Starting phenix.real_space_refine on Fri Mar 15 11:11:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t57_25697/03_2024/7t57_25697_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t57_25697/03_2024/7t57_25697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t57_25697/03_2024/7t57_25697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t57_25697/03_2024/7t57_25697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t57_25697/03_2024/7t57_25697_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t57_25697/03_2024/7t57_25697_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 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 60 5.16 5 C 7382 2.51 5 N 1870 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 143": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B GLU 585": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 706": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11460 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "D" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 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: 7.16, per 1000 atoms: 0.62 Number of scatterers: 11460 At special positions: 0 Unit cell: (106.09, 98.88, 143.17, 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 60 16.00 P 6 15.00 Mg 2 11.99 O 2140 8.00 N 1870 7.00 C 7382 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: 4.83 Conformation dependent library (CDL) restraints added in 2.4 seconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 6 sheets defined 56.6% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 154 through 195 removed outlier: 4.757A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 6.374A pdb=" N LYS A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 215 through 252 removed outlier: 3.782A pdb=" N LYS A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 264 through 280 removed outlier: 4.155A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 275 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 304 removed outlier: 4.075A pdb=" N ILE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 353 removed outlier: 4.569A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix removed outlier: 3.601A pdb=" N ALA A 342 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 364 through 417 removed outlier: 3.589A pdb=" N ASP A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 464 removed outlier: 3.512A pdb=" N ALA A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Proline residue: A 438 - end of helix removed outlier: 4.122A pdb=" N GLN A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Proline residue: A 447 - end of helix removed outlier: 4.343A pdb=" N ILE A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 471 No H-bonds generated for 'chain 'A' and resid 468 through 471' Processing helix chain 'A' and resid 526 through 532 Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 555 through 561 Processing helix chain 'A' and resid 576 through 580 Processing helix chain 'A' and resid 589 through 598 Processing helix chain 'A' and resid 602 through 605 No H-bonds generated for 'chain 'A' and resid 602 through 605' Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 625 through 639 removed outlier: 3.827A pdb=" N LYS A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 651 No H-bonds generated for 'chain 'A' and resid 649 through 651' Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 704 through 710 Processing helix chain 'A' and resid 713 through 721 Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 55 through 65 Processing helix chain 'B' and resid 125 through 131 Processing helix chain 'B' and resid 155 through 195 removed outlier: 4.856A pdb=" N GLY B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU B 162 " --> pdb=" O PHE B 158 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Proline residue: B 164 - end of helix removed outlier: 6.488A pdb=" N LYS B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N THR B 168 " --> pdb=" O PRO B 164 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 215 through 252 removed outlier: 3.842A pdb=" N LYS B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 263 through 280 removed outlier: 4.056A pdb=" N ARG B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 275 " --> pdb=" O MET B 271 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 304 removed outlier: 3.917A pdb=" N ILE B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 353 removed outlier: 4.645A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 3.872A pdb=" N LYS B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B 345 " --> pdb=" O ASN B 341 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 364 through 417 removed outlier: 3.545A pdb=" N ASP B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 459 removed