Starting phenix.real_space_refine on Fri Dec 8 02:26:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/12_2023/8q8w_18263.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/12_2023/8q8w_18263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/12_2023/8q8w_18263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/12_2023/8q8w_18263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/12_2023/8q8w_18263.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8w_18263/12_2023/8q8w_18263.pdb" } resolution = 2.85 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= 0.002 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 S 6 5.16 5 C 2034 2.51 5 N 594 2.21 5 O 612 1.98 5 H 3372 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6618 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "B" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "D" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "F" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 3.24, per 1000 atoms: 0.49 Number of scatterers: 6618 At special positions: 0 Unit cell: (121.952, 140.904, 45.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 612 8.00 N 594 7.00 C 2034 6.00 H 3372 1.00 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: 4.82 Conformation dependent library (CDL) restraints added in 663.2 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 51.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 309 through 310 removed outlier: 6.620A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.702A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.363A pdb=" N VAL C 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LYS E 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER C 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLY E 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N CYS C 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU E 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER C 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N SER E 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N CYS E 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER E 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY A 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.546A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 336 through 342 removed outlier: 6.518A pdb=" N GLN A 336 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N VAL E 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU A 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER E 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS A 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.397A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.592A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.771A pdb=" N ASP A 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N THR E 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 368 through 374 Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.522A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.753A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.305A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.606A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 333 through 334 removed outlier: 6.777A pdb=" N GLY B 333 " --> pdb=" O GLY D 334 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 342 Processing sheet with id=AB7, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.592A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.290A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.273A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.376A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 231 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3366 1.12 - 1.29: 546 1.29 - 1.47: 1076 1.47 - 1.64: 1675 1.64 - 1.81: 6 Bond restraints: 6669 Sorted by residual: bond pdb=" NE2 GLN E 336 " pdb="HE22 GLN E 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY B 326 " pdb=" H GLY B 326 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY C 333 " pdb=" H GLY C 333 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN B 327 " pdb="HD21 ASN B 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY A 355 " pdb=" H GLY A 355 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 95.96 - 102.61: 23 102.61 - 109.26: 4362 109.26 - 115.90: 4371 115.90 - 122.55: 2731 122.55 - 129.20: 681 Bond angle restraints: 12168 Sorted by residual: angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 118.44 -5.84 1.00e+00 1.00e+00 3.41e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.63 -5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 117.47 -4.87 1.00e+00 1.00e+00 2.38e+01 angle pdb=" OE1 GLN F 336 " pdb=" CD GLN F 336 " pdb=" NE2 GLN F 336 " ideal model delta sigma weight residual 122.60 117.91 4.69 1.00e+00 1.00e+00 2.20e+01 angle pdb=" OE1 GLN D 336 " pdb=" CD GLN D 336 " pdb=" NE2 GLN D 336 " ideal model delta sigma weight residual 122.60 118.05 4.55 1.00e+00 1.00e+00 2.07e+01 ... (remaining 12163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.72: 2647 13.72 - 27.45: 157 27.45 - 41.17: 50 41.17 - 54.89: 22 54.89 - 68.61: 64 Dihedral angle restraints: 2940 sinusoidal: 1626 harmonic: 1314 Sorted by residual: dihedral pdb=" CA ASP D 358 " pdb=" C ASP D 358 " pdb=" N ASN D 359 " pdb=" CA ASN D 359 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU D 372 " pdb=" C GLU D 372 " pdb=" N THR D 373 " pdb=" CA THR D 373 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU F 372 " pdb=" C GLU F 372 " pdb=" N THR F 373 " pdb=" CA THR F 373 " ideal model delta harmonic sigma weight residual 180.00 160.49 19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 2937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 220 0.053 - 0.106: 180 0.106 - 0.160: 61 0.160 - 0.213: 26 0.213 - 0.266: 8 Chirality restraints: 495 Sorted by residual: chirality pdb=" CA LYS A 347 " pdb=" N LYS A 347 " pdb=" C LYS A 347 " pdb=" CB LYS A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA SER B 352 " pdb=" N SER B 352 " pdb=" C SER B 352 " pdb=" CB SER B 352 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA LYS F 347 " pdb=" N LYS F 347 " pdb=" C LYS F 347 " pdb=" CB LYS F 347 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 492 not shown) Planarity restraints: 966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 368 " -0.052 2.00e-02 2.50e+03 4.88e-02 3.58e+01 pdb=" CG ASN A 368 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 368 " 0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN A 368 " 0.048 2.00e-02 2.50e+03 pdb="HD21 ASN A 368 " 0.035 2.00e-02 2.50e+03 pdb="HD22 ASN A 368 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 362 " -0.061 2.00e-02 2.50e+03 3.69e-02 3.06e+01 pdb=" CG HIS D 362 " 0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS D 362 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS D 362 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 HIS D 362 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS D 362 " 0.028 2.00e-02 2.50e+03 pdb=" HD2 HIS D 362 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 HIS D 362 " -0.023 2.00e-02 2.50e+03 pdb=" HE2 HIS D 362 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.066 2.00e-02 2.50e+03 2.96e-02 2.62e+01 pdb=" CG TYR E 310 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.058 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " -0.002 2.00e-02 2.50e+03 ... (remaining 963 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 395 2.14 - 2.76: 10601 2.76 - 3.37: 17256 3.37 - 3.99: 23349 3.99 - 4.60: 32273 Nonbonded interactions: 83874 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.526 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.553 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.571 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.571 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.614 