Starting phenix.real_space_refine on Wed Feb 14 13:20:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zay_14582/02_2024/7zay_14582_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zay_14582/02_2024/7zay_14582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zay_14582/02_2024/7zay_14582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zay_14582/02_2024/7zay_14582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zay_14582/02_2024/7zay_14582_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zay_14582/02_2024/7zay_14582_updated.pdb" } resolution = 2.8 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 P 2 5.49 5 S 46 5.16 5 C 6010 2.51 5 N 1571 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9339 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4573 Classifications: {'peptide': 566} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 539} Chain breaks: 4 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4688 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.29, per 1000 atoms: 0.57 Number of scatterers: 9339 At special positions: 0 Unit cell: (97.44, 102.48, 102.48, 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 46 16.00 P 2 15.00 O 1710 8.00 N 1571 7.00 C 6010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.04 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.04 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 800 " - " ASN A 330 " " NAG C 1 " - " ASN B 637 " Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.6 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 13 sheets defined 30.5% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 313 through 319 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 383 through 395 removed outlier: 3.765A pdb=" N LEU A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU A 387 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Proline residue: A 390 - end of helix Processing helix chain 'A' and resid 398 through 415 Processing helix chain 'A' and resid 419 through 432 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 547 through 550 Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 699 through 712 Processing helix chain 'B' and resid 128 through 139 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.978A pdb=" N GLU B 239 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 275 removed outlier: 3.994A pdb=" N LYS B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.849A pdb=" N GLU B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 314' Processing helix chain 'B' and resid 330 through 336 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 370 through 379 removed outlier: 3.525A pdb=" N VAL B 373 " --> pdb=" O MET B 370 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TYR B 374 " --> pdb=" O SER B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.826A pdb=" N GLY B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 478 removed outlier: 4.242A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 523 Processing helix chain 'B' and resid 546 through 558 removed outlier: 3.589A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 removed outlier: 3.627A pdb=" N THR B 609 " --> pdb=" O TYR B 606 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR B 610 " --> pdb=" O LEU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 622 Processing helix chain 'B' and resid 627 through 639 removed outlier: 3.571A pdb=" N MET B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASN B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 684 Processing sheet with id= A, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.499A pdb=" N LEU A 153 " --> pdb=" O TYR A 117 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 191 through 194 removed outlier: 6.854A pdb=" N MET A 215 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASN A 194 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA A 217 " --> pdb=" O ASN A 194 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL A 232 " --> pdb=" O LYS A 218 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 264 through 267 Processing sheet with id= D, first strand: chain 'A' and resid 333 through 337 removed outlier: 5.812A pdb=" N VAL A 356 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 336 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 358 " --> pdb=" O VAL A 336 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 625 through 627 removed outlier: 7.232A pdb=" N ALA A 482 