Starting phenix.real_space_refine on Fri Sep 11 16:18:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y90_10731/09_2026/6y90_10731.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y90_10731/09_2026/6y90_10731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y90_10731/09_2026/6y90_10731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y90_10731/09_2026/6y90_10731.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6y90_10731/09_2026/6y90_10731.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y90_10731/09_2026/6y90_10731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y90_10731/09_2026/6y90_10731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y90_10731/09_2026/6y90_10731.map" } resolution = 3.69 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= 0.004 sd= 0.057 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 P 2 5.49 5 S 56 5.16 5 C 6368 2.51 5 N 1520 2.21 5 O 1832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9778 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1341 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "B" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1341 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "C" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1669 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 210} Chain: "D" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1623 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199} Chain: "A" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 256 Unusual residues: {'MYS': 5, 'PC1': 1, 'Y01': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 256 Unusual residues: {'MYS': 5, 'PC1': 1, 'Y01': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: H, L Time building chain proxies: 2.66, per 1000 atoms: 0.27 Number of scatterers: 9778 At special positions: 0 Unit cell: (103.378, 142.45, 134.31, 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 56 16.00 P 2 15.00 O 1832 8.00 N 1520 7.00 C 6368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 224 " - pdb=" SG CYS D 213 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 224 " - pdb=" SG CYS L 213 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 395.8 milliseconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 20 sheets defined 24.7% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 48 through 70 Processing helix chain 'A' and resid 79 through 84 removed outlier: 4.004A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 102 removed outlier: 3.805A pdb=" N TRP A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 143 removed outlier: 4.010A pdb=" N MET A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 177 through 215 removed outlier: 3.859A pdb=" N CYS A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 71 removed outlier: 3.567A pdb=" N LEU B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.707A pdb=" N VAL B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 102 removed outlier: 3.889A pdb=" N TRP B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 143 removed outlier: 4.054A pdb=" N MET B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 177 through 215 removed outlier: 3.729A pdb=" N CYS B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.540A pdb=" N LEU D 124 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY D 127 " --> pdb=" O GLN D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 188 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'L' and resid 120 through 127 removed outlier: 3.539A pdb=" N LEU L 124 " --> pdb=" O SER L 120 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY L 127 " --> pdb=" O GLN L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 188 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.752A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 59 removed outlier: 3.620A pdb=" N ILE C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.817A pdb=" N ASP C 105 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.881A pdb=" N SER C 128 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY C 147 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER C 188 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N SER C 185 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA C 176 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER C 187 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 159 through 160 removed outlier: 3.537A pdb=" N THR C 159 " --> pdb=" O ASN C 207 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.668A pdb=" N THR D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 19 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.558A pdb=" N LEU D 11 