Starting phenix.real_space_refine on Thu Feb 5 23:14:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jo7_61645/02_2026/9jo7_61645.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jo7_61645/02_2026/9jo7_61645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jo7_61645/02_2026/9jo7_61645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jo7_61645/02_2026/9jo7_61645.map" model { file = "/net/cci-nas-00/data/ceres_data/9jo7_61645/02_2026/9jo7_61645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jo7_61645/02_2026/9jo7_61645.cif" } resolution = 3.68 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= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 8100 2.51 5 N 2085 2.21 5 O 2435 1.98 5 H 7960 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20620 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "J" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 900 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "B" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 900 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "D" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "E" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 900 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "F" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "G" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 900 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "H" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3224 Classifications: {'peptide': 206} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "I" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 900 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Time building chain proxies: 4.37, per 1000 atoms: 0.21 Number of scatterers: 20620 At special positions: 0 Unit cell: (117.135, 115.425, 86.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 O 2435 8.00 N 2085 7.00 C 8100 6.00 H 7960 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " distance=2.37 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.22 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 97 " distance=2.37 Simple disulfide: pdb=" SG CYS F 36 " - pdb=" SG CYS F 97 " distance=2.37 Simple disulfide: pdb=" SG CYS H 36 " - pdb=" SG CYS H 97 " distance=2.36 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: 2.03 Conformation dependent library (CDL) restraints added in 693.6 milliseconds 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 30 sheets defined 8.1% alpha, 41.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.894A 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 'J' and resid 87 through 91 Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.893A 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 'C' and resid 87 through 91 Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.894A 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 177 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.893A pdb=" N SER F 45 " --> pdb=" O GLU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 177 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 42 through 46 removed outlier: 3.893A 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 'I' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.841A pdb=" N ILE A 106 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 34 " --> pdb=" O TRP A 162 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS A 38 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN A 158 " --> pdb=" O HIS A 38 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR A 40 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE A 156 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 85 removed outlier: 5.072A pdb=" N ASN A 61 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR A 54 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 63 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE A 52 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE A 65 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER A 50 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 7 through 9 Processing sheet with id=AA5, first strand: chain 'J' and resid 13 through 14 removed outlier: 3.724A pdb=" N GLY J 36 " --> pdb=" O TYR J 97 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N MET J 35 " --> pdb=" O PHE J 51 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE J 51 " --> pdb=" O MET J 35 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP J 37 " --> pdb=" O ALA J 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 13 through 14 Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 115 removed outlier: 3.842A pdb=" N ILE B 106 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B 34 " --> pdb=" O TRP B 162 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS B 38 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ASN B 158 " --> pdb=" O HIS B 38 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR B 40 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE B 156 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 10.374A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 80 through 85 removed outlier: 5.073A pdb=" N ASN B 61 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR B 54 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 63 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE B 52 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE B 65 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N SER B 50 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 7 through 9 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 3.723A pdb=" N GLY C 36 " --> pdb=" O TYR C 97 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N MET C 35 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE C 51 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP C 37 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 Processing sheet with id=AB4, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB5, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.842A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR D 34 " --> pdb=" O TRP D 162 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS D 38 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ASN D 158 " --> pdb=" O HIS D 38 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR D 40 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE D 156 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 80 through 85 removed outlier: 5.073A pdb=" N ASN D 61 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR D 54 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE D 63 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE D 52 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 65 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER D 50 