Starting phenix.real_space_refine on Sun Mar 10 15:33:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg3_16628/03_2024/8cg3_16628.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg3_16628/03_2024/8cg3_16628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg3_16628/03_2024/8cg3_16628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg3_16628/03_2024/8cg3_16628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg3_16628/03_2024/8cg3_16628.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg3_16628/03_2024/8cg3_16628.pdb" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 1785 2.51 5 N 610 2.21 5 O 605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U ARG 272": "NH1" <-> "NH2" Residue "U ARG 275": "NH1" <-> "NH2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 293": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 293": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3040 Number of models: 1 Model: "" Number of chains: 5 Chain: "U" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 608 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "A" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 608 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "B" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 608 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "C" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 608 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "D" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 608 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Time building chain proxies: 1.86, per 1000 atoms: 0.61 Number of scatterers: 3040 At special positions: 0 Unit cell: (77.4, 67.94, 50.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 605 8.00 N 610 7.00 C 1785 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 - 3.50 Amino acid : False - 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: 1.02 Conformation dependent library (CDL) restraints added in 606.6 milliseconds 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 275 removed outlier: 8.696A pdb=" N SER U 273 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG B 275 " --> pdb=" O GLY U 274 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG C 275 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG D 275 " --> pdb=" O GLY C 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 293 removed outlier: 6.781A pdb=" N SER U 292 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER B 292 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER C 292 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 300 removed outlier: 6.769A pdb=" N GLY U 296 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N LEU A 299 " --> pdb=" O GLY U 296 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY U 298 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 308 removed outlier: 6.560A pdb=" N ASN U 306 " --> pdb=" O MET A 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 6.611A pdb=" N MET U 311 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLY B 314 " --> pdb=" O MET U 311 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE U 313 " --> pdb=" O GLY B 314 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET B 311 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLY C 314 " --> pdb=" O MET B 311 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE B 313 " --> pdb=" O GLY C 314 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N MET C 311 " --> pdb=" O ASN D 312 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLY D 314 " --> pdb=" O MET C 311 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE C 313 " --> pdb=" O GLY D 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 336 removed outlier: 6.738A pdb=" N ALA U 321 " --> pdb=" O MET B 322 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ALA B 324 " --> pdb=" O ALA U 321 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET U 323 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ALA B 326 " --> pdb=" O MET U 323 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA U 325 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ALA B 328 " --> pdb=" O ALA U 325 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN U 327 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N LEU B 330 " --> pdb=" O GLN U 327 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA U 329 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N SER B 332 " --> pdb=" O ALA U 329 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN U 331 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N TRP B 334 " --> pdb=" O GLN U 331 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER U 333 " --> pdb=" O TRP B 334 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N MET B 336 " --> pdb=" O SER U 333 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY U 335 " --> pdb=" O MET B 336 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA B 321 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ALA C 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET B 323 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ALA C 326 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA B 325 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ALA C 328 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN B 327 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N LEU C 330 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA B 329 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N SER C 332 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN B 331 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N TRP C 334 " --> pdb=" O GLN B 331 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER B 333 " --> pdb=" O TRP C 334 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N MET C 336 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY