Starting phenix.real_space_refine on Thu Feb 13 12:51:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j0f_35901/02_2025/8j0f_35901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j0f_35901/02_2025/8j0f_35901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j0f_35901/02_2025/8j0f_35901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j0f_35901/02_2025/8j0f_35901.map" model { file = "/net/cci-nas-00/data/ceres_data/8j0f_35901/02_2025/8j0f_35901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j0f_35901/02_2025/8j0f_35901.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 5588 2.51 5 N 1572 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8932 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "F" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "A" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "B" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "G" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "D" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2067 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 2 Chain: "H" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 5.69, per 1000 atoms: 0.64 Number of scatterers: 8932 At special positions: 0 Unit cell: (102.82, 92.22, 94.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 12 15.00 Mg 4 11.99 O 1720 8.00 N 1572 7.00 C 5588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB RGP C 802 " pdb=" CB RGP A 802 " pdb=" CB RGP B 802 " pdb=" CB RGP D 802 " Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 58.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'C' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE C 10 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY C 31 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 51 Processing helix chain 'C' and resid 61 through 78 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER C 101 " --> pdb=" O GLY C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 147 Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS C 285 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 77 Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'A' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE A 10 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY A 31 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 51 Processing helix chain 'A' and resid 61 through 78 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG A 129 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 175 through 187 Processing helix chain 'A' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS A 285 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 Processing helix chain 'E' and resid 79 through 85 Processing helix chain 'B' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE B 10 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY B 31 " --> pdb=" O GLY B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 51 Processing helix chain 'B' and resid 61 through 78 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG B 129 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 175 through 187 Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS B 285 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 79 through 85 Processing helix chain 'D' and resid 5 through 13 removed outlier: 5.346A pdb=" N PHE D 10 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.791A pdb=" N GLY D 31 " --> pdb=" O GLY D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 51 Processing helix chain 'D' and resid 61 through 78 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 91 through 114 removed outlier: 3.705A pdb=" N SER D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.700A pdb=" N ARG D 129 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 147 Processing helix chain 'D' and resid 175 through 187 Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.862A pdb=" N LYS D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 4.350A pdb=" N SER D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 removed outlier: 3.702A pdb=" N HIS D 285 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'H' and resid 79 through 85 Processing sheet with id=AA1, first strand: chain 'C' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR C 117 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL C 152 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA C 119 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN C 154 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET C 121 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL C 55 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG C 16 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE C 193 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL C 18 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 195 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS C 20 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 192 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR C 259 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU C 194 " --> pdb=" O THR C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR A 117 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 152 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA A 119 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN A 154 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 121 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL A 55 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG A 16 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE A 193 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 18 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU A 195 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS A 20 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 192 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR A 259 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU A 194 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR B 117 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL B 152 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA B 119 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN B 154 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET B 121 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL B 55 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG B 16 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE B 193 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 18 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU B 195 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 20 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 192 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR B 259 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU B 194 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 117 through 123 removed outlier: 7.008A pdb=" N THR D 117 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL D 152 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA D 119 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN D 154 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET D 121 " --> pdb=" O ASN D 154 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL D 55 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG D 16 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE D 193 " --> pdb=" O ARG D 16 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL D 18 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU D 195 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS D 20 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU D 192 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR D 259 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU D 194 " --> pdb=" O THR D 259 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1212 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: 2.60 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1788 1.32 - 1.44: 2040 1.44 - 1.56: 5136 1.56 - 1.68: 20 1.68 - 1.80: 64 Bond restraints: 9048 Sorted by residual: bond pdb=" OE2 RGP D 802 " pdb=" PA RGP D 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" OE2 RGP C 802 " pdb=" PA RGP C 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" OE2 RGP A 802 " pdb=" PA RGP A 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" OE2 RGP B 802 " pdb=" PA RGP B 802 " ideal model delta sigma weight residual 1.798 1.608 0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" CD RGP A 802 " pdb=" OE2 RGP A 802 " ideal model delta sigma weight residual 1.302 1.455 -0.153 2.00e-02 2.50e+03 5.86e+01 ... (remaining 9043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 11268 1.67 - 3.34: 620 3.34 - 5.01: 224 5.01 - 6.68: 80 6.68 - 8.34: 20 Bond angle restraints: 12212 Sorted by residual: angle pdb=" N ILE C 150 " pdb=" CA ILE C 150 " pdb=" C ILE C 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N ILE B 150 " pdb=" CA ILE B 150 " pdb=" C ILE B 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N