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 7 through 9 Processing sheet with id=AB8, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.723A pdb=" N GLY E 36 " --> pdb=" O TYR E 97 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET E 35 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE E 51 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP E 37 " --> pdb=" O ALA E 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AC1, first strand: chain 'F' and resid 114 through 115 Processing sheet with id=AC2, first strand: chain 'F' and resid 114 through 115 removed outlier: 3.842A pdb=" N ILE F 106 " --> pdb=" O GLU F 101 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR F 34 " --> pdb=" O TRP F 162 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N HIS F 38 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN F 158 " --> pdb=" O HIS F 38 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR F 40 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE F 156 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASN F 158 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 10.374A pdb=" N LYS F 7 " --> pdb=" O ASN F 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 80 through 85 removed outlier: 5.073A pdb=" N ASN F 61 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR F 54 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE F 63 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE F 52 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE F 65 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER F 50 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE F 133 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 7 through 9 Processing sheet with id=AC5, first strand: chain 'G' and resid 13 through 14 removed outlier: 3.723A pdb=" N GLY G 36 " --> pdb=" O TYR G 97 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N MET G 35 " --> pdb=" O PHE G 51 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE G 51 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP G 37 " --> pdb=" O ALA G 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 13 through 14 Processing sheet with id=AC7, first strand: chain 'H' and resid 114 through 115 Processing sheet with id=AC8, first strand: chain 'H' and resid 114 through 115 removed outlier: 3.841A pdb=" N ILE H 106 " --> pdb=" O GLU H 101 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR H 34 " --> pdb=" O TRP H 162 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS H 38 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ASN H 158 " --> pdb=" O HIS H 38 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR H 40 " --> pdb=" O ILE H 156 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE H 156 " --> pdb=" O TYR H 40 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN H 158 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 10.374A pdb=" N LYS H 7 " --> pdb=" O ASN H 158 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 80 through 85 removed outlier: 5.073A pdb=" N ASN H 61 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR H 54 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE H 63 " --> pdb=" O PHE H 52 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE H 52 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE H 65 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER H 50 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE H 133 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 7 through 9 Processing sheet with id=AD2, first strand: chain 'I' and resid 13 through 14 removed outlier: 3.723A pdb=" N GLY I 36 " --> pdb=" O TYR I 97 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET I 35 " --> pdb=" O PHE I 51 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE I 51 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP I 37 " --> pdb=" O ALA I 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 13 through 14 525 hydrogen bonds defined for protein. 1230 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: 5.72 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 7960 1.02 - 1.22: 5 1.22 - 1.42: 5620 1.42 - 1.62: 7295 1.62 - 1.82: 60 Bond restraints: 20940 Sorted by residual: bond pdb=" C ASN B 158 " pdb=" N VAL B 159 " ideal model delta sigma weight residual 1.329 1.437 -0.108 1.17e-02 7.31e+03 8.48e+01 bond pdb=" C ASN A 158 " pdb=" N VAL A 159 " ideal model delta sigma weight residual 1.329 1.437 -0.108 1.17e-02 7.31e+03 8.48e+01 bond pdb=" C ASN F 158 " pdb=" N VAL F 159 " ideal model delta sigma weight residual 1.329 1.437 -0.108 1.17e-02 7.31e+03 8.47e+01 bond pdb=" C ASN D 158 " pdb=" N VAL D 159 " ideal model delta sigma weight residual 1.329 1.436 -0.107 1.17e-02 7.31e+03 8.38e+01 bond pdb=" C ASN H 158 " pdb=" N VAL H 159 " ideal model delta sigma weight residual 1.329 1.436 -0.107 1.17e-02 7.31e+03 8.36e+01 ... (remaining 20935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 34116 1.65 - 3.30: 1260 3.30 - 4.95: 237 4.95 - 6.60: 121 6.60 - 8.25: 21 Bond angle restraints: 35755 Sorted by residual: angle pdb=" O ILE D 174 " pdb=" C ILE D 174 " pdb=" N TYR D 175 " ideal model delta sigma weight residual 121.87 116.38 5.49 9.70e-01 1.06e+00 3.20e+01 angle pdb=" O ILE B 174 " pdb=" C ILE B 174 " pdb=" N TYR B 175 " ideal model delta sigma weight residual 121.87 116.39 5.48 9.70e-01 1.06e+00 3.19e+01 angle pdb=" C ASP H 169 " pdb=" N GLU H 170 " pdb=" CA GLU H 170 " ideal model delta sigma weight residual 120.29 128.30 -8.01 1.42e+00 4.96e-01 3.18e+01 angle pdb=" C ASP A 169 " pdb=" N GLU A 170 " pdb=" CA GLU A 170 " ideal model delta sigma weight residual 120.29 128.28 -7.99 1.42e+00 4.96e-01 3.17e+01 angle pdb=" C ASP B 169 " pdb=" N GLU B 170 " pdb=" CA GLU B 170 " ideal model delta sigma weight residual 120.29 128.27 -7.98 1.42e+00 4.96e-01 3.16e+01 ... (remaining 35750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 9251 17.07 - 34.13: 846 34.13 - 51.20: 243 51.20 - 68.27: 120 68.27 - 85.33: 35 Dihedral angle restraints: 10495 sinusoidal: 5165 harmonic: 5330 Sorted by residual: dihedral pdb=" CB CYS A 36 " pdb=" SG CYS A 36 " pdb=" SG CYS A 97 " pdb=" CB CYS A 97 " ideal model delta sinusoidal sigma weight residual 93.00 124.37 -31.37 1 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CB CYS D 36 " pdb=" SG CYS D 36 " pdb=" SG CYS D 97 " pdb=" CB CYS D 97 " ideal model delta sinusoidal sigma weight residual 93.00 124.37 -31.37 1 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CB CYS H 36 " pdb=" SG CYS H 36 " pdb=" SG CYS H 97 " pdb=" CB CYS H 97 " ideal model delta sinusoidal sigma weight residual 93.00 124.36 -31.36 1 1.00e+01 1.00e-02 1.40e+01 ... (remaining 10492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1423 0.045 - 0.089: 316 0.089 - 0.134: 146 0.134 - 0.178: 15 0.178 - 