Starting phenix.real_space_refine on Fri Dec 8 15:17:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wam_37397/12_2023/8wam_37397_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wam_37397/12_2023/8wam_37397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wam_37397/12_2023/8wam_37397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wam_37397/12_2023/8wam_37397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wam_37397/12_2023/8wam_37397_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wam_37397/12_2023/8wam_37397_updated.pdb" } resolution = 3.23 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= -0.002 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 5612 2.51 5 N 1448 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 131": "OD1" <-> "OD2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 492": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8650 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4293 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain breaks: 4 Chain: "B" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4293 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain breaks: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.27, per 1000 atoms: 0.61 Number of scatterers: 8650 At special positions: 0 Unit cell: (97.455, 77.745, 124.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 6 15.00 Mg 2 11.99 O 1528 8.00 N 1448 7.00 C 5612 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: 3.43 Conformation dependent library (CDL) restraints added in 1.7 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 4 sheets defined 58.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.906A pdb=" N ARG A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 175 through 188 Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.671A pdb=" N LYS A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 254 Processing helix chain 'A' and resid 269 through 274 removed outlier: 3.810A pdb=" N MET A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 302 removed outlier: 4.336A pdb=" N MET A 296 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 297 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 Processing helix chain 'A' and resid 338 through 356 removed outlier: 4.228A pdb=" N ALA A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Proline residue: A 351 - end of helix Processing helix chain 'A' and resid 380 through 402 Processing helix chain 'A' and resid 408 through 424 removed outlier: 3.760A pdb=" N ALA A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 457 removed outlier: 3.790A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.671A pdb=" N VAL A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 472 removed outlier: 4.715A pdb=" N ALA A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 506 removed outlier: 3.591A pdb=" N LEU A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix removed outlier: 3.553A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 540 Processing helix chain 'A' and resid 546 through 562 removed outlier: 3.802A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 575 through 578 Processing helix chain 'A' and resid 581 through 594 Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.544A pdb=" N LEU A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 604' Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 635 through 659 removed outlier: 3.590A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 114 Processing helix chain 'B' and resid 136 through 141 removed outlier: 3.805A pdb=" N ARG B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 175 through 188 Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.724A pdb=" N LYS B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 254 Processing helix chain 'B' and resid 269 through 274 removed outlier: 3.854A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 302 removed outlier: 3.619A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 320 Processing helix chain 'B' and resid 338 through 357 removed outlier: 4.391A pdb=" N ALA B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) Proline residue: B 351 - end of helix Processing helix chain 'B' and resid 380 through 403 removed outlier: 4.444A pdb=" N HIS B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 424 removed outlier: 3.670A pdb=" N ALA B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 454 removed outlier: 3.754A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 458 through 472 removed outlier: 3.854A pdb=" N GLU B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 467 " --> pdb=" O ARG B 463 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 506 removed outlier: 3.569A pdb=" N LEU B 489 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N VAL B 494 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix removed outlier: 3.592A pdb=" N PHE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 540 Processing helix chain 'B' and resid 546 through 562 Processing helix chain 'B' and resid 575 through 578 Processing helix chain 'B' and resid 581 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.619A pdb=" N LEU B 604 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 635 through 659 removed outlier: 3.614A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 