Starting phenix.real_space_refine on Wed Jul 30 07:19:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vrs_21371/07_2025/6vrs_21371.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrs_21371/07_2025/6vrs_21371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vrs_21371/07_2025/6vrs_21371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrs_21371/07_2025/6vrs_21371.map" model { file = "/net/cci-nas-00/data/ceres_data/6vrs_21371/07_2025/6vrs_21371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrs_21371/07_2025/6vrs_21371.cif" } resolution = 2.7 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= 0.087 sd= 0.769 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 8 7.51 5 S 32 5.16 5 C 7652 2.51 5 N 2200 2.21 5 O 2316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12208 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3046 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367} Chain: "B" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3046 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367} Chain: "C" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3046 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367} Chain: "D" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3046 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 7.87, per 1000 atoms: 0.64 Number of scatterers: 12208 At special positions: 0 Unit cell: (91.91, 84.63, 101.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 8 24.99 S 32 16.00 O 2316 8.00 N 2200 7.00 C 7652 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: 3.14 Conformation dependent library (CDL) restraints added in 1.8 seconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2800 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 58.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 6 through 9 Processing helix chain 'A' and resid 15 through 19 Processing helix chain 'A' and resid 35 through 46 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 64 through 83 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 108 through 129 Processing helix chain 'A' and resid 150 through 173 Processing helix chain 'A' and resid 195 through 204 removed outlier: 3.565A pdb=" N GLU A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 217 through 223 Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 295 through 323 removed outlier: 3.613A pdb=" N MET A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.519A pdb=" N ALA A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 354 through 357 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.602A pdb=" N ARG A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 384 Processing helix chain 'B' and resid 6 through 9 Processing helix chain 'B' and resid 15 through 19 Processing helix chain 'B' and resid 35 through 46 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 64 through 83 Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 108 through 129 Processing helix chain 'B' and resid 150 through 173 Processing helix chain 'B' and resid 195 through 204 removed outlier: 3.569A pdb=" N GLU B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 264 through 279 Processing helix chain 'B' and resid 295 through 323 removed outlier: 3.615A pdb=" N MET B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 333 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.518A pdb=" N ALA B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 354 through 357 Processing helix chain 'B' and resid 361 through 368 removed outlier: 3.602A pdb=" N ARG B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 385 Processing helix chain 'C' and resid 6 through 9 Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 64 through 83 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 108 through 129 Processing helix chain 'C' and resid 150 through 173 Processing helix chain 'C' and resid 195 through 204 removed outlier: 3.570A pdb=" N GLU C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 217 through 223 Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 264 through 279 Processing helix chain 'C' and resid 295 through 323 removed outlier: 3.615A pdb=" N MET C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 333 Processing helix chain 'C' and resid 334 through 339 removed outlier: 3.520A pdb=" N ALA C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 354 through 357 Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.601A pdb=" N ARG C 368 " --> pdb=" O ALA C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 385 Processing helix chain 'D' and resid 6 through 9 Processing helix chain 'D' and resid 15 through 19 Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 64 through 83 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 108 through 129 Processing helix chain 'D' and resid 150 through 173 Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.565A