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 84 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N GLN D 36 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D 48 " --> pdb=" O ASN D 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 113 through 117 removed outlier: 3.516A pdb=" N SER D 113 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN D 136 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 132 " --> pdb=" O PHE D 117 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA D 129 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 180 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER D 176 " --> pdb=" O CYS D 133 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 135 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 174 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 161 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR D 177 " --> pdb=" O GLN D 159 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN D 159 " --> pdb=" O THR D 177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.953A pdb=" N TRP D 147 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS D 144 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU D 194 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR D 191 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE D 208 " --> pdb=" O TYR D 191 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS D 193 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS D 206 " --> pdb=" O CYS D 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.753A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.620A pdb=" N ILE H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 100 through 102 removed outlier: 3.819A pdb=" N ASP H 105 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 128 through 132 removed outlier: 3.881A pdb=" N SER H 128 " --> pdb=" O LYS H 151 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER H 188 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N SER H 185 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA H 176 " --> pdb=" O SER H 185 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER H 187 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 159 through 160 removed outlier: 3.537A pdb=" N THR H 159 " --> pdb=" O ASN H 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.668A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.558A pdb=" N LEU L 11 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR L 84 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N GLN L 36 " --> pdb=" O PRO L 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR L 48 " --> pdb=" O ASN L 52 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 113 through 117 removed outlier: 3.516A pdb=" N SER L 113 " --> pdb=" O ASN L 136 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN L 136 " --> pdb=" O SER L 113 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA L 129 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU L 180 " --> pdb=" O ALA L 129 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER L 176 " --> pdb=" O CYS L 133 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU L 135 " --> pdb=" O LEU L 174 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU L 174 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER L 161 " --> pdb=" O SER L 175 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR L 177 " --> pdb=" O GLN L 159 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN L 159 " --> pdb=" O THR L 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 152 through 154 removed outlier: 3.954A pdb=" N TRP L 147 " --> pdb=" O GLN L 154 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS L 144 " --> pdb=" O THR L 196 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU L 194 " --> pdb=" O GLN L 146 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR L 191 " --> pdb=" O PHE L 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE L 208 " --> pdb=" O TYR L 191 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS L 193 " --> pdb=" O LYS L 206 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS L 206 " --> pdb=" O CYS L 193 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1077 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: 1.48 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1498 1.31 - 1.44: 2686 1.44 - 1.56: 5745 1.56 - 1.69: 5 1.69 - 1.81: 84 Bond restraints: 10018 Sorted by residual: bond pdb=" CAZ Y01 A 303 " pdb=" CBH Y01 A 303 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" CAZ Y01 B 304 " pdb=" CBH Y01 B 304 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" CAZ Y01 A 302 " pdb=" CBH Y01 A 302 " ideal model delta sigma weight residual 1.519 1.406 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" CAZ Y01 B 301 " pdb=" CBH Y01 B 301 " ideal model delta sigma weight residual 1.519 1.406 0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" CAZ Y01 B 302 " pdb=" CBH Y01 B 302 " ideal model delta sigma weight residual 1.519 1.406 0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 10013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 13126 2.83 - 5.67: 438 5.67 - 8.50: 18 8.50 - 11.33: 6 11.33 - 14.16: 2 Bond angle restraints: 13590 Sorted by residual: angle pdb=" O12 PC1 A 304 " pdb=" P PC1 A 304 " pdb=" O14 PC1 A 304 " ideal model delta sigma weight residual 123.67 109.51 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" O12 PC1 B 305 " pdb=" P PC1 B 305 " pdb=" O14 PC1 B 305 " ideal model delta sigma weight residual 123.67 109.53 14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" CAY Y01 A 303 " pdb=" OAW Y01 A 303 " pdb=" CBC Y01 A 303 " ideal model delta sigma weight residual 119.39 109.59 9.80 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CAY Y01 B 304 " pdb=" OAW Y01 B 304 " pdb=" CBC Y01 B 304 " ideal model delta sigma weight residual 119.39 109.65 9.74 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C22 PC1 B 305 " pdb=" C21 PC1 B 305 " pdb=" O21 PC1 B 305 " ideal model delta sigma weight residual 111.12 119.88 -8.76 3.00e+00 1.11e-01 8.52e+00 ... (remaining 13585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 5311 17.33 - 34.66: 506 34.66 - 52.00: 109 52.00 - 69.33: 14 69.33 - 86.66: 12 Dihedral angle restraints: 5952 sinusoidal: 2430 harmonic: 3522 Sorted by residual: dihedral pdb=" CA PHE B 146 " pdb=" C PHE B 146 " pdb=" N LEU B 147 " pdb=" CA LEU B 147 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" N MET H 34 " pdb=" CA MET H 34 " pdb=" CB MET H 34 " pdb=" CG MET H 34 " ideal model delta sinusoidal sigma weight residual -60.00 -119.83 59.83 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N MET C 34 " pdb=" CA MET C 34 " pdb=" CB MET C 34 " pdb=" CG MET C 34 " ideal model delta sinusoidal sigma weight residual -60.00 -119.81 59.81 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1428 0.096 - 0.192: 62 0.192 - 0.288: 5 0.288 - 0.384: 15 0.384 - 0.480: 14 Chirality restraints: 1524 Sorted by residual: chirality pdb=" CBH Y01 B 301 " pdb=" CAT Y01 B 301 " pdb=" CAZ Y01 B 301 " pdb=" CBF Y01 B 301 " both_signs ideal model delta sigma weight residual False -2.85 -2.37 -0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CBH Y01 A 310 " pdb=" CAT Y01 A 310 " pdb=" CAZ Y01 A 310 " pdb=" CBF Y01 A 310 " both_signs ideal model delta sigma weight residual False -2.85 -2.38 -0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CBG Y01 B 301 " pdb=" CAQ Y01 B 301 " pdb=" CBD Y01 B 301 " pdb=" CBI Y01 B 301 " both_signs ideal model delta sigma weight residual False -2.33 -2.81 0.47 2.00e-01 2.50e+01 5.62e+00 ... (remaining 1521 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 94 " -0.007 2.00e-02 2.50e+03 1.03e-02 2.11e+00 pdb=" CG TYR A 94 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 94 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 94 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 94 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 94 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 94 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 94 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 57 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO L 58 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 58 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 58 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 57 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO D 58 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO D 58 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 58 " 0.018 5.00e-02 4.00e+02 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2180 2.79 - 3.32: 8677 3.32 - 3.85: 15209 3.85 - 4.37: 16780 4.37 - 4.90: 29883 Nonbonded interactions: 72729 Sorted by model distance: nonbonded pdb=" O ASN A 163 " pdb=" OH TYR B 182 " model vdw 2.268 3.040 nonbonded pdb=" OD1 ASP C 90 " pdb=" OH TYR C 94 " model vdw 2.279 3.040 nonbonded pdb=" OD1 ASP H 90 " pdb=" OH TYR H 94 " model vdw 2.279 3.040 nonbonded pdb=" OD1 ASN L 136 " pdb=" OG SER L 173 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASN D 136 " pdb=" OG SER D 173 " model vdw 2.287 3.040 ... (remaining 72724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 45 through 303 or resid 306 through 309)) selection = (chain 'B' and (resid 45 through 302 or (resid 303 and (name CAA or name CAB or \ name CAD or name CAE or name CAI or name CAJ or name CAK or name CAL or name CAM \ or name CAN or name CAO or name CAP or name CAQ or name CAR or name CAS or name \ CAT or name CAU or name CAV or name CAX or name CAY or name CAZ or name CBA or \ name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or name CBH \ or name CBI or name OAF or name OAG or name OAH or name OAW)) or resid 306 thro \ ugh 309)) } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'L' } 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.800 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.007 0.114 10032 Z= 0.333 Angle : 0.902 14.163 13614 Z= 0.356 Chirality : 0.068 0.480 1524 Planarity : 0.003 0.032 1642 Dihedral : 14.160 86.662 3664 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: 0.18 (0.25), residues: 1206 helix: 2.02 (0.35), residues: 234 sheet: 0.31 (0.28), residues: 352 loop : -0.72 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 156 TYR 0.024 0.001 TYR A 94 PHE 0.018 0.001 PHE A 62 TRP 0.009 0.001 TRP B 89 HIS 0.002 0.000 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.33 (10018) covalent geometry : angle 0.90266 / 0.36 (13590) SS BOND : bond 0.00553 / 0.31 ( 12) SS BOND : angle 0.50249 / 0.32 ( 24) hydrogen bonds : bond 0.23071 / 15.43 ( 385) hydrogen bonds : angle 8.17755 / 6.11 ( 1077) Misc. bond : bond 0.00363 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.279 Fit side-chains REVERT: B 106 LYS cc_start: 0.8472 (mmmt) cc_final: 0.7931 (pttm) REVERT: B 142 LYS cc_start: 0.8655 (tppt) cc_final: 0.8315 (tptt) REVERT: D 89 GLN cc_start: 0.8320 (pp30) cc_final: 0.8115 (pp30) REVERT: H 62 GLN cc_start: 0.7764 (mt0) cc_final: 0.7519 (mt0) REVERT: L 89 GLN cc_start: 0.8291 (pp30) cc_final: 0.8079 (pp30) outliers start: 2 outliers final: 2 residues processed: 191 average time/residue: 0.0916 time to fit residues: 25.4005 Evaluate side-chains 154 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain H residue 34 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 40.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN A 181 GLN A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS B 166 ASN B 181 GLN B 214 ASN C 207 ASN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN H 33 ASN H 207 ASN H 208 HIS L 1 GLN L 137 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.191266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.151547 restraints weight = 16802.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.150203 restraints weight = 10566.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.150915 restraints weight = 10156.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.152298 restraints weight = 6362.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.152474 restraints weight = 5535.695| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10032 Z= 0.178 Angle : 0.656 7.520 13614 Z= 0.314 Chirality : 0.044 0.227 1524 Planarity : 0.004 0.035 1642 Dihedral : 9.320 71.471 1580 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.35 % Allowed : 10.02 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.05 (0.25), residues: 1206 helix: 1.55 (0.33), residues: 252 sheet: 0.30 (0.28), residues: 372 loop : -0.96 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 76 TYR 0.019 0.002 TYR A 94 PHE 0.017 0.002 PHE B 146 TRP 0.011 0.002 TRP B 89 HIS 0.005 0.001 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (10018) covalent geometry : angle 0.65513 / 0.31 (13590) SS BOND : bond 0.00514 / 0.25 ( 12) SS BOND : angle 1.09456 / 0.75 ( 24) hydrogen bonds : bond 0.04145 / 2.73 ( 385) hydrogen bonds : angle 5.72292 / 4.26 ( 1077) Misc. bond : bond 0.00238 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.375 Fit side-chains REVERT: A 46 MET cc_start: 0.5769 (pmm) cc_final: 0.5569 (ptp) REVERT: A 50 LYS cc_start: 0.8026 (ttmt) cc_final: 0.6934 (pttp) REVERT: A 119 MET cc_start: 0.6745 (mmt) cc_final: 0.6382 (mmt) REVERT: B 106 LYS cc_start: 0.8511 (mmmt) cc_final: 0.7903 (pttp) REVERT: C 48 ILE cc_start: 0.8652 (tp) cc_final: 0.8352 (tp) REVERT: D 168 LYS cc_start: 0.7775 (tttm) cc_final: 0.7158 (tppt) REVERT: H 48 ILE cc_start: 0.8685 (tp) cc_final: 0.8393 (tp) REVERT: H 62 GLN cc_start: 0.8036 (mt0) cc_final: 0.7798 (mt0) REVERT: L 89 GLN cc_start: 0.8437 (pp30) cc_final: 0.8148 (pp30) outliers start: 14 outliers final: 9 residues processed: 176 average time/residue: 0.0877 time to fit residues: 22.7818 Evaluate side-chains 163 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 62 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.0170 chunk 94 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 62 optimal weight: 0.0030 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 overall best weight: 0.7830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN A 181 GLN A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN B 181 GLN C 39 GLN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.192993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.153351 restraints weight = 16676.