (pm20) REVERT: I 155 ASP cc_start: 0.8771 (m-30) cc_final: 0.8455 (m-30) REVERT: I 197 GLU cc_start: 0.7621 (tt0) cc_final: 0.7106 (tt0) REVERT: E 138 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: E 163 ASP cc_start: 0.8730 (p0) cc_final: 0.8441 (p0) REVERT: D 4 MET cc_start: 0.8795 (mmm) cc_final: 0.8511 (mmm) REVERT: C 91 VAL cc_start: 0.8448 (t) cc_final: 0.8224 (p) outliers start: 20 outliers final: 9 residues processed: 175 average time/residue: 1.7248 time to fit residues: 329.5051 Evaluate side-chains 155 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 173 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 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: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.098428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.079267 restraints weight = 65113.478| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 1.85 r_work: 0.2714 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16790 Z= 0.157 Angle : 0.759 15.711 22830 Z= 0.394 Chirality : 0.161 1.737 2470 Planarity : 0.004 0.070 2900 Dihedral : 6.025 41.927 2202 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.11 % Allowed : 7.33 % Favored : 91.56 % 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: -0.31 (0.18), residues: 2040 helix: 2.05 (0.45), residues: 110 sheet: 0.16 (0.16), residues: 890 loop : -0.74 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 58 TYR 0.021 0.001 TYR J 54 PHE 0.013 0.001 PHE E 52 TRP 0.010 0.001 TRP E 110 HIS 0.007 0.002 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00372 (16780) covalent geometry : angle 0.75955 (22810) SS BOND : bond 0.00109 ( 10) SS BOND : angle 0.40887 ( 20) hydrogen bonds : bond 0.04514 ( 664) hydrogen bonds : angle 5.84336 ( 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 177 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: J 193 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7414 (tp30) REVERT: F 197 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: G 193 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6898 (tm-30) REVERT: H 193 GLU cc_start: 0.7925 (tt0) cc_final: 0.7655 (tt0) REVERT: I 13 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8200 (mtmm) REVERT: I 88 GLU cc_start: 0.7291 (pp20) cc_final: 0.6831 (pm20) REVERT: I 155 ASP cc_start: 0.8724 (m-30) cc_final: 0.8360 (m-30) REVERT: E 138 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: E 163 ASP cc_start: 0.8715 (p0) cc_final: 0.8423 (p0) REVERT: C 91 VAL cc_start: 0.8500 (t) cc_final: 0.8268 (p) REVERT: B 108 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8210 (mt-10) outliers start: 20 outliers final: 10 residues processed: 171 average time/residue: 1.6886 time to fit residues: 315.2559 Evaluate side-chains 158 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 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: 0.2980 chunk 3 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.098008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.078500 restraints weight = 64561.820| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.87 r_work: 0.2703 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16790 Z= 0.163 Angle : 0.748 15.752 22830 Z= 0.386 Chirality : 0.161 1.721 2470 Planarity : 0.004 0.074 2900 Dihedral : 5.765 40.910 2202 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.33 % Allowed : 8.39 % 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: -0.32 (0.18), residues: 2040 helix: 2.27 (0.46), residues: 110 sheet: 0.15 (0.16), residues: 890 loop : -0.77 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 58 TYR 0.022 0.001 TYR J 54 PHE 0.013 0.001 PHE E 52 TRP 0.008 0.001 TRP E 110 HIS 0.007 0.002 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00392 (16780) covalent geometry : angle 0.74818 (22810) SS BOND : bond 0.00119 ( 10) SS BOND : angle 0.43156 ( 20) hydrogen bonds : bond 0.04154 ( 664) hydrogen bonds : angle 5.67396 ( 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 174 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: J 193 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7424 (tp30) REVERT: F 88 GLU cc_start: 0.8099 (pp20) cc_final: 0.7230 (mm-30) REVERT: F 197 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: G 147 GLU cc_start: 0.7568 (mt-10) cc_final: 0.6957 (mt-10) REVERT: G 193 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6898 (tm-30) REVERT: H 193 GLU cc_start: 0.7922 (tt0) cc_final: 0.7629 (tt0) REVERT: I 13 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8226 (mtmm) REVERT: I 88 GLU cc_start: 0.7454 (pp20) cc_final: 0.6944 (pm20) REVERT: I 197 GLU cc_start: 0.7640 (tt0) cc_final: 0.7288 (tt0) REVERT: E 138 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: E 163 ASP cc_start: 0.8696 (p0) cc_final: 0.8430 (p0) REVERT: C 91 VAL cc_start: 0.8509 (t) cc_final: 0.8279 (p) REVERT: B 108 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8191 (mt-10) outliers start: 24 outliers final: 15 residues processed: 169 average time/residue: 1.7307 time to fit residues: 319.3062 Evaluate side-chains 161 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 141 SER Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 173 THR 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 38 HIS 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: 1.9990 chunk 55 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 129 optimal weight: 0.0870 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.098598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.079152 restraints weight = 64791.717| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.88 r_work: 0.2716 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16790 Z= 0.141 Angle : 0.731 15.724 22830 Z= 0.376 Chirality : 0.161 1.740 2470 Planarity : 0.004 0.076 2900 Dihedral : 5.523 40.273 2202 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.33 % Allowed : 9.06 % 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: -0.31 (0.18), residues: 2040 helix: 2.43 (0.46), residues: 110 sheet: 0.15 (0.16), residues: 890 loop : -0.78 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 58 TYR 0.021 0.001 TYR J 54 PHE 0.012 0.001 PHE G 52 TRP 0.007 0.001 TRP E 162 HIS 0.007 0.002 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00341 (16780) covalent geometry : angle 0.73170 (22810) SS BOND : bond 0.00084 ( 10) SS BOND : angle 0.35297 ( 20) hydrogen bonds : bond 0.03878 ( 664) hydrogen bonds : angle 5.56609 ( 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 177 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: J 193 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7418 (tp30) REVERT: F 197 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: G 147 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6969 (mt-10) REVERT: G 193 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: H 193 GLU cc_start: 0.7893 (tt0) cc_final: 0.7591 (tt0) REVERT: I 13 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8191 (mtmm) REVERT: I 88 GLU cc_start: 0.7557 (pp20) cc_final: 0.7017 (pm20) REVERT: E 138 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: E 163 ASP cc_start: 0.8661 (p0) cc_final: 0.8409 (p0) REVERT: C 91 VAL cc_start: 0.8481 (t) cc_final: 0.8244 (p) REVERT: B 108 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8250 (mt-10) outliers start: 24 outliers final: 13 residues processed: 171 average time/residue: 1.6511 time to fit residues: 309.0908 Evaluate side-chains 156 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 141 SER Chi-restraints excluded: chain G residue 172 ASN Chi-restraints excluded: chain G residue 173 THR 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 38 HIS 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 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: 0.5980 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 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: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.097492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.077944 restraints weight = 64690.090| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.88 r_work: 0.2692 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16790 Z= 0.179 Angle : 0.744 15.686 22830 Z= 0.384 Chirality : 0.161 1.803 2470 Planarity : 0.004 0.083 2900 Dihedral : 5.545 40.146 2202 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.28 % Allowed : 9.61 % Favored : 89.11 % 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: -0.35 (0.18), residues: 2040 helix: 2.32 (0.47), residues: 110 sheet: 0.16 (0.16), residues: 890 loop : -0.83 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 58 TYR 0.023 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 covalent geometry : bond 0.00429 (16780) covalent geometry : angle 0.74445 (22810) SS BOND : bond 0.00153 ( 10) SS BOND : angle 0.45753 ( 20) hydrogen bonds : bond 0.04005 ( 664) hydrogen bonds : angle 5.60687 ( 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 170 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.984 Fit side-chains REVERT: F 88 GLU cc_start: 0.8068 (pp20) cc_final: 0.7220 (mm-30) REVERT: G 58 ARG cc_start: 0.6851 (mtm110) cc_final: 0.6638 (mtm-85) REVERT: G 147 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6952 (mt-10) REVERT: G 193 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: H 193 GLU cc_start: 0.7940 (tt0) cc_final: 0.7609 (tt0) REVERT: I 13 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8193 (mtmm) REVERT: I 88 GLU cc_start: 0.7519 (pp20) cc_final: 0.7299 (pp20) REVERT: I 149 SER cc_start: 0.8225 (p) cc_final: 0.7818 (m) REVERT: E 138 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: E 163 ASP cc_start: 0.8706 (p0) cc_final: 0.8465 (p0) REVERT: C 91 VAL cc_start: 0.8467 (t) cc_final: 0.8246 (p) REVERT: B 108 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8194 (mt-10) outliers start: 23 outliers final: 14 residues processed: 165 average time/residue: 1.6541 time to fit residues: 299.4925 Evaluate side-chains 163 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 Chi-restraints excluded: chain A residue 126 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 31 optimal weight: 1.9990 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: 0.5980 chunk 52 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.077498 restraints weight = 64914.401| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 1.88 r_work: 0.2684 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2683 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= 0.186 Angle : 0.747 15.688 22830 Z= 0.385 Chirality : 0.161 1.805 2470 Planarity : 0.004 0.086 2900 Dihedral : 5.549 40.203 2202 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.83 % Allowed : 9.67 % Favored : 88.50 % 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: -0.40 (0.18), residues: 2040 helix: 2.22 (0.46), residues: 110 sheet: 0.15 (0.17), residues: 890 loop : -0.89 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 58 TYR 0.023 0.001 TYR J 54 PHE 0.013 0.001 PHE E 52 TRP 0.008 0.001 TRP I 162 HIS 0.007 0.002 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00444 (16780) covalent geometry : angle 0.74672 (22810) SS BOND : bond 0.00154 ( 10) SS BOND : angle 0.43934 ( 20) hydrogen bonds : bond 0.04005 ( 664) hydrogen bonds : angle 5.61106 ( 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 185 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.905 Fit side-chains REVERT: J 193 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7405 (tp30) REVERT: G 58 ARG cc_start: 0.6878 (mtm110) cc_final: 0.6664 (mtm-85) REVERT: G 147 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6978 (mt-10) REVERT: G 193 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: H 193 GLU cc_start: 0.7992 (tt0) cc_final: 0.7648 (tt0) REVERT: I 58 ARG cc_start: 0.6414 (mtp-110) cc_final: 0.6048 (mtm-85) REVERT: I 88 GLU cc_start: 0.7545 (pp20) cc_final: 0.7320 (pp20) REVERT: I 149 SER cc_start: 0.8249 (p) cc_final: 0.7847 (m) REVERT: E 138 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: E 163 ASP cc_start: 0.8708 (p0) cc_final: 0.8459 (p0) REVERT: C 91 VAL cc_start: 0.8497 (t) cc_final: 0.8274 (p) REVERT: B 108 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 138 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7475 (tm-30) outliers start: 33 outliers final: 15 residues processed: 180 average time/residue: 1.6311 time to fit residues: 322.3738 Evaluate side-chains 160 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 G residue 193 GLU 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 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: 0.7980 chunk 131 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.078097 restraints weight = 64758.743| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.88 r_work: 0.2694 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16790 