pdb=" N GLU D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 217 through 223 Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 264 through 279 Processing helix chain 'D' and resid 295 through 323 removed outlier: 3.613A pdb=" N MET D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 334 through 339 removed outlier: 3.519A pdb=" N ALA D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 354 through 357 Processing helix chain 'D' and resid 361 through 368 removed outlier: 3.602A pdb=" N ARG D 368 " --> pdb=" O ALA D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 384 Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 214 removed outlier: 6.655A pdb=" N ALA A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 51 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N THR A 90 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE A 53 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 11 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N THR A 52 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE A 13 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N HIS A 54 " --> pdb=" O PHE A 13 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A 12 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA3, first strand: chain 'B' and resid 212 through 214 removed outlier: 6.655A pdb=" N ALA B 89 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 51 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N THR B 90 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE B 53 " --> pdb=" O THR B 90 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE B 11 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N THR B 52 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE B 13 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N HIS B 54 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B 12 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 143 Processing sheet with id=AA5, first strand: chain 'C' and resid 212 through 214 removed outlier: 6.651A pdb=" N ALA C 89 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 51 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N THR C 90 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE C 53 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE C 11 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N THR C 52 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE C 13 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N HIS C 54 " --> pdb=" O PHE C 13 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR C 12 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AA7, first strand: chain 'D' and resid 212 through 214 removed outlier: 6.655A pdb=" N ALA D 89 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL D 51 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR D 90 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE D 53 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE D 11 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N THR D 52 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE D 13 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N HIS D 54 " --> pdb=" O PHE D 13 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR D 12 " --> pdb=" O PHE D 286 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 142 through 143 614 hydrogen bonds defined for protein. 1782 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: 3.98 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2162 1.30 - 1.43: 3361 1.43 - 1.56: 6886 1.56 - 1.69: 3 1.69 - 1.82: 60 Bond restraints: 12472 Sorted by residual: bond pdb=" NE ARG D 177 " pdb=" CZ ARG D 177 " ideal model delta sigma weight residual 1.326 1.369 -0.043 1.10e-02 8.26e+03 1.51e+01 bond pdb=" CG ASP B 255 " pdb=" OD1 ASP B 255 " ideal model delta sigma weight residual 1.249 1.176 0.073 1.90e-02 2.77e+03 1.50e+01 bond pdb=" CG ASP B 255 " pdb=" OD2 ASP B 255 " ideal model delta sigma weight residual 1.249 1.177 0.072 1.90e-02 2.77e+03 1.45e+01 bond pdb=" NE ARG B 177 " pdb=" CZ ARG B 177 " ideal model delta sigma weight residual 1.326 1.363 -0.037 1.10e-02 8.26e+03 1.15e+01 bond pdb=" CE1 HIS B 49 " pdb=" NE2 HIS B 49 " ideal model delta sigma weight residual 1.321 1.352 -0.031 1.00e-02 1.00e+04 9.56e+00 ... (remaining 12467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 16287 3.34 - 6.67: 548 6.67 - 10.01: 34 10.01 - 13.35: 12 13.35 - 16.68: 3 Bond angle restraints: 16884 Sorted by residual: angle pdb=" CB ARG B 42 " pdb=" CG ARG B 42 " pdb=" CD ARG B 42 " ideal model delta sigma weight residual 111.30 127.98 -16.68 2.30e+00 1.89e-01 5.26e+01 angle pdb=" CB ARG D 42 " pdb=" CG ARG D 42 " pdb=" CD ARG D 42 " ideal model delta sigma weight residual 111.30 127.79 -16.49 2.30e+00 1.89e-01 5.14e+01 angle pdb=" CB ARG D 387 " pdb=" CG ARG D 387 " pdb=" CD ARG D 387 " ideal model