ILE D 150 " pdb=" CA ILE D 150 " pdb=" C ILE D 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N ILE A 150 " pdb=" CA ILE A 150 " pdb=" C ILE A 150 " ideal model delta sigma weight residual 107.56 112.87 -5.31 9.10e-01 1.21e+00 3.40e+01 angle pdb=" N VAL B 254 " pdb=" CA VAL B 254 " pdb=" C VAL B 254 " ideal model delta sigma weight residual 107.55 112.76 -5.21 9.90e-01 1.02e+00 2.77e+01 ... (remaining 12207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 5260 34.62 - 69.24: 178 69.24 - 103.86: 16 103.86 - 138.48: 8 138.48 - 173.11: 2 Dihedral angle restraints: 5464 sinusoidal: 2216 harmonic: 3248 Sorted by residual: dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 113.10 -173.11 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PB ADP C 801 " pdb=" PA ADP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 113.10 -173.11 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP D 801 " pdb=" O5' ADP D 801 " pdb=" PA ADP D 801 " pdb=" O2A ADP D 801 " ideal model delta sinusoidal sigma weight residual 300.00 170.94 129.07 1 2.00e+01 2.50e-03 3.91e+01 ... (remaining 5461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 972 0.043 - 0.085: 320 0.085 - 0.128: 96 0.128 - 0.170: 8 0.170 - 0.213: 12 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA MET D 110 " pdb=" N MET D 110 " pdb=" C MET D 110 " pdb=" CB MET D 110 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA MET C 110 " pdb=" N MET C 110 " pdb=" C MET C 110 " pdb=" CB MET C 110 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA MET B 110 " pdb=" N MET B 110 " pdb=" C MET B 110 " pdb=" CB MET B 110 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1405 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 115 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP A 115 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP A 115 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 115 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 115 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP C 115 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP C 115 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP C 115 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 115 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" CG ASP D 115 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP D 115 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP D 115 " 0.013 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2014 2.77 - 3.31: 9110 3.31 - 3.84: 14972 3.84 - 4.37: 17476 4.37 - 4.90: 28944 Nonbonded interactions: 72516 Sorted by model distance: nonbonded pdb=" N GLU D 265 " pdb=" OE1 GLU D 265 " model vdw 2.242 3.120 nonbonded pdb=" N GLU B 265 " pdb=" OE1 GLU B 265 " model vdw 2.242 3.120 nonbonded pdb=" N GLU A 265 " pdb=" OE1 GLU A 265 " model vdw 2.242 3.120 nonbonded pdb=" N GLU C 265 " pdb=" OE1 GLU C 265 " model vdw 2.242 3.120 nonbonded pdb=" OD2 ASP B 208 " pdb=" OG1 THR B 210 " model vdw 2.246 3.040 ... (remaining 72511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.540 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.009 0.190 9048 Z= 0.639 Angle : 1.064 8.344 12212 Z= 0.653 Chirality : 0.047 0.213 1408 Planarity : 0.005 0.047 1544 Dihedral : 18.094 173.106 3368 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.13 % Allowed : 20.43 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 1108 helix: 0.35 (0.22), residues: 580 sheet: -0.20 (0.41), residues: 188 loop : 0.56 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 174 HIS 0.006 0.001 HIS B 222 PHE 0.019 0.001 PHE B 153 TYR 0.024 0.002 TYR D 106 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 1.196 Fit side-chains REVERT: C 68 GLN cc_start: 0.8657 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 68 GLN cc_start: 0.8651 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 68 GLN cc_start: 0.8641 (tm-30) cc_final: 0.7797 (tm-30) REVERT: D 68 GLN cc_start: 0.8648 (tm-30) cc_final: 0.7791 (tm-30) outliers start: 20 outliers final: 0 residues processed: 194 average time/residue: 0.2529 time to fit residues: 65.0845 Evaluate side-chains 179 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.091691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.071427 restraints weight = 21669.133| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.08 r_work: 0.2925 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9048 Z= 0.198 Angle : 0.676 9.348 12212 Z= 0.326 Chirality : 0.042 0.142 1408 Planarity : 0.003 0.023 1544 Dihedral : 13.507 178.735 1300 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.28 % Allowed : 19.89 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1108 helix: 1.08 (0.21), residues: 596 sheet: 0.02 (0.41), residues: 188 loop : 0.85 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 287 HIS 0.003 0.001 HIS C 222 PHE 0.022 0.002 PHE F 80 TYR 0.023 0.002 TYR D 106 ARG 0.002 0.000 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 1.078 Fit side-chains REVERT: C 80 PHE cc_start: 0.9388 (t80) cc_final: 0.9146 (t80) REVERT: C 115 ASP cc_start: 0.8946 (t0) cc_final: 0.8742 (t0) REVERT: C 186 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8331 (tm-30) REVERT: C 228 PHE cc_start: 0.8311 (m-10) cc_final: 0.8089 (m-10) REVERT: A 115 ASP cc_start: 0.8944 (t0) cc_final: 0.8733 (t0) REVERT: A 131 LYS cc_start: 0.9236 (pttm) cc_final: 0.8959 (mmmt) REVERT: A 228 PHE cc_start: 0.8286 (m-10) cc_final: 0.8047 (m-10) REVERT: B 54 GLU cc_start: 0.8689 (mp0) cc_final: 0.8030 (pm20) REVERT: B 115 ASP cc_start: 0.8973 (t0) cc_final: 0.8748 (t0) REVERT: B 132 ASP cc_start: 0.8875 (t0) cc_final: 0.8600 (t0) REVERT: B 157 ASP cc_start: 0.8752 (m-30) cc_final: 0.8551 (m-30) REVERT: B 220 GLU cc_start: 0.9481 (tp30) cc_final: 0.9156 (tm-30) REVERT: B 239 MET cc_start: 0.8857 (tpp) cc_final: 0.7419 (tpp) REVERT: B 251 TYR cc_start: 0.8650 (m-80) cc_final: 0.8317 (m-80) REVERT: D 115 ASP cc_start: 0.8932 (t0) cc_final: 0.8721 (t0) REVERT: D 132 ASP cc_start: 0.8901 (t0) cc_final: 0.8645 (t0) REVERT: D 157 ASP cc_start: 0.8764 (m-30) cc_final: 0.8548 (m-30) REVERT: D 186 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8341 (tm-30) REVERT: D 251 TYR cc_start: 0.8684 (m-80) cc_final: 0.8362 (m-80) outliers start: 12 outliers final: 4 residues processed: 206 average time/residue: 0.2335 time to fit residues: 64.6004 Evaluate side-chains 177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 173 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain D residue 23 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 64 optimal weight: 0.0670 chunk 18 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.067942 restraints weight = 22116.212| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 4.25 r_work: 0.2847 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9048 Z= 0.190 Angle : 0.630 11.118 12212 Z= 0.301 Chirality : 0.040 0.137 1408 Planarity : 0.003 0.025 1544 Dihedral : 12.490 158.061 1300 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.66 % Allowed : 20.00 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.26), residues: 1108 helix: 1.47 (0.21), residues: 596 sheet: 0.19 (0.41), residues: 188 loop : 0.90 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 174 HIS 0.003 0.001 HIS B 222 PHE 0.027 0.002 PHE E 80 TYR 0.032 0.002 TYR C 106 ARG 0.002 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: C 115 ASP cc_start: 0.8984 (t0) cc_final: 0.8707 (t0) REVERT: C 121 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8025 (mmm) REVERT: C 186 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8483 (tm-30) REVERT: C 239 MET cc_start: 0.8317 (mmm) cc_final: 0.7896 (ttm) REVERT: F 80 PHE cc_start: 0.8591 (t80) cc_final: 0.8355 (t80) REVERT: A 110 MET cc_start: 0.8668 (mtt) cc_final: 0.8267 (mtm) REVERT: A 115 ASP cc_start: 0.8995 (t0) cc_final: 0.8701 (t0) REVERT: A 121 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8092 (mmm) REVERT: A 186 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8456 (tm-30) REVERT: A 239 MET cc_start: 0.8266 (mmm) cc_final: 0.7866 (ttm) REVERT: E 80 PHE cc_start: 0.8632 (t80) cc_final: 0.8372 (t80) REVERT: B 83 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9131 (mp) REVERT: B 115 ASP cc_start: 0.8961 (t0) cc_final: 0.8682 (t0) REVERT: B 121 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8005 (mmm) REVERT: B 239 MET cc_start: 0.8728 (tpp) cc_final: 0.7116 (tpp) REVERT: D 115 ASP cc_start: 0.8950 (t0) cc_final: 0.8678 (t0) REVERT: D 121 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.7992 (mmm) REVERT: D 186 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8479 (tm-30) REVERT: D 239 MET cc_start: 0.8428 (mmm) cc_final: 0.7928 (ttm) REVERT: H 80 PHE cc_start: 0.8627 (t80) cc_final: 0.8388 (t80) outliers start: 25 outliers final: 6 residues processed: 202 average time/residue: 0.2304 time to fit residues: 62.7997 Evaluate side-chains 185 