1.850 ... (remaining 83869 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' and resid 308 through 375) selection = chain 'C' selection = (chain 'D' and resid 308 through 375) selection = chain 'E' selection = (chain 'F' and resid 308 through 375) } 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: 2.360 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: 0.100 Extract box with map and model: 11.490 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.940 Find NCS groups from input model: 0.370 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:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 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 : 0.011 0.035 3297 Z= 0.715 Angle : 1.754 6.483 4410 Z= 1.171 Chirality : 0.085 0.266 495 Planarity : 0.009 0.034 561 Dihedral : 11.104 67.181 1263 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.35), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS E 330 PHE 0.051 0.020 PHE F 346 TYR 0.061 0.013 TYR E 310 ARG 0.005 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 3.1282 time to fit residues: 383.0928 Evaluate side-chains 71 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 327 ASN B 336 GLN D 307 GLN D 327 ASN D 336 GLN F 307 GLN F 327 ASN F 336 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3297 Z= 0.235 Angle : 0.630 6.028 4410 Z= 0.318 Chirality : 0.050 0.129 495 Planarity : 0.004 0.027 561 Dihedral : 6.176 15.944 435 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.81 % Allowed : 13.44 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.007 0.001 PHE D 346 TYR 0.008 0.001 TYR B 310 ARG 0.003 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 66 average time/residue: 2.9242 time to fit residues: 197.5623 Evaluate side-chains 55 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN F 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3297 Z= 0.190 Angle : 0.543 6.090 4410 Z= 0.271 Chirality : 0.051 0.137 495 Planarity : 0.003 0.023 561 Dihedral : 5.481 15.226 435 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.08 % Allowed : 14.52 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.65 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 329 PHE 0.008 0.001 PHE B 346 TYR 0.009 0.002 TYR B 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.586 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 60 average time/residue: 2.8353 time to fit residues: 174.5415 Evaluate side-chains 55 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3297 Z= 0.266 Angle : 0.535 5.895 4410 Z= 0.269 Chirality : 0.050 0.136 495 Planarity : 0.003 0.021 561 Dihedral : 5.280 14.515 435 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.81 % Allowed : 15.59 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.65 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 329 PHE 0.008 0.002 PHE B 346 TYR 0.009 0.002 TYR B 310 ARG 0.003 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.590 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 54 average time/residue: 2.7152 time to fit residues: 150.5881 Evaluate side-chains 49 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.515 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3297 Z= 0.161 Angle : 0.495 5.911 4410 Z= 0.245 Chirality : 0.051 0.133 495 Planarity : 0.003 0.019 561 Dihedral : 5.028 15.243 435 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.81 % Allowed : 15.32 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 329 PHE 0.005 0.001 PHE B 346 TYR 0.007 0.001 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.624 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 2.8318 time to fit residues: 162.6844 Evaluate side-chains 51 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.7160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3297 Z= 0.301 Angle : 0.528 5.890 4410 Z= 0.265 Chirality : 0.050 0.129 495 Planarity : 0.003 0.021 561 Dihedral : 5.032 16.098 435 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.54 % Allowed : 15.59 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.009 0.002 PHE D 346 TYR 0.011 0.002 TYR B 310 ARG 0.003 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.510 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 3.1283 time to fit residues: 166.3429 Evaluate side-chains 48 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3297 Z= 0.141 Angle : 0.475 5.817 4410 Z= 0.236 Chirality : 0.051 0.129 495 Planarity : 0.003 0.029 561 Dihedral : 4.708 15.077 435 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.54 % Allowed : 15.59 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.61 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 362 PHE 0.004 0.001 PHE B 346 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.596 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 2.9197 time to fit residues: 158.6526 Evaluate side-chains 51 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN D 307 GLN F 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3297 Z= 0.172 Angle : 0.463 5.261 4410 Z= 0.231 Chirality : 0.050 0.125 495 Planarity : 0.003 0.038 561 Dihedral : 4.488 13.950 435 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.54 % Allowed : 16.94 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 374 PHE 0.005 0.001 PHE F 346 TYR 0.007 0.001 TYR B 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.630 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 3.0625 time to fit residues: 156.8831 Evaluate side-chains 55 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN D 307 GLN F 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3297 Z= 0.220 Angle : 0.477 5.389 4410 Z= 0.238 Chirality : 0.050 0.124 495 Planarity : 0.003 0.037 561 Dihedral : 4.527 14.034 435 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.27 % Allowed : 16.94 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.60 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 374 PHE 0.007 0.001 PHE F 346 TYR 0.009 0.002 TYR B 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.634 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 3.0836 time to fit residues: 161.0920 Evaluate side-chains 50 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 0.3980 chunk 9 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN D 307 GLN F 307 GLN F 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3297 Z= 0.150 Angle : 0.461 5.279 4410 Z= 0.229 Chirality : 0.051 0.127 495 Planarity : 0.003 0.041 561 Dihedral : 4.368 13.403 435 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.27 % Allowed : 17.20 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 362 PHE 0.004 0.001 PHE B 346 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG B 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.624 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 2.8752 time to fit residues: 153.3475 Evaluate side-chains 52 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.7132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 23 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN D 307 GLN F 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.116184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107799 restraints weight = 13735.105| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.56 r_work: 0.3572 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3297 Z= 0.132 Angle : 0.443 4.943 4410 Z= 0.218 Chirality : 0.051 0.125 495 Planarity : 0.003 0.050 561 Dihedral : 4.121 12.429 435 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.27 % Allowed : 17.74 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.63 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 374 PHE 0.003 0.000 PHE F 346 TYR 0.005 0.001 TYR B 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4369.92 seconds wall clock time: 80 minutes 55.42 seconds (4855.42 seconds total)