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE A 513 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE A 484 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 596 through 600 Processing sheet with id= G, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.542A pdb=" N LEU B 152 " --> pdb=" O TYR B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 187 through 190 removed outlier: 6.757A pdb=" N LEU B 211 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASN B 190 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 213 " --> pdb=" O ASN B 190 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 255 through 257 removed outlier: 6.179A pdb=" N LEU B 281 " --> pdb=" O SER B 256 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 298 through 300 Processing sheet with id= K, first strand: chain 'B' and resid 317 through 320 removed outlier: 6.200A pdb=" N VAL B 340 " --> pdb=" O CYS B 318 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 320 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL B 342 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 511 through 513 removed outlier: 8.801A pdb=" N VAL B 512 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 487 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LEU B 486 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 458 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL B 488 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 460 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 533 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE B 459 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 535 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU B 461 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE B 537 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 570 through 574 removed outlier: 3.589A pdb=" N LEU B 572 " --> pdb=" O LYS B 581 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 576 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: 2.50 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2958 1.34 - 1.46: 2340 1.46 - 1.58: 4214 1.58 - 1.70: 2 1.70 - 1.82: 71 Bond restraints: 9585 Sorted by residual: bond pdb=" O1A UDP A 801 " pdb=" PA UDP A 801 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.96e+01 bond pdb=" O2A UDP A 801 " pdb=" PA UDP A 801 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.80e-02 3.09e+03 6.21e+00 bond pdb=" C1 NAG A 800 " pdb=" O5 NAG A 800 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.79e+00 ... (remaining 9580 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.89: 345 106.89 - 113.67: 5149 113.67 - 120.44: 3618 120.44 - 127.22: 3793 127.22 - 133.99: 124 Bond angle restraints: 13029 Sorted by residual: angle pdb=" C GLY B 260 " pdb=" N LEU B 261 " pdb=" CA LEU B 261 " ideal model delta sigma weight residual 121.54 132.03 -10.49 1.91e+00 2.74e-01 3.02e+01 angle pdb=" O5' UDP A 801 " pdb=" PA UDP A 801 " pdb=" O1A UDP A 801 " ideal model delta sigma weight residual 106.70 111.08 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" O2A UDP A 801 " pdb=" PA UDP A 801 " pdb=" O3A UDP A 801 " ideal model delta sigma weight residual 105.97 110.23 -4.26 1.00e+00 1.00e+00 1.81e+01 angle pdb=" N LEU B 261 " pdb=" CA LEU B 261 " pdb=" CB LEU B 261 " ideal model delta sigma weight residual 110.49 117.47 -6.98 1.69e+00 3.50e-01 1.70e+01 angle pdb=" CA LEU B 261 " pdb=" CB LEU B 261 " pdb=" CG LEU B 261 " ideal model delta sigma weight residual 116.30 130.73 -14.43 3.50e+00 8.16e-02 1.70e+01 ... (remaining 13024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 5486 21.82 - 43.64: 256 43.64 - 65.46: 37 65.46 - 87.28: 12 87.28 - 109.10: 6 Dihedral angle restraints: 5797 sinusoidal: 2410 harmonic: 3387 Sorted by residual: dihedral pdb=" CD ARG A 723 " pdb=" NE ARG A 723 " pdb=" CZ ARG A 723 " pdb=" NH1 ARG A 723 " ideal model delta sinusoidal sigma weight residual 0.00 71.37 -71.37 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CA ALA B 202 " pdb=" C ALA B 202 " pdb=" N LEU B 203 " pdb=" CA LEU B 203 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.61 109.10 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 5794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1178 0.054 - 0.108: 217 0.108 - 0.161: 34 0.161 - 0.215: 3 0.215 - 0.269: 1 Chirality restraints: 1433 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA PRO B 263 " pdb=" N PRO B 263 " pdb=" C PRO B 263 " pdb=" CB PRO B 263 