delta sigma weight residual 111.30 126.46 -15.16 2.30e+00 1.89e-01 4.34e+01 angle pdb=" CA ASP C 245 " pdb=" CB ASP C 245 " pdb=" CG ASP C 245 " ideal model delta sigma weight residual 112.60 118.80 -6.20 1.00e+00 1.00e+00 3.84e+01 angle pdb=" CA ASP D 245 " pdb=" CB ASP D 245 " pdb=" CG ASP D 245 " ideal model delta sigma weight residual 112.60 118.80 -6.20 1.00e+00 1.00e+00 3.84e+01 ... (remaining 16879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 6746 17.06 - 34.12: 468 34.12 - 51.17: 94 51.17 - 68.23: 54 68.23 - 85.29: 26 Dihedral angle restraints: 7388 sinusoidal: 3008 harmonic: 4380 Sorted by residual: dihedral pdb=" CA PHE D 53 " pdb=" C PHE D 53 " pdb=" N HIS D 54 " pdb=" CA HIS D 54 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA PHE A 53 " pdb=" C PHE A 53 " pdb=" N HIS A 54 " pdb=" CA HIS A 54 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA PHE C 53 " pdb=" C PHE C 53 " pdb=" N HIS C 54 " pdb=" CA HIS C 54 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 7385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 904 0.072 - 0.144: 521 0.144 - 0.215: 216 0.215 - 0.287: 56 0.287 - 0.359: 43 Chirality restraints: 1740 Sorted by residual: chirality pdb=" CA PRO C 97 " pdb=" N PRO C 97 " pdb=" C PRO C 97 " pdb=" CB PRO C 97 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA PRO D 97 " pdb=" N PRO D 97 " pdb=" C PRO D 97 " pdb=" CB PRO D 97 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA PRO B 97 " pdb=" N PRO B 97 " pdb=" C PRO B 97 " pdb=" CB PRO B 97 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.34 2.00e-01 2.50e+01 2.98e+00 ... (remaining 1737 not shown) Planarity restraints: 2300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 185 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" CG ASN C 185 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN C 185 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 185 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 288 " -0.029 2.00e-02 2.50e+03 2.39e-02 9.98e+00 pdb=" CG PHE B 288 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 288 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 288 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE B 288 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE B 288 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 288 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 288 " 0.030 2.00e-02 2.50e+03 2.38e-02 9.94e+00 pdb=" CG PHE C 288 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE C 288 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 288 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE C 288 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE C 288 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 288 " 0.043 2.00e-02 2.50e+03 ... (remaining 2297 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 61 2.59 - 3.17: 10145 3.17 - 3.74: 20178 3.74 - 4.32: 29889 4.32 - 4.90: 47192 Nonbonded interactions: 107465 Sorted by model distance: nonbonded pdb=" OD2 ASP C 287 " pdb="MN MN C 401 " model vdw 2.012 2.320 nonbonded pdb=" OD2 ASP B 287 " pdb="MN MN B 402 " model vdw 2.014 2.320 nonbonded pdb=" OD2 ASP A 287 " pdb="MN MN A 402 " model vdw 2.047 2.320 nonbonded pdb=" OD2 ASP D 287 " pdb="MN MN D 402 " model vdw 2.048 2.320 nonbonded pdb=" OE2 GLU A 181 " pdb="MN MN A 402 " model vdw 2.056 2.320 ... (remaining 107460 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: 0.10 Found NCS groups: 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: 1.460 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: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 31.190 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 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 : 0.008 0.082 12472 Z= 0.548 Angle : 1.490 16.684 16884 Z= 0.968 Chirality : 0.110 0.359 1740 Planarity : 0.008 0.041 2300 Dihedral : 14.484 85.288 4588 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.12 % Favored : 96.62 % Rotamer: Outliers : 1.82 % Allowed : 2.56 % Favored : 95.63 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 5.26 % 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: -0.31 (0.20), residues: 1540 helix: 0.40 (0.16), residues: 804 sheet: -2.25 (0.54), residues: 88 loop : -0.52 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.008 TRP B 300 HIS 0.020 0.006 HIS C 54 PHE 0.043 0.009 PHE B 288 TYR 0.039 0.011 TYR A 134 ARG 0.022 0.002 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.17734 ( 614) hydrogen bonds : angle 5.69095 ( 1782) covalent geometry : bond 0.00833 (12472) covalent geometry : angle 1.48974 (16884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 0 residues processed: 105 average time/residue: 1.5057 time to fit residues: 170.4413 Evaluate side-chains 42 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS A 285 HIS B 230 HIS B 285 HIS C 230 