Starting phenix.real_space_refine on Sun Mar 17 12:38:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2w_23143/03_2024/7l2w_23143_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2w_23143/03_2024/7l2w_23143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2w_23143/03_2024/7l2w_23143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2w_23143/03_2024/7l2w_23143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2w_23143/03_2024/7l2w_23143_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2w_23143/03_2024/7l2w_23143_updated.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 Na 1 4.78 5 C 11648 2.51 5 N 2816 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 575": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17737 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "D" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "B" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "C" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'6EU': 1, '6IY': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {' NA': 1, '6EU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 168 Unusual residues: {'6EU': 2, '6IY': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.69, per 1000 atoms: 0.55 Number of scatterers: 17737 At special positions: 0 Unit cell: (124.415, 132.765, 111.055, 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 100 16.00 P 4 15.00 Na 1 11.00 O 3168 8.00 N 2816 7.00 C 11648 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: 5.75 Conformation dependent library (CDL) restraints added in 2.8 seconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 4 sheets defined 56.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 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 416 through 428 Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 556 removed outlier: 4.127A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN A 551 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 598 removed outlier: 3.544A pdb=" N ARG A 575 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP A 576 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU A 577 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N CYS A 578 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 579 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET A 581 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 582 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 592 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'A' and resid 693 through 711 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 416 through 428 Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 4.229A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 598 removed outlier: 3.538A pdb=" N ARG D 575 " --> pdb=" O MET D 572 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP D 576 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU D 577 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS D 578 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET D 581 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE D 582 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 589 " --> pdb=" O VAL D 586 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 592 " --> pdb=" O PHE D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 673 through 688 Processing helix chain 'D' and resid 693 through 710 removed outlier: 3.821A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 535 through 556 removed outlier: 3.857A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 598 removed outlier: 3.784A pdb=" N ALA B 566 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 575 " --> pdb=" O MET B 572 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP B 576 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU B 577 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N CYS B 578 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 579 " --> pdb=" O ASP B 576 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET B 581 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 582 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 589 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 592 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 673 through 688 Processing helix chain 'B' and resid 691 through 710 removed outlier: 4.401A pdb=" N LYS B 694 " --> pdb=" O GLN B 691 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP B 697 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 416 through 428 Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 4.145A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 598 removed outlier: 3.824A pdb=" N ALA C 566 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C 575 " --> pdb=" O MET C 572 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP C 576 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU C 577 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS C 578 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET C 581 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE C 582 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C 589 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 592 " --> pdb=" O PHE C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 673 through 688 Processing helix chain 'C' and resid 693 through 710 Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 6.643A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 742 through 747 removed outlier: 6.483A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 742 through 747 removed outlier: 6.507A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 742 through 747 removed outlier: 6.571A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) 861 hydrogen bonds defined for protein. 2010 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: 5.42 Time building geometry restraints manager: 6.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2720 1.30 - 1.43: 5153 1.43 - 1.56: 10122 1.56 - 1.69: 9 1.69 - 1.81: 164 Bond restraints: 18168 Sorted by residual: bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CBK 6EU C 903 " pdb=" OAF 6EU C 903 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.452 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C13 6IY C 902 " pdb=" O6 6IY C 902 " ideal model delta sigma weight residual 1.333 1.421 -0.088 2.00e-02 2.50e+03 1.92e+01 ... (remaining 18163 not shown) Histogram of bond angle deviations from ideal: 96.74 - 104.19: 226 104.19 - 111.65: 8081 111.65 - 119.11: 6632 119.11 - 126.57: 9491 126.57 - 134.02: 186 Bond angle restraints: 24616 Sorted by residual: angle pdb=" O3 6IY A 903 " pdb=" P 6IY A 903 " pdb=" O4 6IY A 903 " ideal model delta sigma weight residual 123.06 100.61 22.45 3.00e+00 1.11e-01 5.60e+01 angle pdb=" O3 6IY C 902 " pdb=" P 6IY C 902 " pdb=" O4 6IY C 902 " ideal model delta sigma weight residual 123.06 100.73 22.33 3.00e+00 1.11e-01 5.54e+01 angle pdb=" O3 6IY A 902 " pdb=" P 6IY A 902 " pdb=" O4 6IY A 902 " ideal model delta sigma weight residual 123.06 100.86 22.20 3.00e+00 1.11e-01 5.48e+01 angle pdb=" O3 6IY C 904 " pdb=" P 6IY C 904 " pdb=" O4 6IY C 904 " ideal model delta sigma weight residual 123.06 102.01 21.05 3.00e+00 1.11e-01 4.92e+01 angle pdb=" C14 6IY C 902 " pdb=" C13 6IY C 902 " pdb=" O6 6IY C 902 " ideal model delta sigma weight residual 110.42 126.01 -15.59 3.00e+00 1.11e-01 2.70e+01 ... (remaining 24611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.24: 10734 28.24 - 56.49: 214 56.49 - 84.73: 50 84.73 - 112.98: 29 112.98 - 141.22: 5 Dihedral angle restraints: 11032 sinusoidal: 4712 harmonic: 6320 Sorted by residual: dihedral pdb=" CA PHE A 712 " pdb=" C PHE A 712 " pdb=" N LEU A 713 " pdb=" CA LEU A 713 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA VAL B 415 " pdb=" C VAL B 415 " pdb=" N GLU B 416 " pdb=" CA GLU B 416 " ideal model delta harmonic sigma weight residual -180.00 -156.61 -23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA VAL C 415 " pdb=" C VAL C 415 " pdb=" N GLU C 416 " pdb=" CA GLU C 416 " ideal model delta harmonic sigma weight residual -180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 11029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2510 0.087 - 0.174: 238 0.174 - 0.261: 0 0.261 - 0.348: 0 0.348 - 0.435: 4 Chirality restraints: 2752 Sorted by residual: chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CAO 6EU C 903 " pdb=" CAJ 6EU C 903 " pdb=" CAR 6EU C 903 " pdb=" CAW 6EU C 903 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CAO 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAR 6EU B 901 " pdb=" CAW 6EU B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.62e+00 ... (remaining 2749 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 544 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C SER B 544 " 0.045 2.00e-02 2.50e+03 pdb=" O SER B 544 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU B 545 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 545 