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.152137 restraints weight = 10100.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.153099 restraints weight = 9522.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.153514 restraints weight = 5960.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.156065 restraints weight = 5309.605| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10032 Z= 0.112 Angle : 0.562 7.967 13614 Z= 0.268 Chirality : 0.042 0.242 1524 Planarity : 0.004 0.041 1642 Dihedral : 8.848 70.191 1574 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.64 % Allowed : 14.45 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.00 (0.25), residues: 1206 helix: 1.48 (0.33), residues: 250 sheet: 0.27 (0.27), residues: 370 loop : -0.81 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 60 TYR 0.016 0.001 TYR A 94 PHE 0.018 0.001 PHE B 146 TRP 0.012 0.001 TRP B 89 HIS 0.002 0.000 HIS L 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (10018) covalent geometry : angle 0.56140 / 0.27 (13590) SS BOND : bond 0.00355 / 0.17 ( 12) SS BOND : angle 0.87396 / 0.60 ( 24) hydrogen bonds : bond 0.03520 / 2.36 ( 385) hydrogen bonds : angle 5.24723 / 3.90 ( 1077) Misc. bond : bond 0.00231 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.426 Fit side-chains REVERT: A 50 LYS cc_start: 0.8304 (ttmt) cc_final: 0.6802 (pttp) REVERT: B 50 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7335 (ttmm) REVERT: B 106 LYS cc_start: 0.8459 (mmmt) cc_final: 0.7843 (pttm) REVERT: C 48 ILE cc_start: 0.8561 (tp) cc_final: 0.8335 (tp) REVERT: C 64 PHE cc_start: 0.6325 (m-10) cc_final: 0.5813 (m-10) REVERT: D 89 GLN cc_start: 0.8373 (pp30) cc_final: 0.8142 (pp30) REVERT: H 48 ILE cc_start: 0.8632 (tp) cc_final: 0.8340 (tp) REVERT: H 64 PHE cc_start: 0.6417 (m-10) cc_final: 0.5934 (m-10) REVERT: L 89 GLN cc_start: 0.8386 (pp30) cc_final: 0.8127 (pp30) outliers start: 17 outliers final: 10 residues processed: 172 average time/residue: 0.0870 time to fit residues: 22.3256 Evaluate side-chains 161 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 0.0170 chunk 111 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 ASN A 181 GLN A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN C 39 GLN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN L 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.190250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.150297 restraints weight = 16993.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.148202 restraints weight = 11184.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.148655 restraints weight = 11688.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.150131 restraints weight = 6841.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.150392 restraints weight = 5657.558| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10032 Z= 0.127 Angle : 0.569 14.997 13614 Z= 0.272 Chirality : 0.042 0.225 1524 Planarity : 0.004 0.041 1642 Dihedral : 8.861 71.336 1574 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.31 % Allowed : 16.47 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: 0.13 (0.25), residues: 1206 helix: 1.47 (0.33), residues: 248 sheet: 0.32 (0.26), residues: 412 loop : -0.70 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 60 TYR 0.015 0.001 TYR A 94 PHE 0.015 0.001 PHE B 146 TRP 0.011 0.001 TRP B 89 HIS 0.002 0.001 HIS H 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (10018) covalent geometry : angle 0.56868 / 0.27 (13590) SS BOND : bond 0.00299 / 0.14 ( 12) SS BOND : angle 0.78352 / 0.57 ( 24) hydrogen bonds : bond 0.03331 / 2.23 ( 385) hydrogen bonds : angle 4.91360 / 3.66 ( 1077) Misc. bond : bond 0.00290 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.383 Fit side-chains REVERT: A 50 LYS cc_start: 0.8293 (ttmt) cc_final: 0.6822 (pttp) REVERT: B 106 LYS cc_start: 0.8501 (mmmt) cc_final: 0.7764 (pttm) REVERT: C 48 ILE cc_start: 0.8500 (tp) cc_final: 0.8287 (tp) REVERT: C 64 PHE cc_start: 0.6552 (m-80) cc_final: 0.6207 (m-10) REVERT: D 89 GLN cc_start: 0.8351 (pp30) cc_final: 0.8106 (pp30) REVERT: H 64 PHE cc_start: 0.6704 (m-80) cc_final: 0.6321 (m-10) REVERT: L 89 GLN cc_start: 0.8357 (pp30) cc_final: 0.8089 (pp30) outliers start: 24 outliers final: 14 residues processed: 172 average time/residue: 0.0866 time to fit residues: 21.8848 Evaluate side-chains 160 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 70 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 ASN A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN C 33 ASN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN L 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.180711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.134551 restraints weight = 16828.