0.223: 10 Chirality restraints: 1910 Sorted by residual: chirality pdb=" CG LEU E 48 " pdb=" CB LEU E 48 " pdb=" CD1 LEU E 48 " pdb=" CD2 LEU E 48 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU G 48 " pdb=" CB LEU G 48 " pdb=" CD1 LEU G 48 " pdb=" CD2 LEU G 48 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CG LEU J 48 " pdb=" CB LEU J 48 " pdb=" CD1 LEU J 48 " pdb=" CD2 LEU J 48 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1907 not shown) Planarity restraints: 3235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 1 " 0.242 2.00e-02 2.50e+03 3.27e-01 1.61e+03 pdb=" CD GLN B 1 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN B 1 " -0.230 2.00e-02 2.50e+03 pdb=" NE2 GLN B 1 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 1 " -0.513 2.00e-02 2.50e+03 pdb="HE22 GLN B 1 " 0.518 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 1 " 0.242 2.00e-02 2.50e+03 3.27e-01 1.61e+03 pdb=" CD GLN A 1 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN A 1 " -0.230 2.00e-02 2.50e+03 pdb=" NE2 GLN A 1 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 1 " -0.512 2.00e-02 2.50e+03 pdb="HE22 GLN A 1 " 0.518 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 1 " 0.242 2.00e-02 2.50e+03 3.27e-01 1.61e+03 pdb=" CD GLN H 1 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN H 1 " -0.230 2.00e-02 2.50e+03 pdb=" NE2 GLN H 1 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN H 1 " -0.512 2.00e-02 2.50e+03 pdb="HE22 GLN H 1 " 0.518 2.00e-02 2.50e+03 ... (remaining 3232 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 260 2.10 - 2.72: 27489 2.72 - 3.35: 51350 3.35 - 3.97: 67388 3.97 - 4.60: 102810 Nonbonded interactions: 249297 Sorted by model distance: nonbonded pdb="HG21 THR B 34 " pdb=" HB2 SER B 99 " model vdw 1.470 2.440 nonbonded pdb="HG21 THR A 34 " pdb=" HB2 SER A 99 " model vdw 1.471 2.440 nonbonded pdb="HG21 THR H 34 " pdb=" HB2 SER H 99 " model vdw 1.471 2.440 nonbonded pdb="HG21 THR F 34 " pdb=" HB2 SER F 99 " model vdw 1.471 2.440 nonbonded pdb="HG21 THR D 34 " pdb=" HB2 SER D 99 " model vdw 1.472 2.440 ... (remaining 249292 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.150 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.840 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.011 0.336 12985 Z= 0.709 Angle : 1.001 12.618 17640 Z= 0.646 Chirality : 0.048 0.223 1910 Planarity : 0.005 0.031 2265 Dihedral : 15.332 85.331 4660 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 27.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.36 % Allowed : 17.26 % Favored : 82.38 % 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: -1.72 (0.21), residues: 1585 helix: -0.60 (0.55), residues: 85 sheet: -1.29 (0.19), residues: 715 loop : -0.90 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 58 TYR 0.008 0.001 TYR H 175 PHE 0.009 0.001 PHE B 109 TRP 0.007 0.001 TRP A 110 HIS 0.004 0.002 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00882 (12980) covalent geometry : angle 0.98083 (17630) SS BOND : bond 0.31133 ( 5) SS BOND : angle 8.41286 ( 10) hydrogen bonds : bond 0.16195 ( 490) hydrogen bonds : angle 7.15726 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 398 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.9390 (m-30) cc_final: 0.9164 (m-30) REVERT: A 170 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8664 (mp0) REVERT: J 15 GLN cc_start: 0.8372 (mm110) cc_final: 0.8058 (mm-40) REVERT: J 32 ASP cc_start: 0.9137 (p0) cc_final: 0.8736 (p0) REVERT: J 65 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8841 (mtmm) REVERT: J 101 ASN cc_start: 0.7770 (p0) cc_final: 0.7510 (p0) REVERT: B 70 ASP cc_start: 0.9373 (m-30) cc_final: 0.9109 (m-30) REVERT: B 130 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6991 (pp20) REVERT: B 170 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8722 (mp0) REVERT: C 15 GLN cc_start: 0.8403 (mm110) cc_final: 0.8059 (mm-40) REVERT: C 32 ASP cc_start: 0.9090 (p0) cc_final: 0.8568 (p0) REVERT: C 101 ASN cc_start: 0.7863 (p0) cc_final: 0.7635 (p0) REVERT: D 70 ASP cc_start: 0.9421 (m-30) cc_final: 0.9146 (m-30) REVERT: D 170 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8703 (mp0) REVERT: E 15 GLN cc_start: 0.8401 (mm110) cc_final: 0.8069 (mm-40) REVERT: E 101 ASN cc_start: 0.7845 (p0) cc_final: 0.7546 (p0) REVERT: F 70 ASP cc_start: 0.9391 (m-30) cc_final: 0.9125 (m-30) REVERT: F 130 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7125 (pp20) REVERT: F 170 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8758 (mp0) REVERT: G 15 GLN cc_start: 0.8289 (mm110) cc_final: 0.7945 (mm-40) REVERT: G 32 ASP cc_start: 0.9151 (p0) cc_final: 0.8870 (p0) REVERT: G 101 ASN cc_start: 0.7900 (p0) cc_final: 0.7590 (p0) REVERT: H 70 ASP cc_start: 0.9384 (m-30) cc_final: 0.9098 (m-30) REVERT: H 130 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7069 (pp20) REVERT: H 170 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8750 (mp0) REVERT: I 15 GLN cc_start: 0.8365 (mm110) cc_final: 0.8021 (mm-40) REVERT: I 32 ASP cc_start: 0.9114 (p0) cc_final: 0.8656 (p0) REVERT: I 90 ASP cc_start: 0.9528 (m-30) cc_final: 0.9302 (m-30) REVERT: I 101 ASN cc_start: 0.7913 (p0) cc_final: 0.7618 (p0) outliers start: 5 outliers final: 0 residues processed: 403 average time/residue: 0.1926 time to fit residues: 115.4489 Evaluate side-chains 342 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.2980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.067038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.048254 restraints weight = 81984.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.051201 restraints weight = 31366.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.053254 restraints weight = 16858.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.054638 restraints weight = 10775.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.055483 restraints weight = 7746.311| |-----------------------------------------------------------------------------| r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12985 Z= 0.179 Angle : 0.567 6.628 17640 Z= 0.302 Chirality : 0.044 0.163 1910 Planarity : 0.003 0.037 2265 Dihedral : 4.058 14.757 1750 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 27.