outlier: 4.194A pdb=" N LEU B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA B 433 " --> pdb=" O ASN B 429 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Proline residue: B 438 - end of helix removed outlier: 4.000A pdb=" N GLN B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 468 through 471 No H-bonds generated for 'chain 'B' and resid 468 through 471' Processing helix chain 'B' and resid 526 through 533 Processing helix chain 'B' and resid 555 through 561 Processing helix chain 'B' and resid 576 through 580 Processing helix chain 'B' and resid 589 through 598 Processing helix chain 'B' and resid 604 through 607 Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 625 through 639 removed outlier: 3.931A pdb=" N LYS B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 651 No H-bonds generated for 'chain 'B' and resid 649 through 651' Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 704 through 710 Processing helix chain 'B' and resid 713 through 719 Processing helix chain 'D' and resid 15 through 20 removed outlier: 3.639A pdb=" N GLU D 20 " --> pdb=" O GLU D 16 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 67 through 72 removed outlier: 6.999A pdb=" N THR A 112 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILE A 106 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 506 through 509 Processing sheet with id= C, first strand: chain 'A' and resid 697 through 702 removed outlier: 6.759A pdb=" N LEU A 692 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER A 701 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 690 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 519 " --> pdb=" O ALA A 678 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 67 through 72 removed outlier: 7.049A pdb=" N THR B 112 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE B 106 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 506 through 509 Processing sheet with id= F, first strand: chain 'B' and resid 697 through 702 removed outlier: 6.588A pdb=" N LEU B 692 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER B 701 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE B 690 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY B 519 " --> pdb=" O ALA B 678 " (cutoff:3.500A) 619 hydrogen bonds defined for protein. 1812 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: 4.19 Time building geometry restraints manager: 5.22 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: 3592 1.34 - 1.46: 1450 1.46 - 1.57: 6482 1.57 - 1.69: 8 1.69 - 1.81: 104 Bond restraints: 11636 Sorted by residual: bond pdb=" O2B ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 1.529 1.459 0.070 2.20e-02 2.07e+03 1.01e+01 bond pdb=" N ARG A 84 " pdb=" CA ARG A 84 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.94e+00 bond pdb=" N LEU A 80 " pdb=" CA LEU A 80 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.25e-02 6.40e+03 6.72e+00 bond pdb=" N PHE A 83 " pdb=" CA PHE A 83 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.18e-02 7.18e+03 6.25e+00 bond pdb=" O2A ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 1.529 1.474 0.055 2.20e-02 2.07e+03 6.20e+00 ... (remaining 11631 not shown) Histogram of bond angle deviations from ideal: 98.99 - 107.17: 224 107.17 - 115.34: 7258 115.34 - 123.52: 8010 123.52 - 131.70: 194 131.70 - 139.87: 10 Bond angle restraints: 15696 Sorted by residual: angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 115.66 24.21 1.00e+00 1.00e+00 5.86e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 117.68 19.15 1.00e+00 1.00e+00 3.67e+02 angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 103.55 17.72 1.00e+00 1.00e+00 3.14e+02 angle pdb=" N VAL B 479 " pdb=" CA VAL B 479 " pdb=" C VAL B 479 " ideal model delta sigma weight residual 108.11 115.53 -7.42 1.40e+00 5.10e-01 2.81e+01 angle pdb=" N SER A 549 " pdb=" CA SER A 549 " pdb=" C SER A 549 " ideal model delta sigma weight residual 110.19 116.71 -6.52 1.24e+00 6.50e-01 2.77e+01 ... (remaining 15691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 6311 16.69 - 33.38: 566 33.38 - 50.06: 147 50.06 - 66.75: 31 66.75 - 83.44: 13 Dihedral angle restraints: 7068 sinusoidal: 2846 harmonic: 4222 Sorted by residual: dihedral pdb=" CA ILE B 110 " pdb=" C ILE B 110 " pdb=" N ILE B 111 " pdb=" CA ILE B 111 " ideal model delta harmonic sigma weight residual -180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ILE A 110 " pdb=" C ILE A 110 " pdb=" N ILE A 111 " pdb=" CA ILE A 111 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ASP B 94 " pdb=" CB ASP B 94 " pdb=" CG ASP B 94 " pdb=" OD1 ASP B 94 " ideal model delta sinusoidal sigma weight residual -30.00 -89.94 59.94 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 7065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1580 