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135038 restraints weight = 9629.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.135844 restraints weight = 6683.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.135985 restraints weight = 5303.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.136796 restraints weight = 4767.272| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10032 Z= 0.252 Angle : 0.711 10.256 13614 Z= 0.347 Chirality : 0.047 0.259 1524 Planarity : 0.004 0.037 1642 Dihedral : 9.721 75.031 1574 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.08 % Allowed : 18.40 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.25), residues: 1206 helix: 1.00 (0.32), residues: 254 sheet: 0.20 (0.26), residues: 414 loop : -1.04 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 60 TYR 0.027 0.002 TYR C 107 PHE 0.016 0.002 PHE B 45 TRP 0.015 0.002 TRP B 89 HIS 0.006 0.001 HIS H 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (10018) covalent geometry : angle 0.70976 / 0.35 (13590) SS BOND : bond 0.00346 / 0.17 ( 12) SS BOND : angle 1.10359 / 0.77 ( 24) hydrogen bonds : bond 0.04115 / 2.70 ( 385) hydrogen bonds : angle 5.30150 / 3.96 ( 1077) Misc. bond : bond 0.00361 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.333 Fit side-chains REVERT: A 50 LYS cc_start: 0.8339 (ttmt) cc_final: 0.6889 (pttp) REVERT: B 106 LYS cc_start: 0.8600 (mmmt) cc_final: 0.7666 (pttm) REVERT: D 32 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8126 (tp) REVERT: L 89 GLN cc_start: 0.8473 (pp30) cc_final: 0.8119 (pp30) outliers start: 32 outliers final: 19 residues processed: 182 average time/residue: 0.0896 time to fit residues: 23.8263 Evaluate side-chains 165 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN B 56 GLN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS B 166 ASN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN L 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.181917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.135885 restraints weight = 16774.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.136687 restraints weight = 9274.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137371 restraints weight = 6515.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.137508 restraints weight = 5427.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.137829 restraints weight = 4668.529| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10032 Z= 0.192 Angle : 0.657 10.423 13614 Z= 0.316 Chirality : 0.045 0.232 1524 Planarity : 0.004 0.035 1642 Dihedral : 9.528 72.131 1574 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.08 % Allowed : 21.00 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.25), residues: 1206 helix: 0.95 (0.32), residues: 254 sheet: 0.22 (0.26), residues: 412 loop : -1.10 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 109 TYR 0.019 0.002 TYR C 107 PHE 0.014 0.001 PHE C 154 TRP 0.016 0.002 TRP B 89 HIS 0.003 0.001 HIS H 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (10018) covalent geometry : angle 0.65647 / 0.32 (13590) SS BOND : bond 0.00314 / 0.15 ( 12) SS BOND : angle 1.08610 / 0.74 ( 24) hydrogen bonds : bond 0.03688 / 2.46 ( 385) hydrogen bonds : angle 5.10473 / 3.81 ( 1077) Misc. bond : bond 0.00289 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.315 Fit side-chains REVERT: A 50 LYS cc_start: 0.8297 (ttmt) cc_final: 0.6869 (pttp) REVERT: A 81 CYS cc_start: 0.8823 (m) cc_final: 0.8565 (t) REVERT: B 193 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8643 (mt) REVERT: D 32 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8067 (tp) REVERT: D 89 GLN cc_start: 0.8393 (pp30) cc_final: 0.8154 (pp30) REVERT: L 89 GLN cc_start: 0.8392 (pp30) cc_final: 0.8163 (pp30) outliers start: 32 outliers final: 23 residues processed: 174 average time/residue: 0.0854 time to fit residues: 21.7891 Evaluate side-chains 170 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 82 optimal weight: 0.2980 chunk 68 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN B 56 GLN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS D 37 GLN L 1 GLN L 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.184839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.138964 restraints weight = 16655.