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.37e+00 pdb=" C LEU B 545 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU B 545 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 546 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 544 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C SER A 544 " -0.042 2.00e-02 2.50e+03 pdb=" O SER A 544 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 545 " 0.014 2.00e-02 2.50e+03 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 215 2.64 - 3.20: 16983 3.20 - 3.77: 26424 3.77 - 4.33: 36646 4.33 - 4.90: 61743 Nonbonded interactions: 142011 Sorted by model distance: nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.075 2.440 nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.093 2.440 nonbonded pdb=" OG1 THR A 731 " pdb=" OD1 ASP A 733 " model vdw 2.116 2.440 nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.128 2.440 nonbonded pdb=" O LYS C 688 " pdb=" NE2 GLN C 691 " model vdw 2.231 2.520 ... (remaining 142006 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 193 through 751) selection = (chain 'B' and resid 193 through 751) selection = (chain 'C' and resid 193 through 751) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.110 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 46.720 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.110 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.125 18168 Z= 0.706 Angle : 1.031 22.453 24616 Z= 0.510 Chirality : 0.053 0.435 2752 Planarity : 0.005 0.044 3020 Dihedral : 14.672 141.220 6976 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.47 % Allowed : 1.79 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.57 (0.18), residues: 2136 helix: 1.51 (0.14), residues: 1248 sheet: -0.60 (0.55), residues: 64 loop : -1.34 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 372 HIS 0.007 0.001 HIS D 410 PHE 0.030 0.003 PHE A 712 TYR 0.037 0.003 TYR A 653 ARG 0.012 0.001 ARG A 739 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 533 time to evaluate : 2.070 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 354 GLN cc_start: 0.8297 (mt0) cc_final: 0.7752 (mt0) REVERT: A 378 HIS cc_start: 0.7815 (p-80) cc_final: 0.6428 (p-80) REVERT: A 397 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 506 LEU cc_start: 0.9123 (tp) cc_final: 0.8845 (tp) REVERT: A 650 THR cc_start: 0.8997 (p) cc_final: 0.8545 (m) REVERT: D 234 ASP cc_start: 0.8458 (m-30) cc_final: 0.8211 (p0) REVERT: D 389 THR cc_start: 0.8792 (m) cc_final: 0.8532 (p) REVERT: D 424 ASP cc_start: 0.8816 (t70) cc_final: 0.8289 (t0) REVERT: D 506 LEU cc_start: 0.9108 (tp) cc_final: 0.8870 (tp) REVERT: D 571 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8658 (mmtp) REVERT: D 740 TRP cc_start: 0.8549 (m100) cc_final: 0.8258 (m100) REVERT: B 253 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8330 (p) REVERT: B 378 HIS cc_start: 0.7967 (p-80) cc_final: 0.7123 (p-80) REVERT: B 389 THR cc_start: 0.8799 (m) cc_final: 0.8479 (p) REVERT: B 424 ASP cc_start: 0.8882 (t70) cc_final: 0.8548 (t70) REVERT: B 740 TRP cc_start: 0.8723 (m100) cc_final: 0.8245 (m100) REVERT: B 745 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: C 253 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8437 (p) REVERT: C 378 HIS cc_start: 0.7992 (p-80) cc_final: 0.7210 (p-80) REVERT: C 389 THR cc_start: 0.8859 (m) cc_final: 0.8629 (p) REVERT: C 506 LEU cc_start: 0.9133 (tp) cc_final: 0.8914 (tp) REVERT: C 571 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8595 (mmtt) REVERT: C 740 TRP cc_start: 0.8480 (m100) cc_final: 0.7758 (m100) outliers start: 9 outliers final: 0 residues processed: 541 average time/residue: 0.3318 time to fit residues: 257.5893 Evaluate side-chains 393 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 390 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 166 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 GLN D 393 ASN B 206 HIS B 289 HIS ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS C 354 GLN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18168 Z= 0.173 Angle : 0.558 10.807 24616 Z= 0.291 Chirality : 0.037 0.145 2752 Planarity : 0.005 0.045 3020 Dihedral : 12.143 95.335 2908 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.27 % Rotamer: Outliers : 1.32 % Allowed : 8.02 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.18), residues: 2136 helix: 2.05 (0.14), residues: 1228 sheet: -0.14 (0.52), residues: 64 loop : -1.27 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 