89 through 91 Processing sheet with id= B, first strand: chain 'A' and resid 277 through 281 removed outlier: 3.607A pdb=" N VAL A 260 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 89 through 91 Processing sheet with id= D, first strand: chain 'B' and resid 286 through 291 removed outlier: 6.517A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 260 " --> pdb=" O GLU B 95 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1275 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: 2.45 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2689 1.34 - 1.46: 1657 1.46 - 1.58: 4386 1.58 - 1.69: 10 1.69 - 1.81: 88 Bond restraints: 8830 Sorted by residual: bond pdb=" CA PHE A 646 " pdb=" C PHE A 646 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.30e-02 5.92e+03 1.13e+00 bond pdb=" CA PHE A 647 " pdb=" C PHE A 647 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.27e-02 6.20e+03 8.79e-01 bond pdb=" C GLU B 599 " pdb=" O GLU B 599 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.26e-02 6.30e+03 7.70e-01 bond pdb=" C ILE B 383 " pdb=" O ILE B 383 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.13e-02 7.83e+03 6.73e-01 bond pdb=" CE1 PHE A 646 " pdb=" CZ PHE A 646 " ideal model delta sigma weight residual 1.382 1.404 -0.022 3.00e-02 1.11e+03 5.17e-01 ... (remaining 8825 not shown) Histogram of bond angle deviations from ideal: 99.16 - 107.30: 276 107.30 - 115.45: 5449 115.45 - 123.60: 6038 123.60 - 131.75: 197 131.75 - 139.90: 20 Bond angle restraints: 11980 Sorted by residual: angle pdb=" CA GLU B 492 " pdb=" CB GLU B 492 " pdb=" CG GLU B 492 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C VAL B 43 " pdb=" N ASP B 44 " pdb=" CA ASP B 44 " ideal model delta sigma weight residual 122.46 125.78 -3.32 1.41e+00 5.03e-01 5.56e+00 angle pdb=" C VAL A 43 " pdb=" N ASP A 44 " pdb=" CA ASP A 44 " ideal model delta sigma weight residual 122.46 125.72 -3.26 1.41e+00 5.03e-01 5.35e+00 angle pdb=" N PHE A 647 " pdb=" CA PHE A 647 " pdb=" C PHE A 647 " ideal model delta sigma weight residual 111.07 112.96 -1.89 1.07e+00 8.73e-01 3.12e+00 angle pdb=" C PHE A 646 " pdb=" CA PHE A 646 " pdb=" CB PHE A 646 " ideal model delta sigma weight residual 110.79 113.68 -2.89 1.66e+00 3.63e-01 3.04e+00 ... (remaining 11975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4369 17.92 - 35.84: 637 35.84 - 53.77: 186 53.77 - 71.69: 25 71.69 - 89.61: 7 Dihedral angle restraints: 5224 sinusoidal: 2072 harmonic: 3152 Sorted by residual: dihedral pdb=" CA TRP B 447 " pdb=" C TRP B 447 " pdb=" N GLY B 448 " pdb=" CA GLY B 448 " ideal model delta harmonic sigma weight residual 180.00 163.29 16.71 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CG ARG A 171 " pdb=" CD ARG A 171 " pdb=" NE ARG A 171 " pdb=" CZ ARG A 171 " ideal model delta sinusoidal sigma weight residual 180.00 135.33 44.67 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA ASP A 44 " pdb=" CB ASP A 44 " pdb=" CG ASP A 44 " pdb=" OD1 ASP A 44 " ideal model delta sinusoidal sigma weight residual -30.00 -85.64 55.64 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 5221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 898 0.026 - 0.052: 303 0.052 - 0.078: 145 0.078 - 0.104: 56 0.104 - 0.130: 18 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA ILE B 129 " pdb=" N ILE B 129 " pdb=" C ILE B 129 " pdb=" CB ILE B 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE A 129 " pdb=" N ILE A 129 " pdb=" C ILE A 129 " pdb=" CB ILE A 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA VAL A 261 " pdb=" N VAL A 261 " pdb=" C VAL A 261 " pdb=" CB VAL A 261 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1417 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 646 " 0.014 2.00e-02 2.50e+03 1.53e-02 4.08e+00 pdb=" CG PHE A 646 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE A 646 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 646 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 646 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 646 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 646 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 492 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C GLU B 492 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU B 492 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 493 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 305 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO A 306 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 306 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 306 " -0.026 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 902 2.75 - 3.29: 8191 3.29 - 3.82: 14319 3.82 - 4.36: 15316 4.36 - 4.90: 27952 Nonbonded interactions: 66680 Sorted by model distance: nonbonded pdb=" OG SER A 108 " pdb=" OD2 ASP A 231 " model vdw 2.211 2.440 nonbonded pdb=" O GLU B 599 " pdb=" NE ARG B 602 " model vdw 2.232 2.520 nonbonded pdb=" O SER B 596 " pdb=" OG SER B 596 " model vdw 2.395 2.440 nonbonded pdb=" OG1 THR A 240 " pdb=" OD1 ASN B 321 " model vdw 2.400 2.440 nonbonded pdb=" O SER B 548 " pdb=" OG1 THR B 552 " model vdw 2.405 2.440 ... (remaining 66675 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' } 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.920 