HIS C 285 HIS D 230 HIS D 285 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.072269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.061557 restraints weight = 33886.592| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.59 r_work: 0.2683 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12472 Z= 0.226 Angle : 0.571 6.022 16884 Z= 0.298 Chirality : 0.043 0.181 1740 Planarity : 0.005 0.042 2300 Dihedral : 4.588 32.118 1724 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.56 % Favored : 98.38 % Rotamer: Outliers : 0.74 % Allowed : 5.78 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 3.95 % 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: 1.29 (0.22), residues: 1540 helix: 2.09 (0.17), residues: 836 sheet: -2.73 (0.54), residues: 68 loop : -0.39 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 300 HIS 0.007 0.002 HIS C 54 PHE 0.010 0.002 PHE B 75 TYR 0.011 0.001 TYR C 134 ARG 0.003 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 614) hydrogen bonds : angle 4.10367 ( 1782) covalent geometry : bond 0.00525 (12472) covalent geometry : angle 0.57101 (16884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.9186 (tt0) cc_final: 0.8921 (tt0) outliers start: 9 outliers final: 0 residues processed: 46 average time/residue: 1.4281 time to fit residues: 72.5186 Evaluate side-chains 40 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 91 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 59 optimal weight: 0.2980 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.074946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.064299 restraints weight = 33918.921| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.61 r_work: 0.2747 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12472 Z= 0.107 Angle : 0.457 6.706 16884 Z= 0.236 Chirality : 0.038 0.192 1740 Planarity : 0.004 0.043 2300 Dihedral : 4.042 28.523 1724 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.33 % Allowed : 6.60 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.85 (0.22), residues: 1540 helix: 2.61 (0.18), residues: 836 sheet: -2.56 (0.53), residues: 68 loop : -0.20 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 300 HIS 0.005 0.001 HIS C 54 PHE 0.009 0.001 PHE B 75 TYR 0.009 0.001 TYR D 168 ARG 0.002 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 614) hydrogen bonds : angle 3.66574 ( 1782) covalent geometry : bond 0.00245 (12472) covalent geometry : angle 0.45729 (16884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 1.490 Fit side-chains REVERT: D 186 GLU cc_start: 0.8982 (tt0) cc_final: 0.8779 (tt0) REVERT: D 264 ASP cc_start: 0.8602 (t70) cc_final: 0.8370 (t70) outliers start: 4 outliers final: 0 residues processed: 48 average time/residue: 1.4617 time to fit residues: 77.3489 Evaluate side-chains 41 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 102 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.061230 restraints weight = 33488.072| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.67 r_work: 0.2724 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12472 Z= 0.109 Angle : 0.436 5.861 16884 Z= 0.225 Chirality : 0.037 0.172 1740 Planarity : 0.004 0.044 2300 Dihedral : 3.910 30.286 1724 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.33 % Allowed : 7.43 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: 2.02 (0.22), residues: 1540 helix: 2.74 (0.18), residues: 836 sheet: -2.37 (0.55), residues: 68 loop : -0.14 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 300 HIS 0.004 0.001 HIS C 54 PHE 0.007 0.001 PHE B 75 TYR 0.009 0.001 TYR D 168 ARG 0.001 0.000 ARG A 259 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 614) hydrogen bonds : angle 3.55131 ( 1782) covalent geometry : bond 0.00252 (12472) covalent geometry : angle 0.43632 (16884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 2.240 Fit side-chains REVERT: A 207 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: A 264 ASP cc_start: 0.8679 (t70) cc_final: 0.8411 (t70) REVERT: D 207 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7972 (tt0) outliers start: 4 outliers final: 0 residues processed: 44 average time/residue: 1.7910 time to fit residues: 85.9338 Evaluate side-chains 42 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain D residue 207 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 127 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.067592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.056669 restraints weight = 34512.300| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.74 r_work: 0.2724 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12472 Z= 0.104 Angle : 0.423 6.440 16884 Z= 0.217 Chirality : 0.037 0.186 1740 Planarity : 0.004 0.044 2300 Dihedral : 3.727 28.422 1724 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.41 % Allowed : 7.18 