740 HIS 0.005 0.001 HIS A 378 PHE 0.023 0.001 PHE A 712 TYR 0.022 0.001 TYR C 309 ARG 0.004 0.000 ARG C 701 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 440 time to evaluate : 2.055 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 234 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8050 (p0) REVERT: A 397 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7837 (mt-10) REVERT: A 491 ARG cc_start: 0.8228 (mmm160) cc_final: 0.8021 (mmm160) REVERT: A 650 THR cc_start: 0.9009 (p) cc_final: 0.8566 (m) REVERT: D 234 ASP cc_start: 0.8410 (m-30) cc_final: 0.8126 (p0) REVERT: D 389 THR cc_start: 0.8754 (m) cc_final: 0.8456 (p) REVERT: D 424 ASP cc_start: 0.8900 (t70) cc_final: 0.8439 (t70) REVERT: B 374 TYR cc_start: 0.6998 (m-80) cc_final: 0.6507 (m-80) REVERT: B 389 THR cc_start: 0.8756 (m) cc_final: 0.8448 (p) REVERT: B 424 ASP cc_start: 0.8954 (t70) cc_final: 0.8550 (t70) REVERT: B 740 TRP cc_start: 0.8472 (m100) cc_final: 0.7884 (m100) REVERT: B 745 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: C 211 ARG cc_start: 0.8394 (mmp80) cc_final: 0.8146 (mmm160) REVERT: C 280 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7715 (ttm110) REVERT: C 378 HIS cc_start: 0.7465 (p-80) cc_final: 0.7225 (p-80) REVERT: C 389 THR cc_start: 0.8905 (m) cc_final: 0.8643 (p) REVERT: C 392 LYS cc_start: 0.8462 (mmtm) cc_final: 0.8128 (tptp) REVERT: C 424 ASP cc_start: 0.9033 (t70) cc_final: 0.8675 (t0) REVERT: C 571 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8376 (mmtt) REVERT: C 575 ARG cc_start: 0.7950 (ttp-110) cc_final: 0.7679 (mtp85) REVERT: C 694 LYS cc_start: 0.8156 (mttp) cc_final: 0.7939 (mttp) outliers start: 25 outliers final: 10 residues processed: 449 average time/residue: 0.3056 time to fit residues: 204.8699 Evaluate side-chains 391 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 378 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 30.0000 chunk 59 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 192 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 191 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 154 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN B 206 HIS B 378 HIS ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS B 700 GLN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS C 700 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18168 Z= 0.168 Angle : 0.526 9.555 24616 Z= 0.269 Chirality : 0.037 0.182 2752 Planarity : 0.004 0.046 3020 Dihedral : 10.900 89.770 2906 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.85 % Allowed : 10.18 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.17 (0.19), residues: 2136 helix: 2.11 (0.15), residues: 1236 sheet: 0.05 (0.52), residues: 64 loop : -1.28 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 372 HIS 0.005 0.001 HIS D 378 PHE 0.019 0.001 PHE A 712 TYR 0.013 0.001 TYR C 738 ARG 0.002 0.000 ARG C 701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 413 time to evaluate : 1.848 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 234 ASP cc_start: 0.8401 (m-30) cc_final: 0.8072 (p0) REVERT: A 397 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7748 (mt-10) REVERT: A 491 ARG cc_start: 0.8234 (mmm160) cc_final: 0.7989 (mmm160) REVERT: A 650 THR cc_start: 0.8984 (p) cc_final: 0.8555 (m) REVERT: D 234 ASP cc_start: 0.8368 (m-30) cc_final: 0.8083 (p0) REVERT: D 389 THR cc_start: 0.8754 (m) cc_final: 0.8435 (p) REVERT: D 424 ASP cc_start: 0.8948 (t70) cc_final: 0.8367 (t0) REVERT: D 740 TRP cc_start: 0.8501 (m100) cc_final: 0.7986 (m100) REVERT: B 260 GLN cc_start: 0.6943 (mt0) cc_final: 0.6524 (mt0) REVERT: B 389 THR cc_start: 0.8781 (m) cc_final: 0.8473 (p) REVERT: B 424 ASP cc_start: 0.8998 (t70) cc_final: 0.8609 (t70) REVERT: B 471 ASP cc_start: 0.7882 (m-30) cc_final: 0.7679 (t0) REVERT: B 740 TRP cc_start: 0.8450 (m100) cc_final: 0.7904 (m100) REVERT: C 211 ARG cc_start: 0.8401 (mmp80) cc_final: 0.8142 (mmm160) REVERT: C 288 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8574 (mt) REVERT: C 378 HIS cc_start: 0.7471 (p-80) cc_final: 0.7267 (p-80) REVERT: C 389 THR cc_start: 0.8872 (m) cc_final: 0.8615 (p) REVERT: C 392 LYS cc_start: 0.8498 (mmtm) cc_final: 0.8133 (tptp) REVERT: C 424 ASP cc_start: 0.9064 (t70) cc_final: 0.8703 (t0) REVERT: C 694 LYS cc_start: 0.8131 (mttp) cc_final: 0.7929 (mttp) outliers start: 35 outliers final: 22 residues processed: 427 average time/residue: 0.2905 time to fit residues: 187.1413 Evaluate side-chains 408 