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB ILE B 344 " pdb=" CA ILE B 344 " pdb=" CG1 ILE B 344 " pdb=" CG2 ILE B 344 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 1430 not shown) Planarity restraints: 1652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 723 " 0.882 9.50e-02 1.11e+02 3.97e-01 1.07e+02 pdb=" NE ARG A 723 " -0.075 2.00e-02 2.50e+03 pdb=" CZ ARG A 723 " 0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG A 723 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 723 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 562 " -0.225 9.50e-02 1.11e+02 1.02e-01 8.22e+00 pdb=" NE ARG B 562 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 562 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG B 562 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 562 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 196 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO B 197 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 197 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 197 " 0.025 5.00e-02 4.00e+02 ... (remaining 1649 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 874 2.74 - 3.28: 9574 3.28 - 3.82: 15911 3.82 - 4.36: 19950 4.36 - 4.90: 32664 Nonbonded interactions: 78973 Sorted by model distance: nonbonded pdb=" O ILE B 376 " pdb=" OG SER B 379 " model vdw 2.203 2.440 nonbonded pdb=" OH TYR A 271 " pdb=" O3B UDP A 801 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR A 223 " pdb=" NE2 HIS B 88 " model vdw 2.238 2.520 nonbonded pdb=" O PRO B 560 " pdb=" ND1 HIS B 601 " model vdw 2.253 2.520 nonbonded pdb=" OH TYR A 626 " pdb=" NE2 HIS A 631 " model vdw 2.261 2.520 ... (remaining 78968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.000 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.450 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 : 0.003 0.045 9585 Z= 0.163 Angle : 0.611 14.426 13029 Z= 0.310 Chirality : 0.044 0.269 1433 Planarity : 0.011 0.397 1650 Dihedral : 13.247 109.101 3579 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.82 % Favored : 92.01 % Rotamer: Outliers : 1.09 % Allowed : 7.42 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.32 (0.25), residues: 1126 helix: 0.29 (0.29), residues: 354 sheet: -2.14 (0.49), residues: 105 loop : -1.33 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 711 HIS 0.010 0.001 HIS B 694 PHE 0.009 0.001 PHE B 400 TYR 0.009 0.001 TYR A 608 ARG 0.060 0.001 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 258 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7245 (m-80) cc_final: 0.7040 (m-80) REVERT: A 420 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7468 (tm-30) REVERT: A 478 SER cc_start: 0.7735 (p) cc_final: 0.7275 (t) REVERT: A 670 ILE cc_start: 0.8002 (mm) cc_final: 0.7766 (mm) REVERT: B 388 MET cc_start: 0.7140 (mtp) cc_final: 0.6859 (mtp) REVERT: B 484 LYS cc_start: 0.4508 (OUTLIER) cc_final: 0.4284 (ttmm) REVERT: B 695 ARG cc_start: 0.7137 (ptt-90) cc_final: 0.6737 (ptt-90) outliers start: 11 outliers final: 1 residues processed: 264 average time/residue: 1.0978 time to fit residues: 312.2578 Evaluate side-chains 195 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 193 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 484 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 471 ASN A 636 HIS B 162 GLN B 200 ASN B 262 HIS B 412 GLN B 454 GLN B 550 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9585 Z= 0.233 Angle : 0.649 12.704 13029 Z= 0.319 Chirality : 0.045 0.220 1433 Planarity : 0.005 0.053 1650 Dihedral : 9.124 85.314 1379 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Rotamer: Outliers : 3.86 % Allowed : 15.03 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.20 (0.25), residues: 1126 helix: 0.24 (0.28), residues: 360 sheet: -1.79 (0.51), residues: 98 loop : -1.24 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 711 HIS 0.006 0.001 HIS B 694 PHE 0.017 0.002 PHE A 577 TYR 0.012 0.001 TYR A 592 ARG 0.007 0.001 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.6756 (mpp-170) cc_final: 0.6530 (mpp-170) REVERT: A 262 TYR cc_start: 0.7367 (m-80) cc_final: 0.7141 (m-80) REVERT: A 478 SER cc_start: 0.7734 (p) cc_final: 0.7282 (t) REVERT: A 674 GLN cc_start: 0.7547 (pm20) cc_final: 0.7224 (pt0) REVERT: B 310 GLN cc_start: 0.7641 (tm-30) cc_final: 0.6786 (tm-30) REVERT: B 388 MET cc_start: 0.7176 (mtp) cc_final: 0.6927 (mtp) REVERT: B 624 MET cc_start: 0.7242 (mmm) cc_final: 0.6985 (mmt) REVERT: B 695 ARG cc_start: 0.7053 (ptt-90) cc_final: 0.6788 (ptt-90) outliers start: 39 outliers final: 21 residues processed: 217 average time/residue: 0.9081 time to fit residues: 214.7842 Evaluate side-chains 195 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 539 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 0.0570 chunk 83 optimal weight: 1.