0.061 - 0.122: 238 0.122 - 0.182: 27 0.182 - 0.243: 6 0.243 - 0.304: 1 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CA TYR A 150 " pdb=" N TYR A 150 " pdb=" C TYR A 150 " pdb=" CB TYR A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA PHE B 478 " pdb=" N PHE B 478 " pdb=" C PHE B 478 " pdb=" CB PHE B 478 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ASN A 552 " pdb=" N ASN A 552 " pdb=" C ASN A 552 " pdb=" CB ASN A 552 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1849 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 548 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C HIS A 548 " -0.049 2.00e-02 2.50e+03 pdb=" O HIS A 548 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 549 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 550 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C ILE A 550 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE A 550 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS A 551 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 551 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C LYS A 551 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS A 551 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 552 " 0.011 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 33 2.44 - 3.06: 7574 3.06 - 3.67: 16775 3.67 - 4.29: 24134 4.29 - 4.90: 39894 Nonbonded interactions: 88410 Sorted by model distance: nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 1.826 2.170 nonbonded pdb=" O2B ATP B 801 " pdb="MG MG B 802 " model vdw 1.923 2.170 nonbonded pdb=" O1B ATP A 801 " pdb="MG MG A 802 " model vdw 2.108 2.170 nonbonded pdb=" O GLY B 282 " pdb=" OG1 THR B 286 " model vdw 2.212 2.440 nonbonded pdb=" O ASP A 476 " pdb=" OD1 ASP A 476 " model vdw 2.226 3.040 ... (remaining 88405 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' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.670 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: 6.210 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 37.100 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 0.070 11636 Z= 0.206 Angle : 0.735 24.206 15696 Z= 0.500 Chirality : 0.045 0.304 1852 Planarity : 0.003 0.029 1944 Dihedral : 14.109 83.440 4356 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.75 % Favored : 97.12 % Rotamer: Outliers : 0.72 % Allowed : 0.64 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.23), residues: 1456 helix: 1.80 (0.19), residues: 832 sheet: -0.21 (0.42), residues: 132 loop : -1.30 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 132 HIS 0.006 0.001 HIS B 99 PHE 0.011 0.001 PHE B 615 TYR 0.012 0.001 TYR A 413 ARG 0.005 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 433 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 MET cc_start: 0.8303 (mmm) cc_final: 0.8025 (tpp) REVERT: B 266 ILE cc_start: 0.8480 (mm) cc_final: 0.8122 (mm) REVERT: B 373 ASP cc_start: 0.7240 (m-30) cc_final: 0.6906 (m-30) REVERT: D 19 MET cc_start: 0.7726 (mmt) cc_final: 0.7197 (mmp) outliers start: 9 outliers final: 4 residues processed: 441 average time/residue: 0.2575 time to fit residues: 155.5018 Evaluate side-chains 268 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 264 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 471 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN B 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11636 Z= 0.236 Angle : 0.617 10.519 15696 Z= 0.318 Chirality : 0.042 0.246 1852 Planarity : 0.003 0.043 1944 Dihedral : 7.058 67.792 1626 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.05 % Allowed : 13.48 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.89 (0.22), residues: 1456 helix: 1.74 (0.18), residues: 844 sheet: -0.16 (0.39), residues: 150 loop : -1.33 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 132 HIS 0.007 0.001 HIS A 602 PHE 0.011 0.001 PHE A 535 TYR 0.020 0.001 TYR A 413 ARG 0.011 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 282 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7929 (pmm) cc_final: 0.7245 (pmm) REVERT: A 644 LEU cc_start: 0.8799 (mp) cc_final: 0.8490 (mp) REVERT: B 615 PHE cc_start: 0.7913 (t80) cc_final: 0.7603 (t80) REVERT: D 19 MET cc_start: 0.7652 (mmt) cc_final: 0.7175 (mmp) outliers start: 38 outliers final: 25 residues processed: 304 average time/residue: 0.2372 time to fit residues: 103.4021 Evaluate side-chains 268 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 243 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 0.0000 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 ASN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11636 Z= 0.164 Angle : 0.563 11.650 15696 Z= 0.288 Chirality : 0.040 0.168 1852 Planarity : 0.003 0.059 1944 Dihedral : 6.516 55.508 1625 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.73 % Allowed : 16.21 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.22), residues: 1456 helix: 1.89 (0.18), residues: 830 sheet: -0.06 (0.39), residues: 150 loop : -1.25 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 132 HIS 0.003 0.001 HIS A 249 PHE 0.008 0.001 PHE A 535 TYR 0.016 0.001 TYR A 413 ARG 0.006 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 263 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7934 (pmm) cc_final: 0.7269 (pmm) REVERT: A 644 LEU cc_start: 0.8808 (mp) cc_final: 0.8501 (mp) REVERT: B 41 LYS cc_start: 0.7870 (mtpt) cc_final: 0.7257 (mtpt) REVERT: B 125 MET cc_start: 0.6829 (tmm) cc_final: 0.6585 (tmm) REVERT: B 290 ASP cc_start: 0.7673 (m-30) cc_final: 0.7464 (m-30) REVERT: B 385 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7610 (tm-30) REVERT: B 615 PHE cc_start: 0.7810 (t80) cc_final: 0.7524 (t80) REVERT: D 19 MET cc_start: 0.7565 (mmt) cc_final: 0.6970 (mmp) outliers start: 34 outliers final: 23 residues processed: 281 average time/residue: 0.2166 time to fit residues: 86.4187 Evaluate side-chains 261 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 238 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11636 Z= 0.275 Angle : 0.612 11.390 15696 Z= 0.314 Chirality : 0.041 0.162 1852 Planarity : 0.003 0.041 1944 Dihedral : 6.173 58.690 1622 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.25 % Allowed : 18.38 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.00 (0.22), residues: 1456 helix: 1.79 (0.18), residues: 832 sheet: -0.03 (0.39), residues: 148 loop : -1.15 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 132 HIS 0.006 0.001 HIS B 249 PHE 0.012 0.002 PHE B 188 TYR 0.013 0.001 TYR B 179 ARG 0.007 0.001 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 253 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8010 (pmm) cc_final: 0.7395 (pmm) REVERT: A 224 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7646 (t0) REVERT: A 274 SER cc_start: 0.8613 (m) cc_final: 0.8373 (p) REVERT: A 647 ASP cc_start: 0.7447 (t0) cc_final: 0.6439 (t0) REVERT: A 648 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7354 (mm-30) REVERT: C 20 GLU cc_start: 0.8196 (mp0) cc_final: 0.7973 (pm20) REVERT: B 41 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7746 (mtpt) REVERT: B 64 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8047 (pp30) REVERT: B 125 MET cc_start: 0.7238 (tmm) cc_final: 0.6990 (tmm) REVERT: B 244 MET cc_start: 0.8175 (mmm) cc_final: 0.7782 (tpp) REVERT: B 250 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8902 (t) REVERT: B 286 THR cc_start: 0.8492 (m) cc_final: 0.8067 (m) REVERT: B 290 ASP cc_start: 0.7992 (m-30) cc_final: 0.7629 (m-30) REVERT: B 385 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 589 MET cc_start: 0.8418 (mmp) cc_final: 0.7916 (mmp) REVERT: D 19 MET cc_start: 0.7911 (mmt) cc_final: 0.7291 (mmp) outliers start: 53 outliers final: 36 residues processed: 284 average time/residue: 0.2169 time to fit residues: 88.9716 Evaluate side-chains 280 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 241 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 682 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 118 optimal weight: 6.9990 chunk 96 optimal weight: 0.0060 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11636 Z= 0.153 Angle : 0.563 14.318 15696 Z= 0.287 Chirality : 0.040 0.161 1852 Planarity : 0.003 0.044 1944 Dihedral : 6.023 59.022 1622 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.81 % Allowed : 21.43 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.08 (0.22), residues: 1456 helix: 1.85 (0.18), residues: 830 sheet: 0.20 (0.40), residues: 146 loop : -1.15 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.002 0.001 HIS B 249 PHE 0.009 0.001 PHE B 128 TYR 0.016 0.001 TYR B 56 ARG 0.014 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 257 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 SER cc_start: 0.8520 (m) cc_final: 0.8304 (p) REVERT: A 368 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6797 (tm-30) REVERT: A 648 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7729 (mm-30) REVERT: B 125 MET cc_start: 0.7167 (tmm) cc_final: 0.6809 (tmm) REVERT: B 194 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7120 (t80) REVERT: B 286 THR cc_start: 0.8351 (m) cc_final: 0.7873 (m) REVERT: B 290 ASP cc_start: 0.8020 (m-30) cc_final: 0.7687 (m-30) REVERT: B 385 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7613 (tm-30) REVERT: D 19 MET cc_start: 0.7537 (mmt) cc_final: 0.7093 (mmp) outliers start: 35 outliers final: 23 residues processed: 273 average time/residue: 0.2305 time to fit residues: 90.1110 Evaluate side-chains 262 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 10.0000 chunk 125 optimal weight: 0.0670 chunk 27 optimal weight: 