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.15 (0.22), residues: 1540 helix: 2.86 (0.18), residues: 836 sheet: -2.23 (0.56), residues: 68 loop : -0.12 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 300 HIS 0.004 0.001 HIS C 54 PHE 0.007 0.001 PHE B 75 TYR 0.008 0.001 TYR D 168 ARG 0.001 0.000 ARG B 259 Details of bonding type rmsd hydrogen bonds : bond 0.03044 ( 614) hydrogen bonds : angle 3.44934 ( 1782) covalent geometry : bond 0.00241 (12472) covalent geometry : angle 0.42312 (16884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 1.328 Fit side-chains REVERT: A 186 GLU cc_start: 0.9085 (tt0) cc_final: 0.8820 (tt0) REVERT: A 207 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: A 264 ASP cc_start: 0.8712 (t70) cc_final: 0.8442 (t70) REVERT: D 207 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7961 (tt0) outliers start: 5 outliers final: 0 residues processed: 45 average time/residue: 2.6955 time to fit residues: 132.6279 Evaluate side-chains 43 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain D residue 207 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 44 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 141 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.066039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.054757 restraints weight = 35026.709| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.84 r_work: 0.2671 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12472 Z= 0.177 Angle : 0.461 5.540 16884 Z= 0.237 Chirality : 0.039 0.181 1740 Planarity : 0.004 0.045 2300 Dihedral : 3.835 29.987 1724 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.50 % Allowed : 6.85 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.06 (0.22), residues: 1540 helix: 2.79 (0.18), residues: 836 sheet: -2.13 (0.57), residues: 68 loop : -0.16 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 270 HIS 0.003 0.001 HIS C 54 PHE 0.008 0.001 PHE A 162 TYR 0.009 0.001 TYR D 168 ARG 0.002 0.000 ARG C 23 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 614) hydrogen bonds : angle 3.56238 ( 1782) covalent geometry : bond 0.00418 (12472) covalent geometry : angle 0.46118 (16884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 1.468 Fit side-chains REVERT: A 186 GLU cc_start: 0.9072 (tt0) cc_final: 0.8802 (tt0) REVERT: A 207 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: D 207 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8000 (tt0) outliers start: 6 outliers final: 2 residues processed: 45 average time/residue: 1.5276 time to fit residues: 76.2897 Evaluate side-chains 43 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 207 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.066720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.055575 restraints weight = 34748.120| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.78 r_work: 0.2686 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12472 Z= 0.148 Angle : 0.444 5.617 16884 Z= 0.228 Chirality : 0.038 0.181 1740 Planarity : 0.004 0.045 2300 Dihedral : 3.788 28.431 1724 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.25 % Allowed : 7.10 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.08 (0.22), residues: 1540 helix: 2.83 (0.18), residues: 836 sheet: -2.13 (0.56), residues: 68 loop : -0.20 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 300 HIS 0.003 0.001 HIS C 54 PHE 0.007 0.001 PHE B 75 TYR 0.008 0.001 TYR D 168 ARG 0.001 0.000 ARG D 266 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 614) hydrogen bonds : angle 3.52452 ( 1782) covalent geometry : bond 0.00350 (12472) covalent geometry : angle 0.44410 (16884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 1.389 Fit side-chains REVERT: A 186 GLU cc_start: 0.9034 (tt0) cc_final: 0.8742 (tt0) REVERT: A 207 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: D 207 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8016 (tt0) outliers start: 3 outliers final: 1 residues processed: 42 average time/residue: 1.5762 time to fit residues: 73.0514 Evaluate side-chains 42 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 207 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 119 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.056827 restraints weight = 34706.017| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.75 r_work: 0.2740 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12472 Z= 0.085 Angle : 0.403 5.837 16884 Z= 0.207 Chirality : 0.036 0.166 1740 Planarity : 0.004 0.043 2300 Dihedral : 3.613 28.021 1724 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.17 % Allowed : 7.18 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.26 (0.23), residues: 1540 helix: 3.02 (0.18), residues: 836 sheet: -2.11 (0.58), residues: 68 loop : -0.17 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 300 HIS 0.003 0.001 HIS C 54 PHE 0.006 0.001 PHE D 269 TYR 