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN B 200 ASN B 389 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 9585 Z= 0.326 Angle : 0.677 11.093 13029 Z= 0.338 Chirality : 0.047 0.267 1433 Planarity : 0.005 0.044 1650 Dihedral : 8.628 86.676 1375 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.82 % Favored : 92.10 % Rotamer: Outliers : 4.35 % Allowed : 16.91 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.40 (0.25), residues: 1126 helix: -0.12 (0.27), residues: 368 sheet: -1.64 (0.53), residues: 93 loop : -1.30 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 394 HIS 0.003 0.001 HIS A 329 PHE 0.017 0.002 PHE B 604 TYR 0.022 0.002 TYR B 107 ARG 0.007 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 179 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.6898 (mpp-170) cc_final: 0.6441 (mpp-170) REVERT: A 478 SER cc_start: 0.7779 (p) cc_final: 0.7315 (t) REVERT: B 80 ARG cc_start: 0.7060 (ttm110) cc_final: 0.6761 (tpp-160) REVERT: B 310 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7397 (tm-30) REVERT: B 388 MET cc_start: 0.7163 (mtp) cc_final: 0.6914 (mtp) REVERT: B 485 LEU cc_start: 0.5561 (OUTLIER) cc_final: 0.5354 (tp) REVERT: B 624 MET cc_start: 0.7314 (mmm) cc_final: 0.7044 (mmm) REVERT: B 695 ARG cc_start: 0.7175 (ptt-90) cc_final: 0.6886 (ptt-90) outliers start: 44 outliers final: 23 residues processed: 210 average time/residue: 0.9892 time to fit residues: 225.6467 Evaluate side-chains 189 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9585 Z= 0.213 Angle : 0.627 10.748 13029 Z= 0.307 Chirality : 0.045 0.353 1433 Planarity : 0.004 0.044 1650 Dihedral : 8.026 85.408 1375 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.75 % Favored : 93.07 % Rotamer: Outliers : 4.06 % Allowed : 18.30 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.19 (0.25), residues: 1126 helix: 0.07 (0.28), residues: 367 sheet: -1.53 (0.52), residues: 103 loop : -1.16 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 394 HIS 0.004 0.001 HIS A 285 PHE 0.032 0.002 PHE A 577 TYR 0.016 0.001 TYR A 467 ARG 0.008 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 177 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 SER cc_start: 0.7671 (p) cc_final: 0.7216 (t) REVERT: A 674 GLN cc_start: 0.7548 (pm20) cc_final: 0.7163 (pt0) REVERT: B 80 ARG cc_start: 0.7026 (ttm110) cc_final: 0.6721 (tpp-160) REVERT: B 310 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7380 (tm-30) REVERT: B 388 MET cc_start: 0.7176 (mtp) cc_final: 0.6876 (mtp) REVERT: B 695 ARG cc_start: 0.7075 (ptt-90) cc_final: 0.6814 (ptt-90) outliers start: 41 outliers final: 22 residues processed: 202 average time/residue: 0.9587 time to fit residues: 211.6041 Evaluate side-chains 189 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.0170 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN B 389 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 9585 Z= 0.346 Angle : 0.679 10.181 13029 Z= 0.341 Chirality : 0.047 0.271 1433 Planarity : 0.005 0.042 1650 Dihedral : 8.297 87.558 1375 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.55 % Favored : 92.27 % Rotamer: Outliers : 4.85 % Allowed : 18.69 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.41 (0.25), residues: 1126 helix: -0.29 (0.27), residues: 370 sheet: -1.54 (0.51), residues: 105 loop : -1.21 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 394 HIS 0.003 0.001 HIS A 285 PHE 0.043 0.002 PHE A 577 TYR 0.022 0.002 TYR A 467 ARG 0.008 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 177 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 SER cc_start: 0.7870 (p) cc_final: 0.7405 (t) REVERT: B 80 ARG cc_start: 0.7091 (ttm110) cc_final: 0.6796 (tpp-160) REVERT: B 310 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7532 (tm-30) REVERT: B 388 MET cc_start: 0.7189 (mtp) cc_final: 0.6937 (mtp) REVERT: B 589 GLU cc_start: 0.7426 (mp0) cc_final: 0.7208 (mp0) REVERT: B 624 MET cc_start: 0.7350 (mmm) cc_final: 0.7062 (mmt) REVERT: B 695 ARG cc_start: 0.7192 (ptt-90) cc_final: 0.6926 (ptt-90) outliers start: 49 outliers