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 385 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 586 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 204 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 HIS ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN C 285 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18168 Z= 0.168 Angle : 0.511 9.216 24616 Z= 0.260 Chirality : 0.036 0.142 2752 Planarity : 0.004 0.041 3020 Dihedral : 9.636 89.773 2904 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.79 % Allowed : 11.13 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.23 (0.19), residues: 2136 helix: 2.17 (0.15), residues: 1236 sheet: 0.24 (0.53), residues: 64 loop : -1.30 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 372 HIS 0.014 0.001 HIS B 378 PHE 0.017 0.001 PHE A 712 TYR 0.011 0.001 TYR B 309 ARG 0.004 0.000 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 408 time to evaluate : 1.763 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 234 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8053 (p0) REVERT: A 374 TYR cc_start: 0.6487 (m-80) cc_final: 0.5507 (m-80) REVERT: A 397 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7873 (mt-10) REVERT: A 491 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7824 (mmm160) REVERT: A 650 THR cc_start: 0.8992 (p) cc_final: 0.8567 (m) REVERT: D 389 THR cc_start: 0.8761 (m) cc_final: 0.8463 (p) REVERT: D 424 ASP cc_start: 0.8902 (t70) cc_final: 0.8349 (t0) REVERT: D 724 LYS cc_start: 0.8433 (tptp) cc_final: 0.8226 (tptt) REVERT: D 740 TRP cc_start: 0.8506 (m100) cc_final: 0.7994 (m100) REVERT: B 206 HIS cc_start: 0.8607 (m90) cc_final: 0.7951 (m-70) REVERT: B 260 GLN cc_start: 0.6956 (mt0) cc_final: 0.6559 (mt0) REVERT: B 389 THR cc_start: 0.8787 (m) cc_final: 0.8464 (p) REVERT: B 424 ASP cc_start: 0.8995 (t70) cc_final: 0.8600 (t70) REVERT: B 471 ASP cc_start: 0.7844 (m-30) cc_final: 0.7612 (t0) REVERT: B 740 TRP cc_start: 0.8424 (m100) cc_final: 0.7912 (m100) REVERT: C 211 ARG cc_start: 0.8435 (mmp80) cc_final: 0.8203 (mmm160) REVERT: C 288 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8604 (mt) REVERT: C 378 HIS cc_start: 0.7402 (p-80) cc_final: 0.7136 (p-80) REVERT: C 389 THR cc_start: 0.8848 (m) cc_final: 0.8584 (p) REVERT: C 392 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8163 (tptp) REVERT: C 424 ASP cc_start: 0.9067 (t70) cc_final: 0.8701 (t0) outliers start: 34 outliers final: 23 residues processed: 420 average time/residue: 0.2806 time to fit residues: 180.9763 Evaluate side-chains 415 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 390 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 632 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 104 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN C 285 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 18168 Z= 0.435 Angle : 0.637 10.623 24616 Z= 0.322 Chirality : 0.041 0.156 2752 Planarity : 0.005 0.043 3020 Dihedral : 9.042 89.928 2904 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.06 % Allowed : 12.13 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.19), residues: 2136 helix: 1.94 (0.15), residues: 1228 sheet: 0.16 (0.53), residues: 64 loop : -1.44 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 372 HIS 0.011 0.001 HIS B 378 PHE 0.020 0.002 PHE A 559 TYR 0.022 0.002 TYR A 309 ARG 0.004 0.000 ARG C 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 391 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8064 (p0) REVERT: A 491 ARG cc_start: 0.8239 (mmm160) cc_final: 0.8005 (mmm160) REVERT: A 499 ARG cc_start: 0.8109 (tpp80) cc_final: 0.7849 (tpp80) REVERT: D 389 THR cc_start: 0.8911 (m) cc_final: 0.8643 (p) REVERT: D 424 ASP cc_start: 0.8938 (t70) cc_final: 0.8391 (t0) REVERT: B 260 GLN cc_start: 0.7121 (mt0) cc_final: 0.6595 (mt0) REVERT: B 389 THR cc_start: 0.8914 (m) cc_final: 0.8651 (p) REVERT: B 424 ASP cc_start: 0.9006 (t70) cc_final: 0.8608 (t70) REVERT: B 471 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7658 (t0) REVERT: B 740 TRP cc_start: 0.8511 (m100) cc_final: 0.8197 (m100) REVERT: C 211 ARG cc_start: 0.8468 (mmp80) cc_final: 0.8193 (mmm160) REVERT: C 288 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8615 (mt) REVERT: C 308 MET cc_start: 0.8929 (mpp) cc_final: 0.8070 (mpp) REVERT: C 378 HIS cc_start: 0.7353 (p-80) cc_final: 0.7073 (p-80) REVERT: C 389 THR cc_start: 0.8930 (m) cc_final: 0.8720 (p) REVERT: C 424 ASP cc_start: 0.9092 (t70) cc_final: 