Starting phenix.real_space_refine on Thu Sep 26 04:33:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrs_21371/09_2024/6vrs_21371.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrs_21371/09_2024/6vrs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrs_21371/09_2024/6vrs_21371.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrs_21371/09_2024/6vrs_21371.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrs_21371/09_2024/6vrs_21371.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrs_21371/09_2024/6vrs_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.81, 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: 3.12 Conformation dependent library (CDL) restraints added in 1.7 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: 1.46 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: 3.66 Time building geometry restraints manager: 3.63 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 2.280 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.370 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.830 ------------------------------------------------------------------------------- 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 *********************** 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 fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 0 residues processed: 105 average time/residue: 1.4195 time to fit residues: 161.2296 Evaluate side-chains 42 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 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= 0.343 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 : 1.75 % Favored : 98.18 % 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 *********************** 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 fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 0 residues processed: 46 average time/residue: 1.3527 time to fit residues: 68.7954 Evaluate side-chains 39 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 0.0370 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 47 optimal weight: 0.0980 chunk 110 optimal weight: 9.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.2304 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= 0.134 Angle : 0.449 6.691 16884 Z= 0.233 Chirality : 0.037 0.188 1740 Planarity : 0.004 0.044 2300 Dihedral : 4.032 28.471 1724 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.33 % Allowed : 6.35 % Favored : 93.32 % 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: -2.57 (0.53), residues: 68 loop : -0.19 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 300 HIS 0.006 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 188 *********************** 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 49 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 1.873 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 49 average time/residue: 1.3496 time to fit residues: 74.7642 Evaluate side-chains 40 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12472 Z= 0.361 Angle : 0.519 5.600 16884 Z= 0.267 Chirality : 0.042 0.186 1740 Planarity : 0.005 0.046 2300 Dihedral : 4.122 30.570 1724 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.34 % Favored : 97.53 % Rotamer: Outliers : 0.91 % Allowed : 6.77 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 1.32 % 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: 1.82 (0.22), residues: 1540 helix: 2.50 (0.17), residues: 836 sheet: -2.64 (0.56), residues: 48 loop : -0.18 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 300 HIS 0.004 0.002 HIS C 54 PHE 0.011 0.001 PHE D 75 TYR 0.013 0.002 TYR C 134 ARG 0.002 0.000 ARG B 23 *********************** 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 47 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 36 time to evaluate : 1.425 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 43 average time/residue: 1.4501 time to fit residues: 68.7094 Evaluate side-chains 40 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 221 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 109 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12472 Z= 0.159 Angle : 0.435 6.509 16884 Z= 0.225 Chirality : 0.037 0.189 1740 Planarity : 0.004 0.045 2300 Dihedral : 3.872 28.362 1724 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.08 % Allowed : 7.43 % 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: 2.03 (0.22), residues: 1540 helix: 2.77 (0.18), residues: 836 sheet: -2.21 (0.55), residues: 68 loop : -0.18 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 A 266 *********************** 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 40 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.432 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 1.3194 time to fit residues: 58.6560 Evaluate side-chains 38 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 0.0470 chunk 36 optimal weight: 0.0980 chunk 147 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12472 Z= 0.147 Angle : 0.416 5.731 16884 Z= 0.214 Chirality : 0.037 0.169 1740 Planarity : 0.004 0.044 2300 Dihedral : 3.697 28.868 1724 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.17 % Allowed : 7.01 % Favored : 92.82 % 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: 2.19 (0.23), residues: 1540 helix: 2.91 (0.18), residues: 836 sheet: -2.11 (0.57), residues: 68 loop : -0.13 (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 0.002 0.000 ARG D 259 *********************** 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 44 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 1.328 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 1.3709 time to fit residues: 67.0563 Evaluate side-chains 41 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.0010 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 90 optimal weight: 0.0980 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12472 Z= 0.305 Angle : 0.478 5.901 16884 Z= 0.246 Chirality : 0.040 0.192 1740 Planarity : 0.005 0.045 2300 Dihedral : 3.866 28.169 1724 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.17 % Allowed : 7.51 % Favored : 92.33 % 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: 2.01 (0.22), residues: 1540 helix: 2.74 (0.18), residues: 836 sheet: -2.11 (0.56), residues: 68 loop : -0.19 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 270 HIS 0.003 0.001 HIS A 54 PHE 0.008 0.001 PHE D 162 TYR 0.010 0.001 TYR D 168 ARG 0.002 0.000 ARG C 23 *********************** 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 41 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 1.482 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 1.3546 time to fit residues: 61.6713 Evaluate side-chains 41 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain C residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.0070 chunk 115 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12472 Z= 0.143 Angle : 0.418 5.776 16884 Z= 0.216 Chirality : 0.037 0.168 1740 Planarity : 0.004 0.043 2300 Dihedral : 3.714 28.555 1724 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.17 % Allowed : 7.51 % Favored : 92.33 % 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: 2.20 (0.23), residues: 1540 helix: 2.95 (0.18), residues: 836 sheet: -2.07 (0.57), residues: 68 loop : -0.19 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 300 HIS 0.003 0.001 HIS A 54 PHE 0.007 0.001 PHE A 269 TYR 0.008 0.001 TYR D 168 ARG 0.001 0.000 ARG C 259 *********************** 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 41 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 1.447 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 1.3126 time to fit residues: 58.7027 Evaluate side-chains 39 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 10.0000 chunk 136 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.2686 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= 0.232 Angle : 0.445 5.680 16884 Z= 0.229 Chirality : 0.038 0.177 1740 Planarity : 0.004 0.044 2300 Dihedral : 3.760 28.413 1724 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 7.59 % 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: 2.12 (0.23), residues: 1540 helix: 2.86 (0.18), residues: 836 sheet: -2.07 (0.57), residues: 68 loop : -0.18 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 270 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 *********************** 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 39 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.372 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 1.4152 time to fit residues: 61.4146 Evaluate side-chains 39 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.2673 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= 0.262 Angle : 0.457 5.666 16884 Z= 0.236 Chirality : 0.039 0.179 1740 Planarity : 0.004 0.044 2300 Dihedral : 3.823 28.578 1724 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % 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: 2.07 (0.23), residues: 1540 helix: 2.82 (0.18), residues: 836 sheet: -2.09 (0.56), residues: 68 loop : -0.21 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 270 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 D 266 ********************** 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 42 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 1.428 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 1.3349 time to fit residues: 62.3078 Evaluate side-chains 40 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3117 r_free = 0.3117 target = 0.068773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.058262 restraints weight = 34573.390| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.58 r_work: 0.2711 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12472 Z= 0.175 Angle : 0.423 5.664 16884 Z= 0.218 Chirality : 0.037 0.170 1740 Planarity : 0.004 0.043 2300 Dihedral : 3.722 28.476 1724 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.17 % Allowed : 7.67 % Favored : 92.16 % 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: 2.19 (0.23), residues: 1540 helix: 2.93 (0.18), residues: 836 sheet: -2.09 (0.57), residues: 68 loop : -0.17 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 300 HIS 0.003 0.001 HIS D 54 PHE 0.007 0.001 PHE B 75 TYR 0.008 0.001 TYR D 168 ARG 0.001 0.000 ARG B 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2537.22 seconds wall clock time: 45 minutes 58.98 seconds (2758.98 seconds total)