0.007 0.001 TYR D 168 ARG 0.001 0.000 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.02682 ( 614) hydrogen bonds : angle 3.35834 ( 1782) covalent geometry : bond 0.00195 (12472) covalent geometry : angle 0.40298 (16884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 1.385 Fit side-chains REVERT: A 207 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: D 207 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7998 (tt0) outliers start: 2 outliers final: 0 residues processed: 45 average time/residue: 1.4855 time to fit residues: 73.3985 Evaluate side-chains 42 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain D residue 207 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 109 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 146 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.068672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.058106 restraints weight = 34588.035| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.59 r_work: 0.2673 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12472 Z= 0.186 Angle : 0.464 5.509 16884 Z= 0.238 Chirality : 0.039 0.187 1740 Planarity : 0.004 0.045 2300 Dihedral : 3.795 28.875 1724 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.75 % Favored : 98.18 % Rotamer: Outliers : 0.33 % Allowed : 7.18 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.09 (0.22), residues: 1540 helix: 2.84 (0.18), residues: 836 sheet: -2.12 (0.56), residues: 68 loop : -0.21 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 270 HIS 0.003 0.001 HIS C 54 PHE 0.008 0.001 PHE D 162 TYR 0.009 0.001 TYR D 168 ARG 0.002 0.000 ARG C 23 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 614) hydrogen bonds : angle 3.52997 ( 1782) covalent geometry : bond 0.00438 (12472) covalent geometry : angle 0.46395 (16884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 1.289 Fit side-chains REVERT: A 207 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: D 207 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8012 (tt0) outliers start: 4 outliers final: 1 residues processed: 43 average time/residue: 1.4709 time to fit residues: 69.4870 Evaluate side-chains 41 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 207 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 103 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.068569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.058019 restraints weight = 34576.638| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.59 r_work: 0.2676 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12472 Z= 0.167 Angle : 0.452 5.535 16884 Z= 0.232 Chirality : 0.039 0.180 1740 Planarity : 0.004 0.045 2300 Dihedral : 3.798 28.904 1724 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.88 % Favored : 98.05 % Rotamer: Outliers : 0.33 % Allowed : 7.26 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.10 (0.23), residues: 1540 helix: 2.85 (0.18), residues: 836 sheet: -2.11 (0.56), residues: 68 loop : -0.20 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 300 HIS 0.003 0.001 HIS C 54 PHE 0.007 0.001 PHE B 75 TYR 0.009 0.001 TYR D 168 ARG 0.002 0.000 ARG B 266 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 614) hydrogen bonds : angle 3.53306 ( 1782) covalent geometry : bond 0.00394 (12472) covalent geometry : angle 0.45163 (16884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 2.491 Fit side-chains REVERT: A 207 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: D 207 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7995 (tt0) outliers start: 4 outliers final: 1 residues processed: 43 average time/residue: 1.7388 time to fit residues: 82.7998 Evaluate side-chains 41 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 207 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 133 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.059404 restraints weight = 34676.422| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.60 r_work: 0.2726 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12472 Z= 0.094 Angle : 0.410 5.588 16884 Z= 0.211 Chirality : 0.036 0.166 1740 Planarity : 0.004 0.043 2300 Dihedral : 3.662 28.319 1724 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 0.17 % Allowed : 7.43 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.28 (0.23), residues: 1540 helix: 3.02 (0.18), residues: 836 sheet: -2.11 (0.57), residues: 68 loop : -0.13 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 300 HIS 0.003 0.001 HIS C 54 PHE 0.007 0.001 PHE B 75 TYR 0.007 0.001 TYR D 168 ARG 0.001 0.000 ARG D 284 Details of bonding type rmsd hydrogen bonds : bond 0.02842 ( 614) hydrogen bonds : angle 3.39675 ( 1782) covalent geometry : bond 0.00219 (12472) covalent geometry : angle 0.41001 (16884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5392.26 seconds wall clock time: 98 minutes 44.28 seconds (5924.28 seconds total)