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.140264 restraints weight = 8891.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.140662 restraints weight = 6256.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140824 restraints weight = 5041.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.141576 restraints weight = 4491.154| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10032 Z= 0.125 Angle : 0.623 12.016 13614 Z= 0.297 Chirality : 0.044 0.199 1524 Planarity : 0.003 0.030 1642 Dihedral : 9.247 71.224 1574 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.50 % Allowed : 21.77 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.25 (0.25), residues: 1206 helix: 1.03 (0.33), residues: 248 sheet: 0.25 (0.26), residues: 404 loop : -1.01 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 60 TYR 0.017 0.001 TYR A 94 PHE 0.013 0.001 PHE B 203 TRP 0.025 0.001 TRP A 85 HIS 0.001 0.001 HIS H 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10018) covalent geometry : angle 0.62255 / 0.30 (13590) SS BOND : bond 0.00324 / 0.15 ( 12) SS BOND : angle 0.86929 / 0.60 ( 24) hydrogen bonds : bond 0.03369 / 2.26 ( 385) hydrogen bonds : angle 4.94166 / 3.69 ( 1077) Misc. bond : bond 0.00248 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.312 Fit side-chains REVERT: A 50 LYS cc_start: 0.8218 (ttmt) cc_final: 0.6799 (pttp) REVERT: A 72 ILE cc_start: 0.9279 (mm) cc_final: 0.8981 (mm) REVERT: B 105 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6630 (mt-10) REVERT: B 106 LYS cc_start: 0.8403 (mmmt) cc_final: 0.6976 (pptt) outliers start: 26 outliers final: 21 residues processed: 176 average time/residue: 0.0831 time to fit residues: 21.3672 Evaluate side-chains 167 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 52 ASN L 1 GLN L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.185769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140027 restraints weight = 16760.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.140796 restraints weight = 8551.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.141972 restraints weight = 5486.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142188 restraints weight = 4921.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142278 restraints weight = 4512.883| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10032 Z= 0.120 Angle : 0.608 9.362 13614 Z= 0.293 Chirality : 0.043 0.198 1524 Planarity : 0.003 0.028 1642 Dihedral : 9.089 71.310 1574 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.41 % Allowed : 22.64 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.18 (0.25), residues: 1206 helix: 1.09 (0.33), residues: 248 sheet: 0.32 (0.26), residues: 404 loop : -0.98 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.027 0.001 TYR B 94 PHE 0.013 0.001 PHE B 203 TRP 0.014 0.001 TRP A 85 HIS 0.001 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (10018) covalent geometry : angle 0.60709 / 0.29 (13590) SS BOND : bond 0.00333 / 0.15 ( 12) SS BOND : angle 0.82542 / 0.56 ( 24) hydrogen bonds : bond 0.03242 / 2.18 ( 385) hydrogen bonds : angle 4.85540 / 3.63 ( 1077) Misc. bond : bond 0.00231 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.226 Fit side-chains REVERT: A 50 LYS cc_start: 0.8200 (ttmt) cc_final: 0.6806 (pttp) REVERT: A 72 ILE cc_start: 0.9218 (mm) cc_final: 0.8928 (mm) REVERT: A 119 MET cc_start: 0.7085 (mmt) cc_final: 0.6728 (mmt) REVERT: B 106 LYS cc_start: 0.8449 (mmmt) cc_final: 0.7082 (pptt) outliers start: 25 outliers final: 20 residues processed: 172 average time/residue: 0.0787 time to fit residues: 19.9389 Evaluate side-chains 169 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN B 56 GLN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN L 1 GLN L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.186089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.145896 restraints weight = 16710.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.145580 restraints weight = 11814.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145763 restraints weight = 12061.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.147808 restraints weight = 6960.