final: 31 residues processed: 210 average time/residue: 0.9618 time to fit residues: 219.7335 Evaluate side-chains 199 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 168 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.0060 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN B 412 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9585 Z= 0.170 Angle : 0.622 11.692 13029 Z= 0.304 Chirality : 0.045 0.370 1433 Planarity : 0.004 0.043 1650 Dihedral : 7.717 83.446 1375 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.39 % Favored : 93.43 % Rotamer: Outliers : 3.96 % Allowed : 20.38 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -0.94 (0.25), residues: 1126 helix: 0.22 (0.28), residues: 362 sheet: -1.34 (0.53), residues: 103 loop : -0.97 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 200 HIS 0.005 0.001 HIS A 285 PHE 0.026 0.001 PHE A 577 TYR 0.017 0.001 TYR A 467 ARG 0.009 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 SER cc_start: 0.7728 (p) cc_final: 0.7250 (t) REVERT: A 577 PHE cc_start: 0.7050 (t80) cc_final: 0.6727 (t80) REVERT: B 80 ARG cc_start: 0.7012 (ttm110) cc_final: 0.6695 (tpp-160) REVERT: B 310 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7650 (tm-30) REVERT: B 388 MET cc_start: 0.7184 (mtp) cc_final: 0.6888 (mtp) REVERT: B 624 MET cc_start: 0.7323 (mmm) cc_final: 0.7060 (mmm) REVERT: B 695 ARG cc_start: 0.7038 (ptt-90) cc_final: 0.6808 (ptt-90) outliers start: 40 outliers final: 24 residues processed: 208 average time/residue: 0.9219 time to fit residues: 209.5328 Evaluate side-chains 192 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 389 GLN B 412 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9585 Z= 0.225 Angle : 0.641 11.420 13029 Z= 0.316 Chirality : 0.045 0.341 1433 Planarity : 0.004 0.041 1650 Dihedral : 7.736 84.651 1375 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.48 % Favored : 93.25 % Rotamer: Outliers : 3.96 % Allowed : 21.56 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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 (0.25), residues: 1126 helix: 0.09 (0.28), residues: 370 sheet: -1.44 (0.53), residues: 104 loop : -0.98 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 200 HIS 0.004 0.001 HIS A 285 PHE 0.026 0.002 PHE A 577 TYR 0.027 0.001 TYR A 467 ARG 0.007 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 175 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 SER cc_start: 0.7729 (p) cc_final: 0.7250 (t) REVERT: B 80 ARG cc_start: 0.7048 (ttm110) cc_final: 0.6720 (tpp-160) REVERT: B 87 MET cc_start: 0.6344 (mmm) cc_final: 0.5683 (mmm) REVERT: B 310 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7737 (tm-30) REVERT: B 388 MET cc_start: 0.7247 (mtp) cc_final: 0.6963 (mtp) REVERT: B 624 MET cc_start: 0.7314 (mmm) cc_final: 0.7052 (mmm) REVERT: B 695 ARG cc_start: 0.7087 (ptt-90) cc_final: 0.6858 (ptt-90) outliers start: 40 outliers final: 28 residues processed: 201 average time/residue: 0.8575 time to fit residues: 188.9312 Evaluate side-chains 192 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 176 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 9585 Z= 0.348 Angle : 0.716 10.602 13029 Z= 0.355 Chirality : 0.048 0.346 1433 Planarity : 0.005 0.041 1650 Dihedral : 8.148 86.141 1375 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.93 % Favored : 92.72 % Rotamer: Outliers : 4.65 % Allowed : 21.07 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.33 (0.25), residues: 1126 helix: -0.25 (0.27), residues: 370 sheet: -1.54 (0.52), residues: 103 loop : -1.12 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 200 HIS 0.003 0.001 HIS A 285 PHE 0.035 0.002 PHE A 577 TYR 0.037 0.002 TYR A 467 ARG 0.007 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 166 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 SER cc_start: 0.7862 (p) cc_final: 0.7394 (t) REVERT: B 80 ARG cc_start: 0.7071 (ttm110) cc_final: 0.6756 (tpp-160) REVERT: B 276 HIS cc_start: 0.5144 (OUTLIER) cc_final: 0.4689 (p90) REVERT: B 310 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B 388 MET cc_start: 0.7189 (mtp) cc_final: 0.6944 (mtp) REVERT: B 624 MET cc_start: 0.7402 (mmm) cc_final: 0.7144 (mmm) outliers start: 47 outliers final: 31 residues processed: 196 average time/residue: 0.8888 time to fit residues: 190.8645 Evaluate side-chains 192 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 686 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 176 