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 121 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 72 optimal weight: 0.0170 chunk 65 optimal weight: 2.9990 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 GLN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.068067 restraints weight = 22674.825| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.05 r_work: 0.2920 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9048 Z= 0.187 Angle : 0.611 6.050 12212 Z= 0.290 Chirality : 0.040 0.144 1408 Planarity : 0.003 0.027 1544 Dihedral : 11.365 135.940 1300 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.09 % Allowed : 21.38 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.26), residues: 1108 helix: 1.70 (0.21), residues: 596 sheet: 0.26 (0.41), residues: 188 loop : 1.18 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 287 HIS 0.002 0.001 HIS A 222 PHE 0.023 0.002 PHE A 80 TYR 0.030 0.002 TYR D 106 ARG 0.001 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 1.129 Fit side-chains REVERT: C 115 ASP cc_start: 0.8951 (t0) cc_final: 0.8641 (t0) REVERT: C 121 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8161 (mmm) REVERT: C 186 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8471 (tm-30) REVERT: C 239 MET cc_start: 0.8481 (mmm) cc_final: 0.7748 (ttm) REVERT: F 80 PHE cc_start: 0.8801 (t80) cc_final: 0.8527 (t80) REVERT: A 83 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9114 (mp) REVERT: A 115 ASP cc_start: 0.8956 (t0) cc_final: 0.8648 (t0) REVERT: A 121 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8249 (mmm) REVERT: A 186 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 239 MET cc_start: 0.8429 (mmm) cc_final: 0.7726 (ttm) REVERT: B 54 GLU cc_start: 0.8634 (mp0) cc_final: 0.8028 (pm20) REVERT: B 115 ASP cc_start: 0.8936 (t0) cc_final: 0.8641 (t0) REVERT: B 121 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8142 (mmm) REVERT: B 136 GLN cc_start: 0.9222 (tt0) cc_final: 0.9013 (tt0) REVERT: B 239 MET cc_start: 0.8943 (tpp) cc_final: 0.7261 (tpp) REVERT: B 248 ASN cc_start: 0.9139 (t0) cc_final: 0.8907 (t0) REVERT: B 251 TYR cc_start: 0.8636 (m-80) cc_final: 0.8303 (m-80) REVERT: D 83 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9218 (mp) REVERT: D 115 ASP cc_start: 0.8938 (t0) cc_final: 0.8614 (t0) REVERT: D 121 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8132 (mmm) REVERT: D 186 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8454 (tm-30) REVERT: D 239 MET cc_start: 0.8382 (mmm) cc_final: 0.7736 (ttm) outliers start: 29 outliers final: 16 residues processed: 198 average time/residue: 0.2310 time to fit residues: 61.5804 Evaluate side-chains 195 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 285 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.085565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.063994 restraints weight = 22239.193| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 4.26 r_work: 0.2721 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9048 Z= 0.344 Angle : 0.688 6.778 12212 Z= 0.329 Chirality : 0.042 0.176 1408 Planarity : 0.003 0.030 1544 Dihedral : 11.195 134.788 1300 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.83 % Allowed : 21.38 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.26), residues: 1108 helix: 1.64 (0.21), residues: 596 sheet: 0.05 (0.39), residues: 188 loop : 1.21 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 287 HIS 0.003 0.001 HIS B 222 PHE 0.024 0.002 PHE H 80 TYR 0.056 0.003 TYR C 106 ARG 0.007 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 106 TYR cc_start: 0.8395 (t80) cc_final: 0.7912 (t80) REVERT: C 110 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.7782 (mtm) REVERT: C 115 ASP cc_start: 0.9066 (t0) cc_final: 0.8769 (t0) REVERT: C 121 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8133 (mmm) REVERT: C 239 MET cc_start: 0.8627 (mmm) cc_final: 0.7747 (ttm) REVERT: A 104 MET cc_start: 0.9485 (tpt) cc_final: 0.9216 (mmm) REVERT: A 115 ASP cc_start: 0.9062 (t0) cc_final: 0.8776 (t0) REVERT: A 121 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8172 (mmm) REVERT: A 239 MET cc_start: 0.8599 (mmm) cc_final: 0.7763 (ttm) REVERT: A 287 TRP cc_start: 0.8010 (m-10) cc_final: 0.7748 (m-10) REVERT: E 80 PHE cc_start: 0.8827 (t80) cc_final: 0.8603 (t80) REVERT: B 115 ASP cc_start: 0.9002 (t0) cc_final: 0.8725 (t0) REVERT: B 121 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8089 (mmm) REVERT: B 287 TRP cc_start: 0.8015 (m-10) cc_final: 0.7771 (m-10) REVERT: D 83 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9104 (mp) REVERT: D 115 ASP cc_start: 0.8988 (t0) cc_final: 0.8709 (t0) REVERT: D 121 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8060 (mmm) REVERT: D 239 MET cc_start: 0.8510 (mmm) cc_final: 0.7603 (tpp) REVERT: D 287 TRP cc_start: 0.7975 (m-10) cc_final: 0.7747 (m-10) outliers start: 36 outliers final: 19 residues processed: 188 average time/residue: 0.2202 time to fit residues: 56.2629 Evaluate side-chains 189 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain H residue 83 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN D 248 ASN ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.085318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.063920 restraints weight = 22361.829| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.18 r_work: 0.2763 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9048 Z= 0.362 Angle : 0.702 10.363 12212 Z= 0.334 Chirality : 0.042 0.141 1408 Planarity : 0.003 0.032 1544 Dihedral : 11.161 132.157 1300 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.04 % Allowed : 22.55 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.26), residues: 1108 helix: 1.43 (0.21), residues: 620 sheet: 0.16 (0.40), residues: 168 loop : 0.69 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP C 287 HIS 0.002 0.001 HIS B 222 PHE 0.031 0.002 PHE F 80 TYR 0.032 0.002 TYR C 106 ARG 0.002 0.000 ARG C 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.880 Fit side-chains REVERT: C 106 TYR cc_start: 0.8771 (t80) cc_final: 0.8526 (t80) REVERT: C 115 ASP cc_start: 0.9080 (t0) cc_final: 0.8766 (t0) REVERT: C 121 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8246 (mmm) REVERT: C 239 MET cc_start: 0.8810 (mmm) cc_final: 0.8352 (tpp) REVERT: A 104 MET cc_start: 0.9548 (tpt) cc_final: 0.9301 (mmm) REVERT: A 110 MET cc_start: 0.8026 (mtm) cc_final: 0.7682 (mtm) REVERT: A 115 ASP cc_start: 0.9022 (t0) cc_final: 0.8752 (t0) REVERT: A 121 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8254 (mmm) REVERT: A 239 MET cc_start: 0.8750 (mmm) cc_final: 0.8266 (tpp) REVERT: A 287 TRP cc_start: 0.8267 (m-10) cc_final: 0.8037 (m-10) REVERT: B 115 ASP cc_start: 0.8996 (t0) cc_final: 0.8742 (t0) REVERT: B 121 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8134 (mmm) REVERT: B 239 MET cc_start: 0.8934 (tpp) cc_final: 0.7454 (tpp) REVERT: D 83 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9060 (mp) REVERT: D 115 ASP cc_start: 0.9056 (t0) cc_final: 0.8751 (t0) REVERT: D 121 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8187 (mmm) REVERT: D 239 MET cc_start: 0.8699 (mmm) cc_final: 0.8248 (tpp) outliers start: 38 outliers final: 22 residues processed: 190 average time/residue: 0.2281 time to fit residues: 58.4310 Evaluate side-chains 190 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 285 HIS Chi-restraints excluded: chain H residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 0.0770 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.089902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.068408 restraints weight = 21938.920| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 4.35 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9048 Z= 0.186 Angle : 0.646 7.246 12212 Z= 0.306 Chirality : 0.040 0.129 1408 Planarity : 0.003 0.029 1544 Dihedral : 10.436 129.264 1300 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.87 % Allowed : 24.04 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.27), residues: 1108 helix: 1.49 (0.21), residues: 620 sheet: 0.42 (0.42), residues: 168 loop : 0.98 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP C 287 HIS 0.001 0.000 HIS B 222 PHE 0.034 0.002 PHE G 80 TYR 0.041 0.002 TYR D 106 ARG 0.001 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.976 Fit side-chains REVERT: C 110 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7941 (mtt) REVERT: C 115 ASP cc_start: 0.8880 (t0) cc_final: 0.8584 (t0) REVERT: C 121 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.7809 (mmm) REVERT: C 219 LYS cc_start: 0.8526 (mttt) cc_final: 0.8065 (mtmt) REVERT: C 239 MET cc_start: 0.8811 (mmm) cc_final: 0.8398 (tpp) REVERT: C 251 TYR cc_start: 0.8423 (m-80) cc_final: 0.7910 (m-80) REVERT: A 85 LYS cc_start: 0.9366 (ptmm) cc_final: 0.9143 (ptpp) REVERT: A 106 TYR cc_start: 0.8742 (t80) cc_final: 0.8384 (t80) REVERT: A 115 ASP cc_start: 0.8796 (t0) cc_final: 0.8542 (t0) REVERT: A 121 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.7842 (mmm) REVERT: A 239 MET cc_start: 0.8871 (mmm) cc_final: 0.8479 (tpp) REVERT: B 115 ASP cc_start: 0.8703 (t0) cc_final: 0.8462 (t0) REVERT: B 121 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.7749 (mmm) REVERT: B 239 MET cc_start: 0.8983 (tpp) cc_final: 0.7569 (tpp) REVERT: D 115 ASP cc_start: 0.8790 (t0) cc_final: 0.8529 (t0) REVERT: D 121 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.7742 (mmm) REVERT: D 239 MET cc_start: 0.8685 (mmm) cc_final: 0.8234 (tpp) outliers start: 27 outliers final: 12 residues processed: 189 average time/residue: 0.2360 time to fit residues: 60.0352 Evaluate side-chains 182 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 285 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 GLN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.089739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.068508 restraints weight = 22236.382| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 4.34 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9048 Z= 0.199 Angle : 0.669 10.046 12212 Z= 0.316 Chirality : 0.040 0.137 1408 Planarity : 0.003 0.028 1544 Dihedral : 10.039 127.396 1300 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.66 % Allowed : 24.15 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.27), residues: 1108 helix: 1.56 (0.22), residues: 620 sheet: 0.49 (0.43), residues: 168 loop : 1.04 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP C 287 HIS 0.001 0.000 HIS C 222 PHE 0.030 0.002 PHE G 80 TYR 0.064 0.002 TYR D 106 ARG 0.002 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.996 Fit side-chains REVERT: C 110 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7824 (mtt) REVERT: C 115 ASP cc_start: 0.8853 (t0) cc_final: 0.8570 (t0) REVERT: C 121 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.7848 (mmm) REVERT: C 186 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8230 (tm-30) REVERT: C 239 MET cc_start: 0.8852 (mmm) cc_final: 0.8398 (tpp) REVERT: A 115 ASP cc_start: 0.8811 (t0) cc_final: 0.8558 (t0) REVERT: A 121 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.7880 (mmm) REVERT: A 239 MET cc_start: 0.8850 (mmm) cc_final: 0.8425 (tpp) REVERT: A 251 TYR cc_start: 0.8442 (m-80) cc_final: 0.8067 (m-80) REVERT: B 120 GLN cc_start: 0.9133 (tt0) cc_final: 0.8750 (tt0) REVERT: B 121 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.7833 (mmm) REVERT: B 239 MET cc_start: 0.9041 (tpp) cc_final: 0.7590 (tpp) REVERT: B 251 TYR cc_start: 0.8420 (m-80) cc_final: 0.8057 (m-80) REVERT: D 115 ASP cc_start: 0.8785 (t0) cc_final: 0.8529 (t0) REVERT: D 121 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.7793 (mmm) REVERT: D 239 MET cc_start: 0.8700 (mmm) cc_final: 0.8124 (tpp) REVERT: D 251 TYR cc_start: 0.8423 (m-80) cc_final: 0.8052 (m-80) outliers start: 25 outliers final: 10 residues processed: 179 average time/residue: 0.2406 time to fit residues: 58.1282 Evaluate side-chains 182 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 285 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.067682 restraints weight = 22169.124| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 4.37 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9048 Z= 0.229 Angle : 0.687 8.998 12212 Z= 0.327 Chirality : 0.040 0.139 1408 Planarity : 0.003 0.030 1544 Dihedral : 9.842 126.394 1300 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.23 % Allowed : 25.00 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.27), residues: 1108 helix: 1.62 (0.22), residues: 620 sheet: 0.54 (0.42), residues: 168 loop : 1.04 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 287 HIS 0.002 0.000 HIS C 285 PHE 0.031 0.002 PHE E 80 TYR 0.047 0.002 TYR D 106 ARG 0.003 0.000 ARG D 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.983 Fit side-chains REVERT: C 87 GLN cc_start: 0.9049 (pm20) cc_final: 0.8838 (pm20) REVERT: C 110 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7487 (mtm) REVERT: C 115 ASP cc_start: 0.8844 (t0) cc_final: 0.8560 (t0) REVERT: C 121 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.7872 (mmm) REVERT: C 186 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8216 (tm-30) REVERT: C 239 MET cc_start: 0.8880 (mmm) cc_final: 0.8404 (tpp) REVERT: C 251 TYR cc_start: 0.8422 (m-80) cc_final: 0.8068 (m-80) REVERT: A 115 ASP cc_start: 0.8825 (t0) cc_final: 0.8576 (t0) REVERT: A 121 