0.0050 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 overall best weight: 0.5132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 ASN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11636 Z= 0.148 Angle : 0.572 15.354 15696 Z= 0.287 Chirality : 0.040 0.160 1852 Planarity : 0.003 0.041 1944 Dihedral : 5.905 58.694 1622 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.65 % Allowed : 23.11 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.22), residues: 1456 helix: 1.87 (0.18), residues: 830 sheet: 0.24 (0.40), residues: 146 loop : -1.13 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 132 HIS 0.007 0.001 HIS B 99 PHE 0.010 0.001 PHE B 83 TYR 0.013 0.001 TYR B 56 ARG 0.008 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 254 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.7819 (mmm-85) REVERT: A 154 MET cc_start: 0.8209 (pmm) cc_final: 0.7245 (pmm) REVERT: A 368 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6817 (tm-30) REVERT: A 648 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7938 (mm-30) REVERT: B 125 MET cc_start: 0.7104 (tmm) cc_final: 0.6784 (tmm) REVERT: B 194 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7247 (t80) REVERT: B 286 THR cc_start: 0.8322 (m) cc_final: 0.7801 (m) REVERT: B 290 ASP cc_start: 0.8024 (m-30) cc_final: 0.7706 (m-30) REVERT: B 385 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7643 (tm-30) REVERT: D 19 MET cc_start: 0.7665 (mmt) cc_final: 0.7253 (mmp) outliers start: 33 outliers final: 26 residues processed: 271 average time/residue: 0.2346 time to fit residues: 91.2681 Evaluate side-chains 260 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 233 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.0970 chunk 79 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11636 Z= 0.166 Angle : 0.587 14.616 15696 Z= 0.295 Chirality : 0.039 0.154 1852 Planarity : 0.003 0.044 1944 Dihedral : 5.827 57.454 1622 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.29 % Allowed : 22.95 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.10 (0.22), residues: 1456 helix: 1.88 (0.18), residues: 830 sheet: 0.16 (0.41), residues: 150 loop : -1.18 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 718 HIS 0.009 0.001 HIS B 99 PHE 0.018 0.001 PHE A 383 TYR 0.020 0.001 TYR B 247 ARG 0.009 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 243 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8425 (mmm) cc_final: 0.7719 (tmm) REVERT: A 155 MET cc_start: 0.7586 (mmm) cc_final: 0.7295 (tpp) REVERT: A 368 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6884 (tm-30) REVERT: A 644 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8669 (mp) REVERT: A 648 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7977 (mm-30) REVERT: B 125 MET cc_start: 0.7079 (tmm) cc_final: 0.6741 (tmm) REVERT: B 194 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7266 (t80) REVERT: B 250 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8589 (t) REVERT: B 385 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7620 (tm-30) REVERT: B 495 TYR cc_start: 0.8508 (t80) cc_final: 0.8170 (t80) REVERT: D 19 MET cc_start: 0.7697 (mmt) cc_final: 0.7462 (mmp) outliers start: 41 outliers final: 27 residues processed: 264 average time/residue: 0.2173 time to fit residues: 83.6340 Evaluate side-chains 264 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 234 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.0980 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11636 Z= 0.185 Angle : 0.612 14.716 15696 Z= 0.304 Chirality : 0.040 0.217 1852 Planarity : 0.003 0.043 1944 Dihedral : 5.748 57.562 1620 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.81 % Allowed : 24.08 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.07 (0.22), residues: 1456 helix: 1.85 (0.18), residues: 828 sheet: 0.24 (0.41), residues: 150 loop : -1.18 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 718 HIS 0.009 0.001 HIS B 99 PHE 0.011 0.001 PHE B 83 TYR 0.020 0.001 TYR B 247 ARG 0.005 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 242 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8421 (mmm) cc_final: 0.7775 (tmm) REVERT: A 155 MET cc_start: 0.7695 (mmm) cc_final: 0.7369 (tpp) REVERT: A 274 SER cc_start: 0.8517 (m) cc_final: 0.8253 (p) REVERT: A 368 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 387 MET cc_start: 0.8183 (mmp) cc_final: 0.7944 (mpp) REVERT: A 644 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8607 (mp) REVERT: A 648 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7861 (mm-30) REVERT: B 125 MET cc_start: 0.7137 (tmm) cc_final: 0.6770 (tmm) REVERT: B 194 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7245 (t80) REVERT: B 250 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8610 (t) REVERT: D 19 MET