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.32 % Allowed : 22.09 % Favored : 74.58 % 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: -1.46 (0.21), residues: 1585 helix: -0.31 (0.55), residues: 85 sheet: -1.14 (0.19), residues: 775 loop : -0.65 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 33 TYR 0.012 0.001 TYR C 80 PHE 0.009 0.001 PHE I 31 TRP 0.008 0.001 TRP A 110 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00403 (12980) covalent geometry : angle 0.56586 (17630) SS BOND : bond 0.00451 ( 5) SS BOND : angle 1.30306 ( 10) hydrogen bonds : bond 0.03732 ( 490) hydrogen bonds : angle 5.62631 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 328 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.9200 (tp30) cc_final: 0.8883 (tp30) REVERT: A 70 ASP cc_start: 0.9269 (m-30) cc_final: 0.9055 (m-30) REVERT: J 15 GLN cc_start: 0.8563 (mm110) cc_final: 0.8031 (mm110) REVERT: J 32 ASP cc_start: 0.8868 (p0) cc_final: 0.8500 (p0) REVERT: J 44 LYS cc_start: 0.8421 (mppt) cc_final: 0.8217 (mppt) REVERT: J 65 LYS cc_start: 0.9304 (ttmm) cc_final: 0.8926 (mtpp) REVERT: B 16 ASP cc_start: 0.9032 (p0) cc_final: 0.8801 (p0) REVERT: B 62 GLU cc_start: 0.9100 (tp30) cc_final: 0.8864 (tp30) REVERT: B 70 ASP cc_start: 0.9249 (m-30) cc_final: 0.8985 (m-30) REVERT: B 130 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7372 (pp20) REVERT: C 15 GLN cc_start: 0.8661 (mm110) cc_final: 0.8072 (mm110) REVERT: C 40 GLN cc_start: 0.7389 (tm-30) cc_final: 0.7173 (tm-30) REVERT: C 65 LYS cc_start: 0.9306 (ttmm) cc_final: 0.8973 (mtpp) REVERT: C 95 PHE cc_start: 0.9377 (m-80) cc_final: 0.8923 (m-80) REVERT: D 62 GLU cc_start: 0.9175 (tp30) cc_final: 0.8878 (tp30) REVERT: D 70 ASP cc_start: 0.9313 (m-30) cc_final: 0.9066 (m-30) REVERT: E 15 GLN cc_start: 0.8652 (mm110) cc_final: 0.8116 (mm110) REVERT: F 62 GLU cc_start: 0.9174 (tp30) cc_final: 0.8907 (tp30) REVERT: F 70 ASP cc_start: 0.9264 (m-30) cc_final: 0.9037 (m-30) REVERT: F 130 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7474 (pp20) REVERT: G 15 GLN cc_start: 0.8662 (mm110) cc_final: 0.8126 (mm110) REVERT: G 65 LYS cc_start: 0.9355 (ttmm) cc_final: 0.8970 (mtpp) REVERT: H 16 ASP cc_start: 0.9085 (p0) cc_final: 0.8880 (p0) REVERT: H 70 ASP cc_start: 0.9276 (m-30) cc_final: 0.9006 (m-30) REVERT: I 15 GLN cc_start: 0.8634 (mm110) cc_final: 0.8050 (mm110) REVERT: I 87 LYS cc_start: 0.9087 (mtmm) cc_final: 0.8565 (mtmm) outliers start: 46 outliers final: 34 residues processed: 336 average time/residue: 0.1965 time to fit residues: 98.3462 Evaluate side-chains 347 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 113 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.068210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.049289 restraints weight = 82093.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.052217 restraints weight = 31135.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.054259 restraints weight = 16681.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.055633 restraints weight = 10641.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.056462 restraints weight = 7666.600| |-----------------------------------------------------------------------------| r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12985 Z= 0.088 Angle : 0.511 5.460 17640 Z= 0.270 Chirality : 0.044 0.151 1910 Planarity : 0.003 0.040 2265 Dihedral : 3.874 15.035 1750 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 24.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.44 % Allowed : 23.25 % Favored : 75.31 % 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: -1.22 (0.22), residues: 1585 helix: 0.08 (0.57), residues: 85 sheet: -1.08 (0.18), residues: 805 loop : -0.32 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 58 TYR 0.007 0.001 TYR E 80 PHE 0.011 0.001 PHE I 31 TRP 0.006 0.001 TRP D 110 HIS 0.003 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00203 (12980) covalent geometry : angle 0.51081 (17630) SS BOND : bond 0.00210 ( 5) SS BOND : angle 0.75484 ( 10) hydrogen bonds : bond 0.02986 ( 490) hydrogen bonds : angle 5.37705 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 355 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.9102 (p0) cc_final: 0.8861 (p0) REVERT: A 70 ASP cc_start: 0.9292 (m-30) cc_final: 0.9070 (m-30) REVERT: J 8 GLU cc_start: 0.7984 (pm20) cc_final: 0.7724 (pt0) REVERT: J 15 GLN cc_start: 0.8576 (mm110) cc_final: 0.8015 (mm110) REVERT: J 32 ASP cc_start: 0.8910 (p0) cc_final: 0.8504 (p0) REVERT: J 44 LYS cc_start: 0.8708 (mppt) cc_final: 0.7806 (mppt) REVERT: J 80 TYR cc_start: 0.9212 (m-80) cc_final: 0.8649 (m-10) REVERT: J 87 LYS cc_start: 0.8819 (mtmm) cc_final: 0.8534 (mtmm) REVERT: B 16 ASP cc_start: 0.9104 (p0) cc_final: 0.8767 (p0) REVERT: B 70 ASP cc_start: 0.9265 (m-30) cc_final: 0.8989 (m-30) REVERT: B 130 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7286 (pp20) REVERT: C 8 GLU cc_start: 0.8048 (pm20) cc_final: 0.7584 (pt0) REVERT: C 15 GLN cc_start: 0.8703 (mm110) cc_final: 0.8130 (mm110) REVERT: C 95 PHE cc_start: 0.9211 (m-80) cc_final: 0.8737 (m-80) REVERT: D 70 ASP cc_start: 0.9324 (m-30) cc_final: 0.9061 (m-30) REVERT: D 101 GLU cc_start: 0.8732 (tt0) cc_final: 0.8354 (tt0) REVERT: E 15 GLN cc_start: 0.8709 (mm110) cc_final: 0.8198 (mm110) REVERT: F 70 ASP cc_start: 0.9282 (m-30) cc_final: 0.9036 (m-30) REVERT: F 130 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7393 (pp20) REVERT: G 15 GLN cc_start: 0.8678 (mm110) cc_final: 0.8151 (mm110) REVERT: G 44 LYS cc_start: 0.8373 (mppt) cc_final: 0.8066 (mppt) REVERT: H 16 ASP cc_start: 0.9150 (p0) cc_final: 0.8867 (p0) REVERT: H 70 ASP cc_start: 0.9284 (m-30) cc_final: 0.8991 (m-30) REVERT: H 130 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7348 (pp20) REVERT: I 8 GLU cc_start: 0.8078 (pm20) cc_final: 0.7775 (pt0) REVERT: I 15 GLN cc_start: 0.8702 (mm110) cc_final: 0.8134 (mm110) outliers start: 20 outliers final: 11 residues processed: 360 average time/residue: 0.1930 time to fit residues: 103.6094 Evaluate side-chains 349 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 338 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain I residue 48 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 122 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.065602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.046949 restraints weight = 82998.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.049783 restraints weight = 31653.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.051768 restraints weight = 17033.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.053000 restraints weight = 10902.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.053984 restraints weight = 7982.382| |-----------------------------------------------------------------------------| r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12985 Z= 0.163 Angle : 0.511 5.131 17640 Z= 0.274 Chirality : 0.043 0.144 1910 Planarity : 0.003 0.029 2265 Dihedral : 3.953 13.987 1750 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 28.