B 335 " --> pdb=" O MET C 336 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA C 321 " --> pdb=" O MET D 322 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ALA D 324 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET C 323 " --> pdb=" O ALA D 324 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ALA D 326 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA C 325 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ALA D 328 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN C 327 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N LEU D 330 " --> pdb=" O GLN C 327 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA C 329 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N SER D 332 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN C 331 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N TRP D 334 " --> pdb=" O GLN C 331 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER C 333 " --> pdb=" O TRP D 334 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N MET D 336 " --> pdb=" O SER C 333 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY C 335 " --> pdb=" O MET D 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 347 removed outlier: 6.609A pdb=" N GLN U 344 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER B 347 " --> pdb=" O GLN U 344 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN U 346 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN B 344 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER C 347 " --> pdb=" O GLN B 344 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN B 346 " --> pdb=" O SER C 347 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN C 344 " --> pdb=" O ASN D 345 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER D 347 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLN C 346 " --> pdb=" O SER D 347 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 353 through 356 removed outlier: 6.878A pdb=" N ASN U 353 " --> pdb=" O GLN A 354 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLN A 356 " --> pdb=" O ASN U 353 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN U 355 " --> pdb=" O GLN A 356 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 162 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: 0.65 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1070 1.35 - 1.48: 805 1.48 - 1.61: 1130 1.61 - 1.74: 0 1.74 - 1.87: 80 Bond restraints: 3085 Sorted by residual: bond pdb=" CA SER D 333 " pdb=" CB SER D 333 " ideal model delta sigma weight residual 1.534 1.484 0.050 1.64e-02 3.72e+03 9.27e+00 bond pdb=" CA SER A 333 " pdb=" CB SER A 333 " ideal model delta sigma weight residual 1.534 1.484 0.050 1.64e-02 3.72e+03 9.26e+00 bond pdb=" CA SER U 333 " pdb=" CB SER U 333 " ideal model delta sigma weight residual 1.534 1.484 0.050 1.64e-02 3.72e+03 9.15e+00 bond pdb=" CA SER B 333 " pdb=" CB SER B 333 " ideal model delta sigma weight residual 1.534 1.484 0.049 1.64e-02 3.72e+03 9.10e+00 bond pdb=" CA SER C 333 " pdb=" CB SER C 333 " ideal model delta sigma weight residual 1.534 1.485 0.049 1.64e-02 3.72e+03 8.90e+00 ... (remaining 3080 not shown) Histogram of bond angle deviations from ideal: 100.19 - 107.04: 148 107.04 - 113.88: 1257 113.88 - 120.73: 1493 120.73 - 127.57: 1187 127.57 - 134.42: 15 Bond angle restraints: 4100 Sorted by residual: angle pdb=" C ASN B 319 " pdb=" CA ASN B 319 " pdb=" CB ASN B 319 " ideal model delta sigma weight residual 110.71 106.12 4.59 9.40e-01 1.13e+00 2.39e+01 angle pdb=" CA ASN D 319 " pdb=" C ASN D 319 " pdb=" N PRO D 320 " ideal model delta sigma weight residual 118.16 121.58 -3.42 7.00e-01 2.04e+00 2.38e+01 angle pdb=" CA ASN C 319 " pdb=" C ASN C 319 " pdb=" N PRO C 320 " ideal model delta sigma weight residual 118.16 121.57 -3.41 7.00e-01 2.04e+00 2.38e+01 angle pdb=" C ASN C 319 " pdb=" CA ASN C 319 " pdb=" CB ASN C 319 " ideal model delta sigma weight residual 110.71 106.13 4.58 9.40e-01 1.13e+00 2.37e+01 angle pdb=" CA ASN U 319 " pdb=" C ASN U 319 " pdb=" N PRO U 320 " ideal model delta sigma weight residual 118.16 121.57 -3.41 7.00e-01 2.04e+00 2.37e+01 ... (remaining 4095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.35: 1510 13.35 - 26.70: 190 26.70 - 40.04: 20 40.04 - 53.39: 10 53.39 - 66.74: 25 Dihedral angle restraints: 1755 sinusoidal: 665 harmonic: 1090 Sorted by residual: dihedral pdb=" CA GLN B 327 " pdb=" C GLN B 327 " pdb=" N ALA B 328 " pdb=" CA ALA B 328 " ideal model delta harmonic sigma weight residual 180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA GLN A 327 " pdb=" C GLN A 327 " pdb=" N ALA A 328 " pdb=" CA ALA A 328 " ideal model delta harmonic sigma weight residual -180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA GLN U 327 " pdb=" C GLN U 327 " pdb=" N ALA U 328 " pdb=" CA ALA U 328 " ideal model delta harmonic sigma weight residual 180.00 -160.68 -19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 1752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 108 0.038 - 0.076: 114 0.076 - 0.113: 88 0.113 - 0.151: 20 0.151 - 0.189: 15 Chirality restraints: 345 Sorted by residual: chirality pdb=" CA GLN B 344 " pdb=" N GLN B 344 " pdb=" C GLN B 344 " pdb=" CB GLN B 344 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA GLN D 344 " pdb=" N GLN D 344 " pdb=" C GLN D 344 " pdb=" CB GLN D 344 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA GLN U 344 " pdb=" N GLN U 344 " pdb=" C GLN U 344 " pdb=" CB GLN U 344 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 342 not shown) Planarity restraints: 615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 334 " -0.029 2.00e-02 2.50e+03 1.82e-02 8.27e+00 pdb=" CG TRP A 334 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 334 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 334 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 334 