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.147827 restraints weight = 5308.689| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10032 Z= 0.124 Angle : 0.609 8.961 13614 Z= 0.296 Chirality : 0.044 0.212 1524 Planarity : 0.003 0.028 1642 Dihedral : 8.978 71.363 1574 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.02 % Allowed : 23.70 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.25 (0.25), residues: 1206 helix: 0.78 (0.32), residues: 260 sheet: 0.37 (0.26), residues: 404 loop : -1.02 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 60 TYR 0.016 0.001 TYR A 94 PHE 0.014 0.001 PHE C 64 TRP 0.014 0.001 TRP B 89 HIS 0.001 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (10018) covalent geometry : angle 0.60852 / 0.30 (13590) SS BOND : bond 0.00284 / 0.13 ( 12) SS BOND : angle 0.81521 / 0.55 ( 24) hydrogen bonds : bond 0.03221 / 2.16 ( 385) hydrogen bonds : angle 4.80756 / 3.59 ( 1077) Misc. bond : bond 0.00222 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.367 Fit side-chains REVERT: A 50 LYS cc_start: 0.8257 (ttmt) cc_final: 0.6858 (pttp) REVERT: A 72 ILE cc_start: 0.9205 (mm) cc_final: 0.8936 (mm) REVERT: B 106 LYS cc_start: 0.8537 (mmmt) cc_final: 0.7210 (pptt) outliers start: 21 outliers final: 16 residues processed: 166 average time/residue: 0.0891 time to fit residues: 21.7190 Evaluate side-chains 165 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 23 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN L 1 GLN L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.184101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.138793 restraints weight = 16723.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139403 restraints weight = 8764.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140561 restraints weight = 5813.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.140671 restraints weight = 4978.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.140938 restraints weight = 4451.553| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10032 Z= 0.165 Angle : 0.634 8.879 13614 Z= 0.310 Chirality : 0.044 0.211 1524 Planarity : 0.004 0.029 1642 Dihedral : 9.069 72.371 1574 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.83 % Allowed : 23.80 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.25), residues: 1206 helix: 0.68 (0.32), residues: 260 sheet: 0.37 (0.27), residues: 406 loop : -1.00 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.029 0.002 TYR A 94 PHE 0.012 0.001 PHE B 203 TRP 0.014 0.001 TRP B 89 HIS 0.002 0.001 HIS H 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (10018) covalent geometry : angle 0.63342 / 0.31 (13590) SS BOND : bond 0.00294 / 0.14 ( 12) SS BOND : angle 0.98850 / 0.68 ( 24) hydrogen bonds : bond 0.03393 / 2.25 ( 385) hydrogen bonds : angle 4.87071 / 3.62 ( 1077) Misc. bond : bond 0.00236 / 0.12 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.365 Fit side-chains REVERT: A 50 LYS cc_start: 0.8343 (ttmt) cc_final: 0.6786 (pttp) REVERT: B 105 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6584 (mt-10) REVERT: B 106 LYS cc_start: 0.8517 (mmmt) cc_final: 0.7175 (pptt) outliers start: 19 outliers final: 17 residues processed: 164 average time/residue: 0.0848 time to fit residues: 20.5618 Evaluate side-chains 165 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 70 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 0.0370 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN A 214 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.187152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.147094 restraints weight = 16654.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.146797 restraints weight = 11988.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147024 restraints weight = 12058.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.148835 restraints weight = 6908.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.148936 restraints weight = 5450.722| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10032 Z= 0.114 Angle : 0.613 9.544 13614 Z= 0.296 Chirality : 0.043 0.198 1524 Planarity : 0.003 0.027 1642 Dihedral : 8.825 70.870 1574 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.93 % Allowed : 23.70 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: -0.20 (0.25), residues: 1206 helix: 0.77 (0.32), residues: 260 sheet: 0.43 (0.27), residues: 404 loop : -0.99 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 47 TYR 0.032 0.001 TYR A 94 PHE 0.014 0.001 PHE C 64 TRP 0.033 0.002 TRP L 147 HIS 0.002 0.001 HIS L 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (10018) covalent geometry : angle 0.61214 / 0.30 (13590) SS BOND : bond 0.00303 / 0.13 ( 12) SS BOND : angle 0.85910 / 0.60 ( 24) hydrogen bonds : bond 0.03216 / 2.14 ( 385) hydrogen bonds : angle 4.79287 / 3.55 ( 1077) Misc. bond : bond 0.00212 / 0.11 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1713.39 seconds wall clock time: 30 minutes 24.15 seconds (1824.15 seconds total)