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.82 % Allowed : 22.38 % Favored : 74.80 % 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: -1.23 (0.22), residues: 1585 helix: 0.24 (0.58), residues: 85 sheet: -1.12 (0.18), residues: 755 loop : -0.38 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 33 TYR 0.013 0.001 TYR E 80 PHE 0.008 0.001 PHE B 52 TRP 0.005 0.001 TRP B 110 HIS 0.006 0.002 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00370 (12980) covalent geometry : angle 0.51044 (17630) SS BOND : bond 0.00430 ( 5) SS BOND : angle 0.75460 ( 10) hydrogen bonds : bond 0.03196 ( 490) hydrogen bonds : angle 5.36532 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 325 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.9155 (p0) cc_final: 0.8881 (p0) REVERT: A 70 ASP cc_start: 0.9327 (m-30) cc_final: 0.9118 (m-30) REVERT: J 8 GLU cc_start: 0.7976 (pm20) cc_final: 0.7662 (pt0) REVERT: J 15 GLN cc_start: 0.8665 (mm110) cc_final: 0.8169 (mm110) REVERT: J 32 ASP cc_start: 0.8908 (p0) cc_final: 0.8529 (p0) REVERT: J 44 LYS cc_start: 0.8651 (mppt) cc_final: 0.8374 (mppt) REVERT: J 65 LYS cc_start: 0.9277 (ttmm) cc_final: 0.8900 (mtpp) REVERT: J 80 TYR cc_start: 0.9197 (m-80) cc_final: 0.8656 (m-10) REVERT: J 87 LYS cc_start: 0.8852 (mtmm) cc_final: 0.8643 (mtmm) REVERT: B 16 ASP cc_start: 0.9189 (p0) cc_final: 0.8806 (p0) REVERT: B 62 GLU cc_start: 0.9140 (tp30) cc_final: 0.8838 (tp30) REVERT: B 70 ASP cc_start: 0.9305 (m-30) cc_final: 0.9060 (m-30) REVERT: B 101 GLU cc_start: 0.8766 (tt0) cc_final: 0.8478 (tt0) REVERT: B 130 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7355 (pp20) REVERT: C 8 GLU cc_start: 0.8039 (pm20) cc_final: 0.7679 (pt0) REVERT: C 15 GLN cc_start: 0.8760 (mm110) cc_final: 0.8205 (mm110) REVERT: C 95 PHE cc_start: 0.9186 (m-80) cc_final: 0.8756 (m-80) REVERT: D 16 ASP cc_start: 0.9132 (p0) cc_final: 0.8858 (p0) REVERT: D 62 GLU cc_start: 0.9201 (tp30) cc_final: 0.8871 (tp30) REVERT: D 70 ASP cc_start: 0.9369 (m-30) cc_final: 0.9122 (m-30) REVERT: E 5 GLN cc_start: 0.9264 (mm-40) cc_final: 0.9025 (mm-40) REVERT: E 15 GLN cc_start: 0.8758 (mm110) cc_final: 0.8246 (mm110) REVERT: E 87 LYS cc_start: 0.8700 (mtmm) cc_final: 0.8340 (mtmm) REVERT: F 70 ASP cc_start: 0.9328 (m-30) cc_final: 0.9095 (m-30) REVERT: G 15 GLN cc_start: 0.8715 (mm110) cc_final: 0.8222 (mm110) REVERT: G 40 GLN cc_start: 0.8664 (tt0) cc_final: 0.8118 (tp40) REVERT: G 44 LYS cc_start: 0.8520 (mppt) cc_final: 0.8227 (mppt) REVERT: H 16 ASP cc_start: 0.9217 (p0) cc_final: 0.8926 (p0) REVERT: H 70 ASP cc_start: 0.9326 (m-30) cc_final: 0.9060 (m-30) REVERT: H 130 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7429 (pp20) REVERT: H 170 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8688 (mp0) REVERT: I 8 GLU cc_start: 0.8049 (pm20) cc_final: 0.7733 (pt0) REVERT: I 15 GLN cc_start: 0.8780 (mm110) cc_final: 0.8281 (mm110) REVERT: I 95 PHE cc_start: 0.9236 (m-10) cc_final: 0.8978 (m-10) outliers start: 39 outliers final: 27 residues processed: 336 average time/residue: 0.1954 time to fit residues: 97.8268 Evaluate side-chains 334 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 307 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 113 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 43 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.065655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.047045 restraints weight = 81984.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.049869 restraints weight = 31085.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.051825 restraints weight = 16689.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.053173 restraints weight = 10682.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.054051 restraints weight = 7718.716| |-----------------------------------------------------------------------------| r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12985 Z= 0.142 Angle : 0.504 5.197 17640 Z= 0.270 Chirality : 0.043 0.141 1910 Planarity : 0.003 0.029 2265 Dihedral : 3.934 14.672 1750 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 28.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.31 % Allowed : 22.89 % Favored : 74.80 % 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: -1.16 (0.21), residues: 1585 helix: 0.37 (0.59), residues: 85 sheet: -0.97 (0.19), residues: 725 loop : -0.52 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 33 TYR 0.008 0.001 TYR E 80 PHE 0.009 0.001 PHE B 52 TRP 0.006 0.001 TRP B 110 HIS 0.006 0.002 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00324 (12980) covalent geometry : angle 0.50363 (17630) SS BOND : bond 0.00401 ( 5) SS BOND : angle 0.69168 ( 10) hydrogen bonds : bond 0.03051 ( 490) hydrogen bonds : angle 5.29766 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 324 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.9179 (p0) cc_final: 0.8888 (p0) REVERT: J 8 GLU cc_start: 0.7897 (pm20) cc_final: 0.7687 (pt0) REVERT: J 32 ASP cc_start: 0.8899 (p0) cc_final: 0.8527 (p0) REVERT: J 65 LYS cc_start: 0.9285 (ttmm) cc_final: 0.8906 (mtpp) REVERT: J 80 TYR cc_start: 0.9205 (m-80) cc_final: 0.8579 (m-10) REVERT: J 87 LYS cc_start: 0.8837 (mtmm) cc_final: 0.8626 (mtmm) REVERT: B 16 ASP cc_start: 0.9187 (p0) cc_final: 0.8772 (p0) REVERT: B 70 ASP cc_start: 0.9323 (m-30) cc_final: 0.9086 (m-30) REVERT: B 130 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7389 (pp20) REVERT: B 170 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8702 (mp0) REVERT: C 8 GLU cc_start: 0.7967 (pm20) cc_final: 0.7558 (pt0) REVERT: C 15 GLN cc_start: 0.8795 (mm110) cc_final: 0.8265 (mm110) REVERT: C 65 LYS cc_start: 0.9276 (ttmm) cc_final: 0.8925 (mtpp) REVERT: C 95 PHE cc_start: 0.9172 (m-80) cc_final: 0.8729 (m-80) REVERT: D 16 ASP cc_start: 0.9195 (p0) cc_final: 0.8877 (p0) REVERT: D 70 ASP cc_start: 0.9380 (m-30) cc_final: 0.9136 (m-30) REVERT: E 5 GLN cc_start: 0.9250 (mm-40) cc_final: 0.9025 (mm-40) REVERT: E 8 GLU cc_start: 0.8016 (pm20) cc_final: 0.7503 (pt0) REVERT: E 87 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8409 (mtmm) REVERT: F 70 ASP cc_start: 0.9350 (m-30) cc_final: 0.9133 (m-30) REVERT: G 15 GLN cc_start: 0.8741 (mm110) cc_final: 0.8192 (mm110) REVERT: G 40 GLN cc_start: 0.8706 (tt0) cc_final: 0.8097 (tp40) REVERT: G 44 LYS cc_start: 0.8507 (mppt) cc_final: 0.7956 (mppt) REVERT: H 16 ASP cc_start: 0.9233 (p0) cc_final: 0.8937 (p0) REVERT: H 62 GLU cc_start: 0.9225 (tp30) cc_final: 0.8956 (tp30) REVERT: H 70 ASP cc_start: 0.9339 (m-30) cc_final: 0.9072 (m-30) REVERT: H 130 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7432 (pp20) REVERT: I 8 GLU cc_start: 0.8006 (pm20) cc_final: 0.7683 (pt0) REVERT: I 15 GLN cc_start: 0.8820 (mm110) cc_final: 0.8313 (mm110) REVERT: I 95 PHE cc_start: 0.9214 (m-10) cc_final: 0.8944 (m-10) outliers start: 32 outliers final: 23 residues processed: 335 average time/residue: 0.1954 time to fit residues: 97.2714 Evaluate side-chains 336 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 313 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 113 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 42 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.064851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2350 r_free = 0.2350 target = 0.046189 restraints weight = 83210.