GLN B 251 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9585 Z= 0.214 Angle : 0.671 9.346 13029 Z= 0.328 Chirality : 0.045 0.312 1433 Planarity : 0.004 0.040 1650 Dihedral : 7.843 83.597 1375 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.13 % Favored : 93.52 % Rotamer: Outliers : 3.86 % Allowed : 21.66 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.04 (0.25), residues: 1126 helix: 0.03 (0.28), residues: 362 sheet: -1.52 (0.53), residues: 104 loop : -0.93 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 200 HIS 0.004 0.001 HIS A 285 PHE 0.035 0.002 PHE A 577 TYR 0.029 0.001 TYR A 467 ARG 0.008 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 171 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 TYR cc_start: 0.7899 (m-10) cc_final: 0.7649 (m-10) REVERT: A 478 SER cc_start: 0.7845 (p) cc_final: 0.7352 (t) REVERT: A 577 PHE cc_start: 0.6634 (t80) cc_final: 0.6165 (t80) REVERT: B 80 ARG cc_start: 0.7054 (ttm110) cc_final: 0.6726 (tpp-160) REVERT: B 276 HIS cc_start: 0.5054 (OUTLIER) cc_final: 0.4580 (p90) REVERT: B 310 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7727 (tm-30) REVERT: B 388 MET cc_start: 0.7185 (mtp) cc_final: 0.6910 (mtt) REVERT: B 624 MET cc_start: 0.7415 (mmm) cc_final: 0.7168 (mmm) REVERT: B 695 ARG cc_start: 0.7130 (ptt-90) cc_final: 0.6905 (ptt-90) outliers start: 39 outliers final: 23 residues processed: 200 average time/residue: 0.9376 time to fit residues: 204.4967 Evaluate side-chains 192 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 0.0570 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.0570 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 176 GLN B 389 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9585 Z= 0.255 Angle : 0.696 10.071 13029 Z= 0.341 Chirality : 0.047 0.315 1433 Planarity : 0.004 0.040 1650 Dihedral : 7.859 82.454 1375 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.48 % Favored : 93.25 % Rotamer: Outliers : 3.46 % Allowed : 22.75 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.11 (0.25), residues: 1126 helix: -0.10 (0.27), residues: 370 sheet: -1.54 (0.52), residues: 104 loop : -0.95 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 200 HIS 0.004 0.001 HIS B 262 PHE 0.043 0.002 PHE A 577 TYR 0.032 0.002 TYR A 467 ARG 0.007 0.000 ARG A 394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 SER cc_start: 0.7858 (p) cc_final: 0.7386 (t) REVERT: A 577 PHE cc_start: 0.6669 (t80) cc_final: 0.6294 (t80) REVERT: A 698 PHE cc_start: 0.5262 (t80) cc_final: 0.4748 (t80) REVERT: B 80 ARG cc_start: 0.7067 (ttm110) cc_final: 0.6737 (tpp-160) REVERT: B 192 LEU cc_start: 0.8231 (mp) cc_final: 0.7864 (mt) REVERT: B 276 HIS cc_start: 0.5113 (OUTLIER) cc_final: 0.4646 (p90) REVERT: B 310 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7790 (tm-30) REVERT: B 388 MET cc_start: 0.7237 (mtp) cc_final: 0.6973 (mtt) REVERT: B 589 GLU cc_start: 0.7324 (mp0) cc_final: 0.7029 (mp0) REVERT: B 695 ARG cc_start: 0.7198 (ptt-90) cc_final: 0.6967 (ptt-90) outliers start: 35 outliers final: 27 residues processed: 193 average time/residue: 0.9314 time to fit residues: 196.2730 Evaluate side-chains 190 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 HIS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 686 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 431 GLN B 176 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.230272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.197310 restraints weight = 11523.931| |-----------------------------------------------------------------------------| r_work (start): 0.4516 rms_B_bonded: 2.72 r_work: 0.4396 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9585 Z= 0.278 Angle : 0.705 10.664 13029 Z= 0.349 Chirality : 0.047 0.310 1433 Planarity : 0.004 0.039 1650 Dihedral : 7.932 81.782 1375 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.48 % Favored : 93.25 % Rotamer: Outliers : 3.56 % Allowed : 22.85 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % 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: -1.13 (0.25), residues: 1126 helix: -0.11 (0.27), residues: 363 sheet: -1.59 (0.53), residues: 104 loop : -0.95 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 200 HIS 0.004 0.001 HIS A 285 PHE 0.041 0.002 PHE A 577 TYR 0.032 0.002 TYR A 467 ARG 0.006 0.000 ARG A 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3959.33 seconds wall clock time: 71 minutes 6.42 seconds (4266.42 seconds total)