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.7920 (mmm) REVERT: A 239 MET cc_start: 0.8887 (mmm) cc_final: 0.8434 (tpp) REVERT: A 251 TYR cc_start: 0.8454 (m-80) cc_final: 0.8064 (m-80) REVERT: B 121 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.7841 (mmm) REVERT: B 239 MET cc_start: 0.9050 (tpp) cc_final: 0.7560 (tpp) REVERT: B 251 TYR cc_start: 0.8402 (m-80) cc_final: 0.8018 (m-80) REVERT: D 115 ASP cc_start: 0.8762 (t0) cc_final: 0.8491 (t0) REVERT: D 121 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.7815 (mmm) REVERT: D 186 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8136 (tm-30) REVERT: D 239 MET cc_start: 0.8745 (mmm) cc_final: 0.8138 (tpp) REVERT: D 251 TYR cc_start: 0.8449 (m-80) cc_final: 0.8097 (m-80) outliers start: 21 outliers final: 11 residues processed: 180 average time/residue: 0.2404 time to fit residues: 58.0494 Evaluate side-chains 183 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 121 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 0.0370 chunk 50 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.087562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.068122 restraints weight = 22716.912| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 4.03 r_work: 0.2890 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9048 Z= 0.208 Angle : 0.693 9.285 12212 Z= 0.333 Chirality : 0.040 0.136 1408 Planarity : 0.003 0.029 1544 Dihedral : 9.600 124.996 1300 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.60 % Allowed : 26.17 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.26), residues: 1108 helix: 1.61 (0.22), residues: 620 sheet: 0.59 (0.42), residues: 168 loop : 1.09 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.005 TRP B 287 HIS 0.007 0.001 HIS A 222 PHE 0.036 0.002 PHE E 80 TYR 0.042 0.002 TYR D 106 ARG 0.002 0.000 ARG A 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: C 87 GLN cc_start: 0.8996 (pm20) cc_final: 0.8793 (pm20) REVERT: C 115 ASP cc_start: 0.8973 (t0) cc_final: 0.8676 (t0) REVERT: C 121 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8325 (mmm) REVERT: C 186 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8671 (tm-30) REVERT: C 239 MET cc_start: 0.8884 (mmm) cc_final: 0.8419 (tpp) REVERT: C 251 TYR cc_start: 0.8675 (m-80) cc_final: 0.8352 (m-80) REVERT: A 115 ASP cc_start: 0.8964 (t0) cc_final: 0.8681 (t0) REVERT: A 121 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8425 (mmm) REVERT: A 239 MET cc_start: 0.8859 (mmm) cc_final: 0.8433 (tpp) REVERT: A 251 TYR cc_start: 0.8674 (m-80) cc_final: 0.8326 (m-80) REVERT: B 120 GLN cc_start: 0.9322 (tt0) cc_final: 0.8838 (tt0) REVERT: B 121 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8264 (mmm) REVERT: B 239 MET cc_start: 0.9134 (tpp) cc_final: 0.7712 (tpp) REVERT: B 251 TYR cc_start: 0.8680 (m-80) cc_final: 0.8338 (m-80) REVERT: D 115 ASP cc_start: 0.8937 (t0) cc_final: 0.8650 (t0) REVERT: D 121 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8249 (mmm) REVERT: D 131 LYS cc_start: 0.9333 (pttm) cc_final: 0.9094 (mmmt) REVERT: D 186 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8568 (tm-30) REVERT: D 239 MET cc_start: 0.8760 (mmm) cc_final: 0.8247 (tpp) REVERT: D 251 TYR cc_start: 0.8701 (m-80) cc_final: 0.8380 (m-80) outliers start: 15 outliers final: 9 residues processed: 177 average time/residue: 0.2431 time to fit residues: 58.7202 Evaluate side-chains 179 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 223 GLN Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 121 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.087369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.067980 restraints weight = 22788.333| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 4.03 r_work: 0.2889 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9048 Z= 0.215 Angle : 0.683 9.654 12212 Z= 0.325 Chirality : 0.040 0.143 1408 Planarity : 0.003 0.029 1544 Dihedral : 9.386 123.641 1300 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.60 % Allowed : 25.74 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.26), residues: 1108 helix: 1.65 (0.22), residues: 620 sheet: 0.66 (0.42), residues: 168 loop : 1.13 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.005 TRP D 287 HIS 0.005 0.001 HIS C 222 PHE 0.032 0.002 PHE E 80 TYR 0.044 0.002 TYR D 106 ARG 0.003 0.000 ARG D 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.10 seconds wall clock time: 61 minutes 39.27 seconds (3699.27 seconds total)