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.048969 restraints weight = 31844.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.050886 restraints weight = 17165.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.052192 restraints weight = 11068.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.053109 restraints weight = 8033.134| |-----------------------------------------------------------------------------| r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 12985 Z= 0.216 Angle : 0.533 4.982 17640 Z= 0.287 Chirality : 0.043 0.141 1910 Planarity : 0.003 0.032 2265 Dihedral : 4.111 15.636 1750 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 29.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.10 % Allowed : 22.89 % Favored : 74.01 % 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: -1.25 (0.21), residues: 1585 helix: 0.30 (0.60), residues: 85 sheet: -0.98 (0.19), residues: 725 loop : -0.64 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 33 TYR 0.018 0.001 TYR G 80 PHE 0.011 0.001 PHE E 31 TRP 0.005 0.001 TRP B 110 HIS 0.005 0.002 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00486 (12980) covalent geometry : angle 0.53254 (17630) SS BOND : bond 0.00475 ( 5) SS BOND : angle 0.76156 ( 10) hydrogen bonds : bond 0.03382 ( 490) hydrogen bonds : angle 5.42511 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 306 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.9249 (tp30) cc_final: 0.8933 (tp30) REVERT: J 32 ASP cc_start: 0.8902 (p0) cc_final: 0.8557 (p0) REVERT: J 65 LYS cc_start: 0.9293 (ttmm) cc_final: 0.8915 (mtpp) REVERT: J 80 TYR cc_start: 0.9199 (m-80) cc_final: 0.8588 (m-10) REVERT: J 87 LYS cc_start: 0.8826 (mtmm) cc_final: 0.8605 (mtmm) REVERT: B 16 ASP cc_start: 0.9225 (p0) cc_final: 0.8812 (p0) REVERT: B 62 GLU cc_start: 0.9205 (tp30) cc_final: 0.8839 (tp30) REVERT: B 70 ASP cc_start: 0.9351 (m-30) cc_final: 0.9126 (m-30) REVERT: C 15 GLN cc_start: 0.8780 (mm110) cc_final: 0.8241 (mm110) REVERT: C 87 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8329 (ptpp) REVERT: C 95 PHE cc_start: 0.9185 (m-80) cc_final: 0.8677 (m-80) REVERT: D 16 ASP cc_start: 0.9237 (p0) cc_final: 0.8886 (p0) REVERT: D 70 ASP cc_start: 0.9405 (m-30) cc_final: 0.9176 (m-30) REVERT: E 5 GLN cc_start: 0.9282 (mm-40) cc_final: 0.9071 (mm-40) REVERT: E 8 GLU cc_start: 0.7961 (pm20) cc_final: 0.7470 (pt0) REVERT: E 15 GLN cc_start: 0.8839 (mm110) cc_final: 0.8322 (mm110) REVERT: E 83 MET cc_start: 0.8663 (mtp) cc_final: 0.8397 (mpp) REVERT: E 87 LYS cc_start: 0.8777 (mtmm) cc_final: 0.8465 (mtmm) REVERT: F 38 HIS cc_start: 0.8707 (OUTLIER) cc_final: 0.8165 (t70) REVERT: F 70 ASP cc_start: 0.9373 (m-30) cc_final: 0.9150 (m-30) REVERT: G 15 GLN cc_start: 0.8772 (mm110) cc_final: 0.8239 (mm110) REVERT: G 40 GLN cc_start: 0.8743 (tt0) cc_final: 0.8113 (tp40) REVERT: G 44 LYS cc_start: 0.8503 (mppt) cc_final: 0.7957 (mppt) REVERT: G 65 LYS cc_start: 0.9362 (ttmm) cc_final: 0.8953 (mtpp) REVERT: G 83 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8479 (mpp) REVERT: H 16 ASP cc_start: 0.9252 (p0) cc_final: 0.8968 (p0) REVERT: H 70 ASP cc_start: 0.9364 (m-30) cc_final: 0.9120 (m-30) REVERT: H 130 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7534 (pp20) REVERT: H 170 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8657 (mp0) REVERT: I 15 GLN cc_start: 0.8827 (mm110) cc_final: 0.8317 (mm110) outliers start: 43 outliers final: 32 residues processed: 322 average time/residue: 0.1929 time to fit residues: 92.1685 Evaluate side-chains 329 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 295 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 113 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 129 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.065544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2370 r_free = 0.2370 target = 0.046914 restraints weight = 81969.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.049728 restraints weight = 31153.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.051658 restraints weight = 16725.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.052983 restraints weight = 10713.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.053884 restraints weight = 7755.957| |-----------------------------------------------------------------------------| r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12985 Z= 0.137 Angle : 0.514 5.568 17640 Z= 0.275 Chirality : 0.043 0.143 1910 Planarity : 0.003 0.031 2265 Dihedral : 3.976 15.930 1750 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 27.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.38 % Allowed : 22.89 % Favored : 74.73 % 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: -1.13 (0.21), residues: 1585 helix: 0.45 (0.60), residues: 85 sheet: -0.90 (0.19), residues: 725 loop : -0.58 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 33 TYR 0.007 0.001 TYR G 80 PHE 0.014 0.001 PHE I 31 TRP 0.006 0.001 TRP B 110 HIS 0.005 0.002 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00312 (12980) covalent geometry : angle 0.51412 (17630) SS BOND : bond 0.00369 ( 5) SS BOND : angle 0.58190 ( 10) hydrogen bonds : bond 0.02989 ( 490) hydrogen bonds : angle 5.30316 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 329 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.9131 (p0) cc_final: 0.8916 (p0) REVERT: A 101 GLU cc_start: 0.8758 (tt0) cc_final: 0.8486 (tt0) REVERT: J 32 ASP cc_start: 0.8907 (p0) cc_final: 0.8547 (p0) REVERT: J 65 LYS cc_start: 0.9285 (ttmm) cc_final: 0.8911 (mtpp) REVERT: J 87 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8561 (mtmm) REVERT: B 16 ASP cc_start: 0.9216 (p0) cc_final: 0.8782 (p0) REVERT: B 70 ASP cc_start: 0.9355 (m-30) cc_final: 0.9133 (m-30) REVERT: B 170 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8687 (mp0) REVERT: C 15 GLN cc_start: 0.8817 (mm110) cc_final: 0.8302 (mm110) REVERT: C 95 PHE cc_start: 0.9160 (m-80) cc_final: 0.8613 (m-80) REVERT: D 16 ASP cc_start: 0.9248 (p0) cc_final: 0.8875 (p0) REVERT: D 70 ASP cc_start: 0.9403 (m-30) cc_final: 0.9173 (m-30) REVERT: E 5 GLN cc_start: 0.9272 (mm-40) cc_final: 0.9059 (mm-40) REVERT: E 15 GLN cc_start: 0.8845 (mm110) cc_final: 0.8332 (mm110) REVERT: E 87 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8487 (mtmm) REVERT: F 70 ASP cc_start: 0.9372 (m-30) cc_final: 0.9144 (m-30) REVERT: G 15 GLN cc_start: 0.8764 (mm110) cc_final: 0.8230 (mm110) REVERT: G 40 GLN cc_start: 0.8759 (tt0) cc_final: 0.8102 (tp-100) REVERT: G 44 LYS cc_start: 0.8486 (mppt) cc_final: 0.7902 (mppt) REVERT: G 65 LYS cc_start: 0.9357 (ttmm) cc_final: 0.8940 (mtpp) REVERT: H 16 ASP cc_start: 0.9251 (p0) cc_final: 0.8968 (p0) REVERT: H 70 ASP cc_start: 0.9357 (m-30) cc_final: 0.9116 (m-30) REVERT: I 8 GLU cc_start: 0.8038 (pm20) cc_final: 0.7628 (pt0) REVERT: I 15 GLN cc_start: 0.8841 (mm110) cc_final: 0.8332 (mm110) REVERT: I 80 TYR cc_start: 0.9180 (m-10) cc_final: 0.8973 (m-10) REVERT: I 87 LYS cc_start: 0.8561 (mtmm) cc_final: 0.8341 (ptpp) outliers start: 33 outliers final: 24 residues processed: 339 average time/residue: 0.1877 time to fit residues: 94.8775 Evaluate side-chains 344 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 320 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 113 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 48 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 103 optimal weight: 0.2980 chunk 115 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.065918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.047300 restraints weight = 82094.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.050104 restraints weight = 31213.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.052033 restraints weight = 16771.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.053357 restraints weight = 10756.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.054152 restraints weight = 7787.823| |-----------------------------------------------------------------------------| r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12985 Z= 0.139 Angle : 0.519 5.536 17640 Z= 0.276 Chirality : 0.043 0.141 1910 Planarity : 0.003 0.033 2265 Dihedral : 3.964 20.095 1750 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 27.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.45 % Allowed : 23.83 % Favored : 73.72 % 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: -1.09 (0.22), residues: 1585 helix: 0.44 (0.60), residues: 85 sheet: -0.85 (0.19), residues: 725 loop : -0.56 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 33 TYR 0.019 0.001 TYR E 80 PHE 0.013 0.001 PHE I 95 TRP 0.006 0.001 TRP B 110 HIS 0.005 0.002 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00319 (12980) covalent geometry : angle 0.51850 (17630) SS BOND : bond 0.00391 ( 5) SS BOND : angle 0.59480 ( 10) hydrogen bonds : bond 0.02956 ( 490) hydrogen bonds : angle 5.25232 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 316 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.9142 (p0) cc_final: 0.8919 (p0) REVERT: J 32 ASP cc_start: 0.8902 (p0) cc_final: 0.8544 (p0) REVERT: J 65 LYS cc_start: 0.9274 (ttmm) cc_final: 0.8903 (mtpp) REVERT: J 87 LYS cc_start: 0.8785 (mtmm) cc_final: 0.8566 (mtmm) REVERT: B 16 ASP cc_start: 0.9211 (p0) cc_final: 0.8773 (p0) REVERT: B 70 ASP cc_start: 0.9350 (m-30) cc_final: 0.9133 (m-30) REVERT: B 170 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8683 (mp0) REVERT: C 95 PHE cc_start: 0.9116 (m-80) cc_final: 0.8580 (m-80) REVERT: D 16 ASP cc_start: 0.9242 (p0) cc_final: 0.8873 (p0) REVERT: D 62 GLU cc_start: 0.9223 (tp30) cc_final: 0.8989 (tp30) REVERT: D 70 ASP cc_start: 0.9396 (m-30) cc_final: 0.9165 (m-30) REVERT: E 5 GLN cc_start: 0.9264 (mm-40) cc_final: 0.9057 (mm-40) REVERT: E 8 GLU cc_start: 0.7963 (pm20) cc_final: 0.7357 (pt0) REVERT: E 87 LYS cc_start: 0.8796 (mtmm) cc_final: 0.8521 (mtmm) REVERT: F 70 ASP cc_start: 0.9371 (m-30) cc_final: 0.9147 (m-30) REVERT: G 15 GLN cc_start: 0.8777 (mm110) cc_final: 0.8105 (tp40) REVERT: G 40 GLN cc_start: 0.8796 (tt0) cc_final: 0.8178 (tp-100) REVERT: G 44 LYS cc_start: 0.8462 (mppt) cc_final: 0.8049 (mppt) REVERT: G 65 LYS cc_start: 0.9355 (ttmm) cc_final: 0.8945 (mtpp) REVERT: H 16 ASP cc_start: 0.9255 (p0) cc_final: 0.8976 (p0) REVERT: H 70 ASP cc_start: 0.9362 (m-30) cc_final: 0.9124 (m-30) REVERT: I 15 GLN cc_start: 0.8838 (mm110) cc_final: 0.8337 (mm110) REVERT: I 65 LYS cc_start: 0.9297 (ttmm) cc_final: 0.8893 (mtpp) REVERT: I 87 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8335 (ptpp) outliers start: 34 outliers final: 25 residues processed: 330 average time/residue: 0.1767 time to fit residues: 87.3531 Evaluate side-chains 337 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 312 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 113 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 146 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.0970 chunk 129 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.066831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.048214 restraints weight = 81888.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.051065 restraints weight = 31003.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.053035 restraints weight = 16481.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.054353 restraints weight = 10511.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.055141 restraints weight = 7583.833| |-----------------------------------------------------------------------------| r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12985 Z= 0.107 Angle : 0.513 5.685 17640 Z= 0.272 Chirality : 0.044 0.141 1910 Planarity : 0.003 0.033 2265 Dihedral : 3.857 20.753 1750 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 26.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.88 % Allowed : 24.33 % Favored : 73.79 % 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: -0.96 (0.22), residues: 1585 helix: 0.53 (0.60), residues: 85 sheet: -0.77 (0.19), residues: 725 loop : -0.46 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 33 TYR 0.029 0.001 TYR E 80 PHE 0.013 0.001 PHE I 95 TRP 0.006 0.001 TRP A 110 HIS 0.005 0.002 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00250 (12980) covalent geometry : angle 0.51340 (17630) SS BOND : bond 0.00336 ( 5) SS BOND : angle 0.51273 ( 10) hydrogen bonds : bond 0.02746 ( 490) hydrogen bonds : angle 5.15032 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 334 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8739 (tt0) cc_final: 0.8487 (tt0) REVERT: J 15 GLN cc_start: 0.8733 (mm110) cc_final: 0.8062 (tp40) REVERT: J 32 ASP cc_start: 0.8923 (p0) cc_final: 0.8552 (p0) REVERT: J 65 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8898 (mtpp) REVERT: J 87 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8564 (mtmm) REVERT: B 16 ASP cc_start: 0.9206 (p0) cc_final: 0.8773 (p0) REVERT: B 70 ASP cc_start: 0.9345 (m-30) cc_final: 0.9125 (m-30) REVERT: B 170 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8686 (mp0) REVERT: C 40 GLN cc_start: 0.8731 (tt0) cc_final: 0.7967 (tp40) REVERT: C 45 GLN cc_start: 0.8940 (mp10) cc_final: 0.8671 (mp10) REVERT: C 80 TYR cc_start: 0.9137 (m-10) cc_final: 0.8874 (m-10) REVERT: C 95 PHE cc_start: 0.9047 (m-80) cc_final: 0.8559 (m-80) REVERT: D 16 ASP cc_start: 0.9239 (p0) cc_final: 0.8863 (p0) REVERT: D 70 ASP cc_start: 0.9389 (m-30) cc_final: 0.9158 (m-30) REVERT: E 5 GLN cc_start: 0.9251 (mm-40) cc_final: 0.9042 (mm-40) REVERT: E 65 LYS cc_start: 0.9304 (ttmm) cc_final: 0.8908 (mtpp) REVERT: E 87 LYS cc_start: 0.8816 (mtmm) cc_final: 0.8564 (mtmm) REVERT: F 70 ASP cc_start: 0.9359 (m-30) cc_final: 0.9155 (m-30) REVERT: G 40 GLN cc_start: 0.8809 (tt0) cc_final: 0.8271 (tt0) REVERT: G 44 LYS cc_start: 0.8482 (mppt) cc_final: 0.8206 (mppt) REVERT: G 65 LYS cc_start: 0.9352 (ttmm) cc_final: 0.8945 (mtpp) REVERT: G 95 PHE cc_start: 0.9212 (m-10) cc_final: 0.8825 (m-10) REVERT: H 16 ASP cc_start: 0.9243 (p0) cc_final: 0.8966 (p0) REVERT: H 62 GLU cc_start: 0.9228 (tp30) cc_final: 0.8958 (tp30) REVERT: H 70 ASP cc_start: 0.9349 (m-30) cc_final: 0.9116 (m-30) REVERT: H 130 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7536 (pp20) REVERT: I 15 GLN cc_start: 0.8825 (mm110) cc_final: 0.8214 (tp40) REVERT: I 37 TRP cc_start: 0.9188 (m100) cc_final: 0.8720 (m100) REVERT: I 40 GLN cc_start: 0.8716 (tt0) cc_final: 0.8090 (tp40) REVERT: I 80 TYR cc_start: 0.9168 (m-10) cc_final: 0.8955 (m-10) REVERT: I 87 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8294 (ptpp) outliers start: 26 outliers final: 16 residues processed: 341 average time/residue: 0.1677 time to fit residues: 85.9146 Evaluate side-chains 343 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 327 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain I residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 113 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.066076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.047409 restraints weight = 81975.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.050219 restraints weight = 31275.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.052152 restraints weight = 16810.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.053451 restraints weight = 10785.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.054360 restraints weight = 7856.762| |-----------------------------------------------------------------------------| r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12985 Z= 0.155 Angle : 0.536 8.575 17640 Z= 0.285 Chirality : 0.043 0.145 1910 Planarity : 0.003 0.033 2265 Dihedral : 3.926 21.439 1750 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 28.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.95 % Allowed : 24.84 % Favored : 73.21 % 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: -1.02 (0.22), residues: 1585 helix: 0.43 (0.60), residues: 85 sheet: -0.83 (0.19), residues: 730 loop : -0.48 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 21 TYR 0.030 0.001 TYR E 80 PHE 0.016 0.001 PHE E 68 TRP 0.005 0.001 TRP B 110 HIS 0.007 0.002 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00356 (12980) covalent geometry : angle 0.53636 (17630) SS BOND : bond 0.00410 ( 5) SS BOND : angle 0.59377 ( 10) hydrogen bonds : bond 0.03036 ( 490) hydrogen bonds : angle 5.22010 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 320 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8766 (tt0) cc_final: 0.8505 (tt0) REVERT: J 32 ASP cc_start: 0.8917 (p0) cc_final: 0.8570 (p0) REVERT: J 65 LYS cc_start: 0.9286 (ttmm) cc_final: 0.8921 (mtpp) REVERT: B 16 ASP cc_start: 0.9220 (p0) cc_final: 0.8780 (p0) REVERT: B 70 ASP cc_start: 0.9352 (m-30) cc_final: 0.9139 (m-30) REVERT: B 170 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8680 (mp0) REVERT: C 95 PHE cc_start: 0.9056 (m-80) cc_final: 0.8853 (m-80) REVERT: D 16 ASP cc_start: 0.9253 (p0) cc_final: 0.8877 (p0) REVERT: D 70 ASP cc_start: 0.9395 (m-30) cc_final: 0.9171 (m-30) REVERT: E 65 LYS cc_start: 0.9336 (ttmm) cc_final: 0.8806 (mtpp) REVERT: E 87 LYS cc_start: 0.8834 (mtmm) cc_final: 0.8595 (mtmm) REVERT: F 70 ASP cc_start: 0.9372 (m-30) cc_final: 0.9149 (m-30) REVERT: G 8 GLU cc_start: 0.7814 (pm20) cc_final: 0.7325 (pt0) REVERT: G 40 GLN cc_start: 0.8779 (tt0) cc_final: 0.8270 (tt0) REVERT: G 44 LYS cc_start: 0.8486 (mppt) cc_final: 0.8193 (mppt) REVERT: G 65 LYS cc_start: 0.9370 (ttmm) cc_final: 0.9045 (mtpp) REVERT: H 16 ASP cc_start: 0.9247 (p0) cc_final: 0.8969 (p0) REVERT: H 70 ASP cc_start: 0.9367 (m-30) cc_final: 0.9134 (m-30) REVERT: H 130 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7567 (pp20) REVERT: H 170 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8610 (mp0) REVERT: I 15 GLN cc_start: 0.8840 (mm110) cc_final: 0.8231 (tp40) REVERT: I 40 GLN cc_start: 0.8724 (tt0) cc_final: 0.8028 (tp40) REVERT: I 80 TYR cc_start: 0.9170 (m-10) cc_final: 0.8949 (m-10) REVERT: I 87 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8291 (ptpp) REVERT: I 95 PHE cc_start: 0.9172 (m-80) cc_final: 0.8834 (m-80) outliers start: 27 outliers final: 16 residues processed: 330 average time/residue: 0.1974 time to fit residues: 97.3141 Evaluate side-chains 330 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 314 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 38 HIS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain H residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.067079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.048372 restraints weight = 80942.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.051208 restraints weight = 30557.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.053154 restraints weight = 16387.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.054485 restraints weight = 10500.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.055287 restraints weight = 7615.634| |-----------------------------------------------------------------------------| r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12985 Z= 0.095 Angle : 0.532 7.147 17640 Z= 0.279 Chirality : 0.044 0.145 1910 Planarity : 0.003 0.033 2265 Dihedral : 3.795 19.689 1750 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.66 % Allowed : 25.49 % Favored : 72.85 % 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: -0.89 (0.22), residues: 1585 helix: 0.60 (0.61), residues: 85 sheet: -0.75 (0.19), residues: 730 loop : -0.39 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 21 TYR 0.026 0.001 TYR E 80 PHE 0.022 0.001 PHE E 68 TRP 0.007 0.001 TRP F 110 HIS 0.006 0.002 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00230 (12980) covalent geometry : angle 0.53160 (17630) SS BOND : bond 0.00301 ( 5) SS BOND : angle 0.45635 ( 10) hydrogen bonds : bond 0.02658 ( 490) hydrogen bonds : angle 5.12626 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3484.13 seconds wall clock time: 60 minutes 38.79 seconds (3638.79 seconds total)