Starting phenix.real_space_refine on Wed Feb 14 12:28:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/02_2024/7n5a_24184_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/02_2024/7n5a_24184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/02_2024/7n5a_24184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/02_2024/7n5a_24184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/02_2024/7n5a_24184_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/02_2024/7n5a_24184_updated.pdb" } resolution = 3.95 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= 0.005 sd= 0.072 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: 7 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5886 2.51 5 N 1586 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 682": "OE1" <-> "OE2" 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: 9254 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4594 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 13, 'TRANS': 575} Chain breaks: 1 Chain: "B" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4594 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 13, 'TRANS': 575} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.33, per 1000 atoms: 0.58 Number of scatterers: 9254 At special positions: 0 Unit cell: (76.26, 92.66, 139.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 2 22.97 S 34 16.00 P 4 15.00 Mg 2 11.99 O 1740 8.00 N 1586 7.00 C 5886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.8 seconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 6 sheets defined 61.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 118 through 131 Processing helix chain 'A' and resid 137 through 174 Proline residue: A 161 - end of helix removed outlier: 4.053A pdb=" N LEU A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 244 removed outlier: 3.785A pdb=" N ARG A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 258 through 278 removed outlier: 3.726A pdb=" N ASN A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.772A pdb=" N ILE A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 347 removed outlier: 4.792A pdb=" N ALA A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 355 Processing helix chain 'A' and resid 358 through 407 removed outlier: 3.721A pdb=" N SER A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 418 through 438 removed outlier: 3.623A pdb=" N LEU A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) Proline residue: A 432 - end of helix removed outlier: 3.926A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 458 removed outlier: 3.659A pdb=" N GLN A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 554 removed outlier: 3.623A pdb=" N SER A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 576 removed outlier: 5.312A pdb=" N GLY A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 591 Processing helix chain 'A' and resid 595 through 600 removed outlier: 4.145A pdb=" N ASN A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 632 removed outlier: 3.521A pdb=" N ALA A 625 " --> pdb=" O LYS A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 660 Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.908A pdb=" N GLY A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.507A pdb=" N GLN A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 131 Processing helix chain 'B' and resid 137 through 174 Proline residue: B 161 - end of helix removed outlier: 4.053A pdb=" N LEU B 166 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 244 removed outlier: 3.786A pdb=" N ARG B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS B 243 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 250 No H-bonds generated for 'chain 'B' and resid 247 through 250' Processing helix chain 'B' and resid 258 through 278 removed outlier: 3.725A pdb=" N ASN B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.772A pdb=" N ILE B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 347 removed outlier: 4.792A pdb=" N ALA B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 338 " --> pdb=" O ALA B 334 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 355 Processing helix chain 'B' and resid 358 through 407 removed outlier: 3.722A pdb=" N SER B 382 " --> pdb=" O GLN B 378 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'B' and resid 418 through 438 removed outlier: 3.624A pdb=" N LEU B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.927A pdb=" N PHE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 458 removed outlier: 3.660A pdb=" N GLN B 445 " --> pdb=" O ARG B 441 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 554 removed outlier: 3.622A pdb=" N SER B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 576 removed outlier: 5.312A pdb=" N GLY B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 591 Processing helix chain 'B' and resid 595 through 600 removed outlier: 4.145A pdb=" N ASN B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 632 removed outlier: 3.522A pdb=" N ALA B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 660 Processing helix chain 'B' and resid 697 through 702 removed outlier: 3.906A pdb=" N GLY B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 removed outlier: 3.507A pdb=" N GLN B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 479 through 482 Processing sheet with id= B, first strand: chain 'A' and resid 682 through 685 removed outlier: 6.740A pdb=" N SER A 667 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ILE A 510 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE A 669 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 484 through 486 removed outlier: 8.395A pdb=" N PHE A 486 