Z= 0.161 Angle : 0.740 15.632 22830 Z= 0.381 Chirality : 0.161 1.777 2470 Planarity : 0.005 0.098 2900 Dihedral : 5.472 39.812 2202 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.28 % Allowed : 10.50 % Favored : 88.22 % 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: -0.39 (0.18), residues: 2040 helix: 2.32 (0.47), residues: 110 sheet: 0.15 (0.17), residues: 890 loop : -0.87 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 58 TYR 0.021 0.001 TYR J 54 PHE 0.013 0.001 PHE E 52 TRP 0.008 0.001 TRP I 162 HIS 0.008 0.002 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00387 (16780) covalent geometry : angle 0.73980 (22810) SS BOND : bond 0.00106 ( 10) SS BOND : angle 0.35629 ( 20) hydrogen bonds : bond 0.03852 ( 664) hydrogen bonds : angle 5.55086 ( 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 163 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.946 Fit side-chains REVERT: J 193 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7404 (tp30) REVERT: F 88 GLU cc_start: 0.8113 (pp20) cc_final: 0.7229 (mm-30) REVERT: G 58 ARG cc_start: 0.6892 (mtm110) cc_final: 0.6681 (mtm-85) REVERT: G 147 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7015 (mt-10) REVERT: G 193 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6930 (tm-30) REVERT: H 193 GLU cc_start: 0.7955 (tt0) cc_final: 0.7587 (tt0) REVERT: I 58 ARG cc_start: 0.6410 (mtp-110) cc_final: 0.6072 (mtm-85) REVERT: I 88 GLU cc_start: 0.7563 (pp20) cc_final: 0.7340 (pp20) REVERT: E 138 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: E 163 ASP cc_start: 0.8687 (p0) cc_final: 0.8436 (p0) REVERT: C 91 VAL cc_start: 0.8469 (t) cc_final: 0.8248 (p) REVERT: B 138 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7405 (tm-30) outliers start: 23 outliers final: 16 residues processed: 161 average time/residue: 1.6865 time to fit residues: 297.4990 Evaluate side-chains 156 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 G residue 193 GLU 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 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: 2.9990 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: 1.9990 chunk 104 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.096550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.076863 restraints weight = 64702.017| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 1.88 r_work: 0.2672 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16790 Z= 0.225 Angle : 0.765 15.716 22830 Z= 0.396 Chirality : 0.161 1.800 2470 Planarity : 0.005 0.096 2900 Dihedral : 5.641 40.367 2202 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.33 % Allowed : 10.78 % Favored : 87.89 % 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: -0.48 (0.18), residues: 2040 helix: 2.09 (0.46), residues: 110 sheet: 0.14 (0.17), residues: 890 loop : -0.97 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 58 TYR 0.024 0.002 TYR J 54 PHE 0.015 0.002 PHE E 52 TRP 0.008 0.001 TRP G 67 HIS 0.008 0.002 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00537 (16780) covalent geometry : angle 0.76557 (22810) SS BOND : bond 0.00221 ( 10) SS BOND : angle 0.56167 ( 20) hydrogen bonds : bond 0.04172 ( 664) hydrogen bonds : angle 5.67258 ( 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 170 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.011 Fit side-chains REVERT: J 58 ARG cc_start: 0.7974 (ttp-110) cc_final: 0.7734 (ttp80) REVERT: F 88 GLU cc_start: 0.8121 (pp20) cc_final: 0.7200 (mm-30) REVERT: G 58 ARG cc_start: 0.6882 (mtm110) cc_final: 0.6673 (mtm-85) REVERT: G 147 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7011 (mt-10) REVERT: G 193 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: H 26 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7182 (tp) REVERT: H 193 GLU cc_start: 0.8020 (tt0) cc_final: 0.7665 (tt0) REVERT: I 88 GLU cc_start: 0.7568 (pp20) cc_final: 0.7349 (pp20) REVERT: I 141 SER cc_start: 0.6809 (OUTLIER) cc_final: 0.6576 (m) REVERT: I 149 SER cc_start: 0.8273 (p) cc_final: 0.7882 (m) REVERT: I 206 PRO cc_start: 0.8268 (Cg_endo) cc_final: 0.7961 (Cg_exo) REVERT: E 138 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: C 91 VAL cc_start: 0.8506 (t) cc_final: 0.8283 (p) REVERT: C 125 TYR cc_start: 0.8665 (t80) cc_final: 