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 334 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 334 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 334 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 334 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 334 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP U 334 " -0.029 2.00e-02 2.50e+03 1.82e-02 8.25e+00 pdb=" CG TRP U 334 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP U 334 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP U 334 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP U 334 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP U 334 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP U 334 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP U 334 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP U 334 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP U 334 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 334 " -0.029 2.00e-02 2.50e+03 1.82e-02 8.24e+00 pdb=" CG TRP C 334 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 334 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP C 334 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 334 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 334 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 334 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 334 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 334 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP C 334 " -0.000 2.00e-02 2.50e+03 ... (remaining 612 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.07: 1732 3.07 - 3.53: 2504 3.53 - 3.99: 4573 3.99 - 4.44: 5320 4.44 - 4.90: 8739 Nonbonded interactions: 22868 Sorted by model distance: nonbonded pdb=" O ASN A 319 " pdb=" CB ASN A 319 " model vdw 2.619 2.752 nonbonded pdb=" O ASN U 319 " pdb=" CB ASN U 319 " model vdw 2.619 2.752 nonbonded pdb=" O ASN B 319 " pdb=" CB ASN B 319 " model vdw 2.619 2.752 nonbonded pdb=" O ASN C 319 " pdb=" CB ASN C 319 " model vdw 2.619 2.752 nonbonded pdb=" O ASN D 319 " pdb=" CB ASN D 319 " model vdw 2.619 2.752 ... (remaining 22863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.000 Extract box with map and model: 3.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.660 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9349 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 : 0.012 0.065 3085 Z= 0.863 Angle : 1.687 6.258 4100 Z= 1.162 Chirality : 0.076 0.189 345 Planarity : 0.008 0.063 615 Dihedral : 14.766 66.738 1105 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.90 (0.19), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.15), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.012 TRP A 334 PHE 0.010 0.003 PHE C 276 ARG 0.003 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.335 Fit side-chains REVERT: B 336 MET cc_start: 0.9327 (ttp) cc_final: 0.9106 (ttm) REVERT: C 339 MET cc_start: 0.8693 (tpt) cc_final: 0.8251 (tpt) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 1.2257 time to fit residues: 80.5185 Evaluate side-chains 58 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 354 GLN A 354 GLN B 354 GLN C 354 GLN D 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9189 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3085 Z= 0.229 Angle : 0.764 4.628 4100 Z= 0.432 Chirality : 0.041 0.134 345 Planarity : 0.003 0.017 615 Dihedral : 5.970 17.876 455 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.19), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.15), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP C 334 PHE 0.012 0.002 PHE B 316 ARG 0.002 0.000 ARG U 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.353 Fit side-chains REVERT: U 311 MET cc_start: 0.9225 (ttt) cc_final: 0.9017 (ttp) REVERT: D 355 ASN cc_start: 0.8836 (m-40) cc_final: 0.8616 (t0) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 1.4077 time to fit residues: 90.8735 Evaluate side-chains 60 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.9243 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3085 Z= 0.383 Angle : 0.956 5.846 4100 Z= 0.545 Chirality : 0.046 0.165 345 Planarity : 0.005 0.031 615 Dihedral : 6.062 20.041 455 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.36 % Allowed : 5.71 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.17), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.13), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP C 334 PHE 0.013 0.003 PHE C 316 ARG 0.002 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.343 Fit side-chains REVERT: C 339 MET cc_start: 0.8667 (tpt) cc_final: 0.8341 (tpt) REVERT: D 355 ASN cc_start: 0.8926 (m-40) cc_final: 0.8695 (t0) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 1.3574 time to fit residues: 82.0084 Evaluate side-chains 59 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 333 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 0.1980 chunk 38 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 6.0390 ------------------------------------------------------------------------------- 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: 0.9236 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3085 Z= 0.355 Angle : 0.918 5.611 4100 Z= 0.521 Chirality : 0.045 0.160 345 Planarity : 0.005 0.030 615 Dihedral : 6.002 19.588 455 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.07 % Allowed : 6.07 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.16), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.12), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP C 334 PHE 0.013 0.003 PHE C 316 ARG 0.002 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.336 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 59 average time/residue: 1.3210 time to fit residues: 79.8616 Evaluate side-chains 56 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.4980 