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP A 496 " --> pdb=" O PHE A 486 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 479 through 482 Processing sheet with id= E, first strand: chain 'B' and resid 682 through 685 removed outlier: 6.740A pdb=" N SER B 667 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ILE B 510 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE B 669 " --> pdb=" O ILE B 510 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 484 through 486 removed outlier: 8.394A pdb=" N PHE B 486 " --> pdb=" O ASP B 496 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP B 496 " --> pdb=" O PHE B 486 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1524 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: 2.76 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3044 1.36 - 1.50: 2362 1.50 - 1.64: 3938 1.64 - 1.77: 0 1.77 - 1.91: 70 Bond restraints: 9414 Sorted by residual: bond pdb=" CA SER B 633 " pdb=" CB SER B 633 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.45e+00 bond pdb=" CA SER A 633 " pdb=" CB SER A 633 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.27e+00 bond pdb=" C4 ADP B 802 " pdb=" C5 ADP B 802 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" C LYS A 632 " pdb=" N SER A 633 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.12e-02 7.97e+03 9.64e-01 ... (remaining 9409 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.71: 118 105.71 - 113.31: 5301 113.31 - 120.91: 4863 120.91 - 128.51: 2416 128.51 - 136.11: 48 Bond angle restraints: 12746 Sorted by residual: angle pdb=" C PRO B 559 " pdb=" N GLN B 560 " pdb=" CA GLN B 560 " ideal model delta sigma weight residual 120.44 123.99 -3.55 1.30e+00 5.92e-01 7.46e+00 angle pdb=" C PRO A 559 " pdb=" N GLN A 560 " pdb=" CA GLN A 560 " ideal model delta sigma weight residual 120.44 123.92 -3.48 1.30e+00 5.92e-01 7.15e+00 angle pdb=" N VAL A 692 " pdb=" CA VAL A 692 " pdb=" C VAL A 692 " ideal model delta sigma weight residual 110.74 113.07 -2.33 9.10e-01 1.21e+00 6.56e+00 angle pdb=" N VAL B 692 " pdb=" CA VAL B 692 " pdb=" C VAL B 692 " ideal model delta sigma weight residual 110.74 113.06 -2.32 9.10e-01 1.21e+00 6.51e+00 angle pdb=" C VAL B 609 " pdb=" CA VAL B 609 " pdb=" CB VAL B 609 " ideal model delta sigma weight residual 111.88 108.80 3.08 1.37e+00 5.33e-01 5.05e+00 ... (remaining 12741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.63: 5299 24.63 - 49.26: 299 49.26 - 73.89: 20 73.89 - 98.53: 2 98.53 - 123.16: 2 Dihedral angle restraints: 5622 sinusoidal: 2212 harmonic: 3410 Sorted by residual: dihedral pdb=" O1B ADP B 802 " pdb=" O3A ADP B 802 " pdb=" PB ADP B 802 " pdb=" PA ADP B 802 " ideal model delta sinusoidal sigma weight residual -60.00 63.15 -123.16 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 63.13 -123.14 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" CA VAL B 691 " pdb=" C VAL B 691 " pdb=" N VAL B 692 " pdb=" CA VAL B 692 " ideal model delta harmonic sigma weight residual 180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 937 0.029 - 0.058: 371 0.058 - 0.087: 110 0.087 - 0.117: 60 0.117 - 0.146: 12 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CG LEU B 456 " pdb=" CB LEU B 456 " pdb=" CD1 LEU B 456 " pdb=" CD2 LEU B 456 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CG LEU A 456 " pdb=" CB LEU A 456 " pdb=" CD1 LEU A 456 " pdb=" CD2 LEU A 456 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA GLN B 413 " pdb=" N GLN B 413 " pdb=" C GLN B 413 " pdb=" CB GLN B 413 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1487 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 427 " 0.015 2.00e-02 2.50e+03 1.28e-02 2.85e+00 pdb=" CG PHE B 427 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 427 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 427 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 427 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 427 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 427 " 0.015 2.00e-02 2.50e+03 1.25e-02 2.74e+00 pdb=" CG PHE A 427 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 427 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 427 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 427 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 427 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 489 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 490 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 490 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 490 " -0.017 5.00e-02 4.00e+02 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 116 2.62 - 3.19: 9021 3.19 - 3.76: 14846 3.76 - 4.33: 19666 4.33 - 4.90: 31555 Nonbonded interactions: 75204 Sorted by model distance: nonbonded pdb="MG MG A 803 " pdb=" O4 VO4 B 803 " model vdw 2.045 2.170 nonbonded pdb=" O4 VO4 A 802 " pdb="MG MG B 801 " model vdw 2.045 2.170 nonbonded pdb="MG MG A 803 " pdb=" O3B ADP B 802 " model vdw 2.066 2.170 nonbonded pdb=" O3B ADP A 801 " pdb="MG MG B 801 " model vdw 2.067 2.170 nonbonded pdb=" OG SER A 487 " pdb=" O ARG A 492 " model vdw 2.133 2.440 ... (remaining 75199 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' and resid 117 through 716) selection = (chain 'B' and resid 117 through 716) } 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: 1.120 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: 6.090 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.060 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 0.029 9414 Z= 0.168 Angle : 0.613 7.847 12746 Z= 0.318 Chirality : 0.039 0.146 1490 Planarity : 0.003 0.031 1606 Dihedral : 14.007 123.157 3418 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.20 % Allowed : 0.80 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1170 helix: 1.49 (0.20), residues: 722 sheet: 0.68 (0.61), residues: 90 loop : -1.20 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 304 HIS 0.009 0.001 HIS A 595 PHE 0.028 0.001 PHE B 427 TYR 0.008 0.001 TYR A 349 ARG 0.005 0.001 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.100 Fit side-chains REVERT: A 253 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.7030 (tpt90) REVERT: A 276 MET cc_start: 0.9332 (mmm) cc_final: 0.8855 (mmm) REVERT: B 253 ARG cc_start: 0.7343 (mtm-85) cc_final: 0.7065 (tpt90) outliers start: 2 outliers final: 0 residues processed: 82 average time/residue: 0.2027 time to fit residues: 24.2949 Evaluate side-chains 61 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN B 560 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9414 Z= 0.223 Angle : 0.624 6.666 12746 Z= 0.317 Chirality : 0.040 0.140 1490 Planarity : 0.004 0.034 1606 Dihedral : 7.320 115.908 1296 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.60 % Allowed : 7.73 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1170 helix: 1.64 (0.19), residues: 722 sheet: 0.87 (0.62), residues: 88 loop : -1.24 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 304 HIS 0.008 0.002 HIS B 697 PHE 0.016 0.002 PHE A 302 TYR 0.023 0.002 TYR B 360 ARG 0.004 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7333 (mtm-85) cc_final: 0.7072 (tpt90) REVERT: B 434 ASN cc_start: 0.8894 (t0) cc_final: 0.8439 (t0) outliers start: 6 outliers final: 1 residues processed: 71 average time/residue: 0.1963 time to fit residues: 20.5793 Evaluate side-chains 60 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 429 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 105 optimal weight: 0.0070 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN B 434 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9414 Z= 0.228 Angle : 0.625 9.175 12746 Z= 0.310 Chirality : 0.040 0.141 1490 Planarity : 0.004 0.042 1606 Dihedral : 7.263 117.306 1296 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.00 % Allowed : 11.95 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1170 helix: 1.59 (0.19), residues: 738 sheet: 0.87 (0.64), residues: 76 loop : -1.41 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 132 HIS 0.005 0.002 HIS B 697 PHE 0.021 0.001 PHE A 302 TYR 0.016 0.002 TYR A 205 ARG 0.004 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7382 (mtm-85) cc_final: 0.7171 (tpt90) REVERT: B 410 MET cc_start: 0.7950 (ppp) cc_final: 0.7634 (ppp) REVERT: B 434 ASN cc_start: 0.8914 (t160) cc_final: 0.8708 (t0) REVERT: B 672 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6911 (p90) outliers start: 10 outliers final: 0 residues processed: 74 average time/residue: 0.1999 time to fit residues: 22.2259 Evaluate side-chains 62 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 672 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.0470 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9414 Z= 0.261 Angle : 0.649 10.286 12746 Z= 0.322 Chirality : 0.041 0.155 1490 Planarity : 0.004 0.042 1606 Dihedral : 7.344 120.217 1296 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.31 % Allowed : 14.66 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1170 helix: 1.56 (0.19), residues: 738 sheet: 0.83 (0.64), residues: 76 loop : -1.43 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 132 HIS 0.007 0.002 HIS A 672 PHE 0.023 0.001 PHE B 302 TYR 0.021 0.002 TYR A 360 ARG 0.004 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7454 (mtm-85) cc_final: 0.7211 (tpt90) REVERT: A 672 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7095 (p90) REVERT: B 289 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7194 (mpp) REVERT: B 434 ASN cc_start: 0.9052 (t160) cc_final: 0.8845 (t0) REVERT: B 672 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7049 (p90) outliers start: 13 outliers final: 8 residues processed: 70 average time/residue: 0.1864 time to fit residues: 20.0583 Evaluate side-chains 70 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 672 HIS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 672 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9414 Z= 0.197 Angle : 0.621 11.540 12746 Z= 0.303 Chirality : 0.040 0.359 1490 Planarity : 0.003 0.042 1606 Dihedral : 7.205 119.546 1296 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.51 % Allowed : 16.47 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1170 helix: 1.65 (0.19), residues: 736 sheet: 0.76 (0.63), residues: 76 loop : -1.32 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 304 HIS 0.006 0.001 HIS A 672 PHE 0.026 0.001 PHE B 302 TYR 0.023 0.002 TYR A 360 ARG 0.004 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.7193 (tpt90) REVERT: B 289 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7406 (mpp) outliers start: 15 outliers final: 7 residues processed: 78 average time/residue: 0.1901 time to fit residues: 22.6458 Evaluate side-chains 65 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.1980 chunk 100 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 108 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9414 Z= 0.152 Angle : 0.608 12.034 12746 Z= 0.294 Chirality : 0.041 0.400 1490 Planarity : 0.003 0.042 1606 Dihedral : 6.988 116.542 1296 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.31 % Allowed : 17.47 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1170 helix: 1.69 (0.19), residues: 738 sheet: 1.53 (0.63), residues: 68 loop : -1.15 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 132 HIS 0.006 0.001 HIS A 672 PHE 0.036 0.001 PHE B 164 TYR 