0.8306 (t80) REVERT: B 138 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7522 (tm-30) outliers start: 24 outliers final: 17 residues processed: 166 average time/residue: 1.6384 time to fit residues: 299.3144 Evaluate side-chains 165 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 193 GLU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 106 ILE 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 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 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: 1.9990 chunk 136 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 131 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.098628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.079063 restraints weight = 64558.566| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 1.89 r_work: 0.2712 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2898 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= 0.126 Angle : 0.726 15.642 22830 Z= 0.372 Chirality : 0.161 1.737 2470 Planarity : 0.005 0.097 2900 Dihedral : 5.305 38.847 2202 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.28 % Allowed : 11.06 % Favored : 87.67 % 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: -0.34 (0.18), residues: 2040 helix: 2.53 (0.47), residues: 110 sheet: 0.16 (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 0.010 0.001 PHE G 52 TRP 0.009 0.001 TRP C 162 HIS 0.007 0.002 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00308 (16780) covalent geometry : angle 0.72618 (22810) SS BOND : bond 0.00051 ( 10) SS BOND : angle 0.28178 ( 20) hydrogen bonds : bond 0.03586 ( 664) hydrogen bonds : angle 5.42274 ( 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: 23 poor density : 147 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: J 58 ARG cc_start: 0.8017 (ttp-110) cc_final: 0.7751 (ttp80) REVERT: F 88 GLU cc_start: 0.8080 (pp20) cc_final: 0.7255 (mm-30) REVERT: G 58 ARG cc_start: 0.6936 (mtm110) cc_final: 0.6715 (mtm-85) REVERT: G 147 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6987 (mt-10) REVERT: G 193 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: H 193 GLU cc_start: 0.7918 (tt0) cc_final: 0.7558 (tt0) REVERT: I 58 ARG cc_start: 0.6469 (mtp-110) cc_final: 0.6142 (mtm-85) REVERT: I 88 GLU cc_start: 0.7611 (pp20) cc_final: 0.7381 (pp20) REVERT: I 141 SER cc_start: 0.6871 (OUTLIER) cc_final: 0.6656 (m) REVERT: I 206 PRO cc_start: 0.8237 (Cg_endo) cc_final: 0.7925 (Cg_exo) REVERT: E 138 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: C 91 VAL cc_start: 0.8455 (t) cc_final: 0.8235 (p) REVERT: B 138 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7366 (tm-30) outliers start: 23 outliers final: 13 residues processed: 165 average time/residue: 1.5765 time to fit residues: 285.6585 Evaluate side-chains 159 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 173 THR Chi-restraints excluded: chain G residue 193 GLU 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 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: 1.9990 chunk 48 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 196 optimal weight: 0.1980 chunk 136 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.077918 restraints weight = 64774.723| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.90 r_work: 0.2692 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2941 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= 0.169 Angle : 0.741 15.682 22830 Z= 0.381 Chirality : 0.161 1.751 2470 Planarity : 0.004 0.080 2900 Dihedral : 5.289 35.707 2200 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.00 % Allowed : 11.50 % 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: -0.37 (0.18), residues: 2040 helix: 2.38 (0.47), residues: 110 sheet: 0.17 (0.17), residues: 890 loop : -0.88 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 188 TYR 0.022 0.001 TYR J 54 PHE 0.013 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 covalent geometry : bond 0.00407 (16780) covalent geometry : angle 0.74089 (22810) SS BOND : bond 0.00128 ( 10) SS BOND : angle 0.41598 ( 20) hydrogen bonds : bond 0.03819 ( 664) hydrogen bonds : angle 5.49116 ( 1638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10289.58 seconds wall clock time: 174 minutes 47.70 seconds (10487.70 seconds total)