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.910 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 : 0.002 0.022 8830 Z= 0.115 Angle : 0.450 6.377 11980 Z= 0.230 Chirality : 0.036 0.130 1420 Planarity : 0.003 0.047 1460 Dihedral : 17.901 89.612 3200 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.11 % Allowed : 27.09 % Favored : 72.81 % 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: 1.70 (0.26), residues: 1082 helix: 2.22 (0.21), residues: 638 sheet: 1.47 (0.62), residues: 80 loop : -1.00 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 505 HIS 0.002 0.000 HIS B 219 PHE 0.021 0.001 PHE A 647 TYR 0.004 0.001 TYR A 430 ARG 0.006 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.110 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.2303 time to fit residues: 35.0307 Evaluate side-chains 110 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0973 time to fit residues: 1.4351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.0050 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 0.0040 overall best weight: 1.0012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN B 147 GLN B 484 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8830 Z= 0.195 Angle : 0.488 5.972 11980 Z= 0.244 Chirality : 0.039 0.139 1420 Planarity : 0.003 0.040 1460 Dihedral : 9.459 88.105 1262 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.03 % Allowed : 26.98 % Favored : 70.99 % 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: 1.55 (0.26), residues: 1082 helix: 1.90 (0.21), residues: 658 sheet: 1.41 (0.60), residues: 80 loop : -0.80 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.003 0.001 HIS B 154 PHE 0.014 0.001 PHE A 499 TYR 0.013 0.001 TYR B 594 ARG 0.004 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.017 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 133 average time/residue: 0.2399 time to fit residues: 43.0378 Evaluate side-chains 118 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0948 time to fit residues: 2.7395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8830 Z= 0.331 Angle : 0.600 7.062 11980 Z= 0.299 Chirality : 0.043 0.221 1420 Planarity : 0.004 0.038 1460 Dihedral : 9.357 87.616 1262 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.32 % Allowed : 25.05 % Favored : 71.63 % 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: 0.96 (0.26), residues: 1082 helix: 1.38 (0.20), residues: 654 sheet: 0.88 (0.58), residues: 82 loop : -0.82 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 575 HIS 0.006 0.001 HIS B 265 PHE 0.019 0.002 PHE A 499 TYR 0.023 0.002 TYR B 594 ARG 0.004 0.001 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 0.889 Fit side-chains outliers start: 31 outliers final: 18 residues processed: 146 average time/residue: 0.2614 time to fit residues: 49.8755 Evaluate side-chains 134 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1354 time to fit residues: 5.5289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 52 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN A 484 HIS B 196 ASN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8830 Z= 0.159 Angle : 0.480 6.306 11980 Z= 0.243 Chirality : 0.038 0.160 1420 Planarity : 0.003 0.036 1460 Dihedral : 8.907 83.986 1262 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.71 % Allowed : 26.34 % Favored : 71.95 % 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: 1.28 (0.26), residues: 1082 helix: 1.69 (0.21), residues: 654 sheet: 0.95 (0.57), residues: 82 loop : -0.80 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 505 HIS 0.004 0.001 HIS A 484 PHE 0.010 0.001 PHE A 441 TYR 0.011 0.001 TYR B 594 ARG 0.005 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.968 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 136 average time/residue: 0.2670 time to fit residues: 47.1997 Evaluate side-chains 123 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1307 time to fit residues: 2.3959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS B 119 HIS ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 8830 Z= 0.509 Angle : 0.703 7.594 11980 Z= 0.356 Chirality : 0.048 0.226 1420 Planarity : 0.005 0.059 1460 Dihedral : 9.345 85.435 1262 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.25 % Allowed : 27.52 % Favored : 70.24 % 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: 0.46 (0.25), residues: 1082 helix: 0.99 (0.20), residues: 646 sheet: 0.40 (0.56), residues: 82 loop : -0.90 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 447 HIS 0.015 0.002 HIS A 265 PHE 0.028 0.003 PHE A 275 TYR 0.028 0.003 TYR B 594 ARG 0.010 0.001 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.936 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 133 average time/residue: 0.3008 time to fit residues: 51.8762 Evaluate side-chains 125 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1086 time to fit residues: 3.3880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 454 ASN B 196 ASN B 219 HIS ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8830 Z= 0.183 Angle : 0.524 6.209 11980 Z= 0.264 Chirality : 0.039 0.139 1420 Planarity : 0.003 0.037 1460 Dihedral : 9.003 83.997 1262 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.28 % Allowed : 28.69 % Favored : 70.02 % 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: 0.90 (0.26), residues: 1082 helix: 1.44 (0.20), residues: 646 sheet: 0.51 (0.56), residues: 82 loop : -0.93 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 505 HIS 0.003 0.001 HIS A 265 PHE 0.013 0.001 PHE A 441 TYR 0.012 0.001 TYR B 594 ARG 0.007 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.001 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 129 average time/residue: 0.2660 time to fit residues: 44.9078 Evaluate side-chains 124 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0860 time to fit residues: 2.4878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.0970 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8830 Z= 0.183 Angle : 0.504 5.862 11980 Z= 0.254 Chirality : 0.039 0.149 1420 Planarity : 0.003 0.038 1460 Dihedral : 8.805 81.351 1262 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.75 % Allowed : 28.59 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1082 helix: 1.57 (0.21), residues: 648 sheet: 0.61 (0.56), residues: 82 loop : -0.94 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 505 HIS 0.002 0.001 HIS B 427 PHE 0.012 0.001 PHE A 275 TYR 0.012 0.001 TYR B 594 ARG 0.008 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 0.991 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 126 average time/residue: 0.2935 time to fit residues: 47.7610 Evaluate side-chains 122 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0828 time to fit residues: 1.8312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 232 GLN A 454 ASN B 196 ASN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8830 Z= 0.214 Angle : 0.537 9.408 11980 Z= 0.268 Chirality : 0.039 0.140 1420 Planarity : 0.003 0.039 1460 Dihedral : 8.801 81.256 1262 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.86 % Allowed : 28.59 % Favored : 70.56 % 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: 0.97 (0.26), residues: 1082 helix: 1.52 (0.20), residues: 648 sheet: 0.58 (0.56), residues: 82 loop : -0.96 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 505 HIS 0.003 0.001 HIS A 265 PHE 0.015 0.001 PHE A 275 TYR 0.013 0.001 TYR B 594 ARG 0.008 0.001 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 1.002 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 124 average time/residue: 0.2639 time to fit residues: 43.0776 Evaluate side-chains 120 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1686 time to fit residues: 1.9679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 265 HIS ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8830 Z= 0.238 Angle : 0.552 8.244 11980 Z= 0.275 Chirality : 0.040 0.150 1420 Planarity : 0.004 0.039 1460 Dihedral : 8.899 81.177 1262 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.64 % Allowed : 29.34 % Favored : 70.02 % 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: 0.91 (0.26), residues: 1082 helix: 1.47 (0.20), residues: 648 sheet: 0.54 (0.56), residues: 82 loop : -0.99 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 505 HIS 0.003 0.001 HIS B 427 PHE 0.016 0.001 PHE A 275 TYR 0.014 0.001 TYR B 594 ARG 0.012 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 0.934 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 122 average time/residue: 0.2757 time to fit residues: 44.0552 Evaluate side-chains 121 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0787 time to fit residues: 1.3705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 265 HIS A 454 ASN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8830 Z= 0.158 Angle : 0.514 8.468 11980 Z= 0.256 Chirality : 0.038 0.135 1420 Planarity : 0.004 0.048 1460 Dihedral : 8.737 80.839 1262 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.11 % Allowed : 29.55 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1082 helix: 1.74 (0.21), residues: 640 sheet: 0.66 (0.57), residues: 82 loop : -1.03 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 505 HIS 0.002 0.001 HIS B 219 PHE 0.012 0.001 PHE A 275 TYR 0.010 0.001 TYR B 594 ARG 0.012 0.001 ARG A 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.941 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.2773 time to fit residues: 43.8336 Evaluate side-chains 116 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0781 time to fit residues: 1.3984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 0.1980 chunk 24 optimal weight: 0.0770 chunk 87 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.185193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147154 restraints weight = 10776.197| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.47 r_work: 0.3571 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8830 Z= 0.211 Angle : 0.540 8.275 11980 Z= 0.268 Chirality : 0.039 0.153 1420 Planarity : 0.004 0.046 1460 Dihedral : 8.737 80.985 1262 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.21 % Allowed : 29.76 % Favored : 70.02 % 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: 1.06 (0.26), residues: 1082 helix: 1.62 (0.20), residues: 646 sheet: 0.65 (0.57), residues: 82 loop : -1.01 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 505 HIS 0.003 0.001 HIS B 219 PHE 0.015 0.001 PHE A 275 TYR 0.012 0.001 TYR B 594 ARG 0.012 0.001 ARG B 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1917.04 seconds wall clock time: 35 minutes 35.10 seconds (2135.10 seconds total)