0.016 0.001 TYR B 205 ARG 0.004 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7443 (mtm-85) cc_final: 0.7196 (tpt90) REVERT: B 289 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7446 (mpp) outliers start: 13 outliers final: 10 residues processed: 71 average time/residue: 0.2211 time to fit residues: 22.3796 Evaluate side-chains 68 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 672 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 672 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9414 Z= 0.391 Angle : 0.742 11.916 12746 Z= 0.368 Chirality : 0.047 0.438 1490 Planarity : 0.005 0.043 1606 Dihedral : 7.537 125.095 1296 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.61 % Allowed : 17.67 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1170 helix: 1.40 (0.19), residues: 746 sheet: 0.74 (0.62), residues: 76 loop : -1.91 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 304 HIS 0.009 0.003 HIS A 672 PHE 0.023 0.002 PHE B 164 TYR 0.019 0.003 TYR B 575 ARG 0.004 0.001 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 60 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7527 (mtm-85) cc_final: 0.7287 (tpt90) REVERT: A 410 MET cc_start: 0.8134 (ppp) cc_final: 0.7714 (ppp) REVERT: A 672 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.7322 (p90) REVERT: B 289 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7543 (mpp) REVERT: B 672 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.7314 (p90) outliers start: 26 outliers final: 19 residues processed: 79 average time/residue: 0.1952 time to fit residues: 24.1534 Evaluate side-chains 78 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 56 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 672 HIS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 672 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 107 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9414 Z= 0.164 Angle : 0.654 14.389 12746 Z= 0.312 Chirality : 0.042 0.358 1490 Planarity : 0.003 0.034 1606 Dihedral : 7.133 120.045 1296 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.71 % Allowed : 19.08 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1170 helix: 1.47 (0.19), residues: 760 sheet: 0.87 (0.62), residues: 76 loop : -1.49 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 132 HIS 0.006 0.001 HIS A 672 PHE 0.031 0.001 PHE A 394 TYR 0.016 0.001 TYR A 205 ARG 0.004 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.7233 (tpt90) REVERT: B 289 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7816 (mpp) outliers start: 17 outliers final: 10 residues processed: 73 average time/residue: 0.2059 time to fit residues: 22.7096 Evaluate side-chains 65 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 672 HIS Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9414 Z= 0.194 Angle : 0.677 14.321 12746 Z= 0.321 Chirality : 0.042 0.332 1490 Planarity : 0.003 0.035 1606 Dihedral : 7.044 118.117 1296 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.71 % Allowed : 19.38 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1170 helix: 1.49 (0.19), residues: 760 sheet: 0.88 (0.63), residues: 76 loop : -1.50 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 132 HIS 0.007 0.001 HIS A 672 PHE 0.053 0.002 PHE A 164 TYR 0.015 0.002 TYR A 205 ARG 0.004 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.7244 (tpt90) REVERT: B 289 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7809 (mpp) outliers start: 17 outliers final: 12 residues processed: 68 average time/residue: 0.1754 time to fit residues: 18.7238 Evaluate side-chains 71 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 672 HIS Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 0.4980 chunk 9 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9414 Z= 0.246 Angle : 0.701 13.740 12746 Z= 0.335 Chirality : 0.043 0.342 1490 Planarity : 0.004 0.036 1606 Dihedral : 7.216 121.372 1296 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.01 % Allowed : 19.38 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1170 helix: 1.42 (0.19), residues: 758 sheet: 0.85 (0.63), residues: 76 loop : -1.68 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 132 HIS 0.008 0.002 HIS A 672 PHE 0.046 0.002 PHE A 164 TYR 0.014 0.002 TYR A 205 ARG 0.003 0.000 ARG A 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 57 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7519 (mtm-85) cc_final: 0.7264 (tpt90) REVERT: B 289 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7874 (mpp) outliers start: 20 outliers final: 12 residues processed: 69 average time/residue: 0.1795 time to fit residues: 19.4889 Evaluate side-chains 67 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.098013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.075396 restraints weight = 25303.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.074491 restraints weight = 19381.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.074345 restraints weight = 19218.519| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9414 Z= 0.378 Angle : 0.777 14.052 12746 Z= 0.380 Chirality : 0.046 0.333 1490 Planarity : 0.005 0.036 1606 Dihedral : 7.721 128.115 1296 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.91 % Allowed : 19.48 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1170 helix: 1.21 (0.19), residues: 744 sheet: 0.70 (0.64), residues: 76 loop : -1.90 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.007 0.002 HIS A 672 PHE 0.045 0.002 PHE A 164 TYR 0.018 0.003 TYR B 575 ARG 0.004 0.001 ARG B 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1663.07 seconds wall clock time: 31 minutes 40.89 seconds (1900.89 seconds total)