chunk 15 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- 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: 0.9220 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3085 Z= 0.295 Angle : 0.837 5.160 4100 Z= 0.474 Chirality : 0.043 0.151 345 Planarity : 0.004 0.027 615 Dihedral : 5.865 19.187 455 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.79 % Allowed : 5.71 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.16), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.12), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP U 334 PHE 0.012 0.002 PHE C 316 ARG 0.002 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.334 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 61 average time/residue: 1.2543 time to fit residues: 78.4697 Evaluate side-chains 57 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 333 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9206 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3085 Z= 0.254 Angle : 0.782 4.986 4100 Z= 0.442 Chirality : 0.042 0.143 345 Planarity : 0.004 0.026 615 Dihedral : 5.734 18.603 455 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.43 % Allowed : 6.07 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.16), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.12), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP U 334 PHE 0.011 0.002 PHE C 316 ARG 0.002 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.324 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 57 average time/residue: 1.3957 time to fit residues: 81.3892 Evaluate side-chains 55 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 333 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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: 0.9251 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3085 Z= 0.448 Angle : 1.009 5.931 4100 Z= 0.575 Chirality : 0.048 0.170 345 Planarity : 0.005 0.032 615 Dihedral : 6.036 20.491 455 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.07 % Allowed : 7.14 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.16), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.12), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP C 334 PHE 0.014 0.003 PHE C 316 ARG 0.003 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.339 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 1.3273 time to fit residues: 80.2398 Evaluate side-chains 57 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 333 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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: 0.9211 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3085 Z= 0.264 Angle : 0.805 5.834 4100 Z= 0.453 Chirality : 0.043 0.145 345 Planarity : 0.004 0.026 615 Dihedral : 5.800 18.897 455 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.36 % Allowed : 8.21 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.16), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.12), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP U 334 PHE 0.011 0.002 PHE C 316 ARG 0.002 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.292 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 1.4428 time to fit residues: 84.1517 Evaluate side-chains 56 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 30.0000 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- 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: 0.9190 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3085 Z= 0.217 Angle : 0.732 4.748 4100 Z= 0.411 Chirality : 0.041 0.135 345 Planarity : 0.004 0.026 615 Dihedral : 5.601 18.322 455 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.36 % Allowed : 8.21 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.74 (0.16), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.13), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP U 334 PHE 0.010 0.002 PHE C 316 ARG 0.001 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.327 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 56 average time/residue: 1.4374 time to fit residues: 82.3520 Evaluate side-chains 57 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 333 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN B 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9248 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3085 Z= 0.440 Angle : 1.004 6.182 4100 Z= 0.569 Chirality : 0.047 0.167 345 Planarity : 0.005 0.032 615 Dihedral : 5.998 20.454 455 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.16), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.12), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP C 334 PHE 0.013 0.003 PHE C 316 ARG 0.003 0.001 ARG A 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.314 Fit side-chains REVERT: A 311 MET cc_start: 0.9116 (ttt) cc_final: 0.8904 (ttt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.3798 time to fit residues: 80.5638 Evaluate side-chains 57 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 25 optimal weight: 0.0470 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.106643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.076962 restraints weight = 2761.006| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.88 r_work: 0.2917 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9178 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3085 Z= 0.241 Angle : 0.775 6.020 4100 Z= 0.434 Chirality : 0.042 0.141 345 Planarity : 0.004 0.026 615 Dihedral : 5.738 18.581 455 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.16), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.12), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP U 334 PHE 0.011 0.002 PHE C 316 ARG 0.002 0.000 ARG A 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1777.87 seconds wall clock time: 32 minutes 5.04 seconds (1925.04 seconds total)