cc_start: 0.7673 (mmt) cc_final: 0.7242 (mmp) outliers start: 35 outliers final: 29 residues processed: 258 average time/residue: 0.2271 time to fit residues: 85.8421 Evaluate side-chains 264 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 232 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.0970 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 77 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11636 Z= 0.161 Angle : 0.628 15.338 15696 Z= 0.307 Chirality : 0.040 0.154 1852 Planarity : 0.003 0.025 1944 Dihedral : 5.704 58.473 1620 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.73 % Allowed : 24.32 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.09 (0.22), residues: 1456 helix: 1.85 (0.19), residues: 826 sheet: 0.32 (0.42), residues: 150 loop : -1.16 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 718 HIS 0.009 0.001 HIS B 99 PHE 0.020 0.001 PHE A 309 TYR 0.009 0.001 TYR A 413 ARG 0.010 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 241 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8396 (mmm) cc_final: 0.7765 (tmm) REVERT: A 155 MET cc_start: 0.7632 (mmm) cc_final: 0.7372 (tpp) REVERT: A 368 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6720 (tm-30) REVERT: A 434 TYR cc_start: 0.8096 (m-80) cc_final: 0.7696 (m-80) REVERT: A 644 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 648 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 125 MET cc_start: 0.7067 (tmm) cc_final: 0.6657 (tmm) REVERT: B 194 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.7182 (t80) REVERT: B 250 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8522 (t) REVERT: B 495 TYR cc_start: 0.8481 (t80) cc_final: 0.8174 (t80) REVERT: D 19 MET cc_start: 0.7697 (mmt) cc_final: 0.7299 (mmp) outliers start: 34 outliers final: 25 residues processed: 255 average time/residue: 0.2179 time to fit residues: 81.8129 Evaluate side-chains 261 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 233 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.0770 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 132 optimal weight: 0.1980 chunk 114 optimal weight: 0.6980 chunk 11 optimal weight: 0.0370 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11636 Z= 0.159 Angle : 0.643 15.386 15696 Z= 0.314 Chirality : 0.040 0.155 1852 Planarity : 0.003 0.023 1944 Dihedral : 5.656 59.363 1620 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.41 % Allowed : 24.16 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.22), residues: 1456 helix: 1.81 (0.19), residues: 828 sheet: 0.32 (0.42), residues: 150 loop : -1.18 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 718 HIS 0.009 0.001 HIS B 99 PHE 0.020 0.001 PHE A 309 TYR 0.024 0.001 TYR B 247 ARG 0.010 0.000 ARG B 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8391 (mmm) cc_final: 0.7751 (tmm) REVERT: A 155 MET cc_start: 0.7744 (mmm) cc_final: 0.7393 (tpp) REVERT: A 434 TYR cc_start: 0.8012 (m-80) cc_final: 0.7638 (m-80) REVERT: A 644 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8686 (mp) REVERT: B 125 MET cc_start: 0.7042 (tmm) cc_final: 0.6661 (tmm) REVERT: B 194 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.7153 (t80) REVERT: B 250 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8590 (p) REVERT: B 495 TYR cc_start: 0.8451 (t80) cc_final: 0.8162 (t80) REVERT: D 19 MET cc_start: 0.7660 (mmt) cc_final: 0.7280 (mmp) outliers start: 30 outliers final: 26 residues processed: 254 average time/residue: 0.2070 time to fit residues: 77.1797 Evaluate side-chains 263 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 234 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 47 optimal weight: 0.0370 chunk 117 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.134038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.113124 restraints weight = 27686.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.115983 restraints weight = 14174.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.117867 restraints weight = 8789.289| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 11636 Z= 0.316 Angle : 0.905 59.146 15696 Z= 0.492 Chirality : 0.045 0.834 1852 Planarity : 0.002 0.021 1944 Dihedral : 5.651 59.377 1620 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.49 % Allowed : 24.00 % Favored : 73.52 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 7.69 % 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: 1.05 (0.22), residues: 1456 helix: 1.80 (0.19), residues: 828 sheet: 0.33 (0.42), residues: 150 loop : -1.17 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 718 HIS 0.004 0.001 HIS B 99 PHE 0.017 0.001 PHE A 309 TYR 0.018 0.001 TYR B 247 ARG 0.015 0.001 ARG B 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2666.10 seconds wall clock time: 48 minutes 44.24 seconds (2924.24 seconds total)