0.8728 (t0) outliers start: 58 outliers final: 37 residues processed: 420 average time/residue: 0.2856 time to fit residues: 182.1511 Evaluate side-chains 416 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 376 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 696 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 205 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 HIS ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 18168 Z= 0.152 Angle : 0.516 8.879 24616 Z= 0.263 Chirality : 0.036 0.154 2752 Planarity : 0.004 0.043 3020 Dihedral : 8.236 86.979 2904 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.42 % Allowed : 14.82 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.19), residues: 2136 helix: 2.02 (0.15), residues: 1240 sheet: 0.43 (0.57), residues: 64 loop : -1.32 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 372 HIS 0.011 0.001 HIS B 378 PHE 0.015 0.001 PHE A 712 TYR 0.017 0.001 TYR D 309 ARG 0.004 0.000 ARG D 575 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 402 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8854 (mmm) cc_final: 0.8639 (mmm) REVERT: A 650 THR cc_start: 0.8942 (p) cc_final: 0.8683 (m) REVERT: D 389 THR cc_start: 0.8922 (m) cc_final: 0.8643 (p) REVERT: D 424 ASP cc_start: 0.8915 (t70) cc_final: 0.8362 (t0) REVERT: D 575 ARG cc_start: 0.8106 (ttp-110) cc_final: 0.7903 (mtp85) REVERT: B 260 GLN cc_start: 0.6861 (mt0) cc_final: 0.6550 (mt0) REVERT: B 288 LEU cc_start: 0.8850 (mt) cc_final: 0.8564 (mt) REVERT: B 389 THR cc_start: 0.8880 (m) cc_final: 0.8605 (p) REVERT: B 424 ASP cc_start: 0.9001 (t70) cc_final: 0.8589 (t70) REVERT: B 471 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7552 (t0) REVERT: B 740 TRP cc_start: 0.8471 (m100) cc_final: 0.8054 (m100) REVERT: C 211 ARG cc_start: 0.8438 (mmp80) cc_final: 0.8203 (mmm160) REVERT: C 288 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8661 (mt) REVERT: C 304 PHE cc_start: 0.7513 (t80) cc_final: 0.6741 (t80) REVERT: C 308 MET cc_start: 0.8861 (mpp) cc_final: 0.7985 (mpp) REVERT: C 378 HIS cc_start: 0.7285 (p-80) cc_final: 0.7058 (p-80) REVERT: C 389 THR cc_start: 0.8856 (m) cc_final: 0.8608 (p) REVERT: C 424 ASP cc_start: 0.9066 (t70) cc_final: 0.8690 (t0) REVERT: C 708 THR cc_start: 0.9554 (m) cc_final: 0.9352 (m) outliers start: 27 outliers final: 15 residues processed: 413 average time/residue: 0.2791 time to fit residues: 177.3153 Evaluate side-chains 406 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 389 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 632 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 126 optimal weight: 0.0470 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN B 206 HIS ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18168 Z= 0.282 Angle : 0.551 10.874 24616 Z= 0.279 Chirality : 0.038 0.177 2752 Planarity : 0.004 0.041 3020 Dihedral : 8.289 89.705 2904 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.95 % Allowed : 14.87 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.19), residues: 2136 helix: 2.03 (0.15), residues: 1228 sheet: 0.47 (0.58), residues: 64 loop : -1.35 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 372 HIS 0.011 0.001 HIS B 378 PHE 0.013 0.001 PHE A 712 TYR 0.014 0.001 TYR D 309 ARG 0.003 0.000 ARG C 575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 388 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 650 THR cc_start: 0.8935 (p) cc_final: 0.8646 (m) REVERT: D 389 THR cc_start: 0.8936 (m) cc_final: 0.8689 (p) REVERT: D 424 ASP cc_start: 0.8925 (t70) cc_final: 0.8377 (t0) REVERT: D 575 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7922 (mtp85) REVERT: B 206 HIS cc_start: 0.8478 (m90) cc_final: 0.8051 (m90) REVERT: B 260 GLN cc_start: 0.7085 (mt0) cc_final: 0.6655 (mt0) REVERT: B 371 GLU cc_start: 0.8209 (tp30) cc_final: 0.7709 (tt0) REVERT: B 389 THR cc_start: 0.8922 (m) cc_final: 0.8688 (p) REVERT: B 424 ASP cc_start: 0.9019 (t70) cc_final: 0.8620 (t70) REVERT: B 471 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7603 (t0) REVERT: B 740 TRP cc_start: 0.8499 (m100) cc_final: 0.8185 (m100) REVERT: C 211 ARG cc_start: 0.8454 (mmp80) cc_final: 0.8200 (mmm160) REVERT: C 288 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8658 (mt) REVERT: C 308 MET cc_start: 0.8895 (mpp) cc_final: 0.8428 (mpp) REVERT: C 378 HIS cc_start: 0.7174 (p-80) cc_final: 0.6912 (p-80) REVERT: C 424 ASP cc_start: 0.9072 (t70) cc_final: 0.8683 (t0) REVERT: C 708 THR cc_start: 0.9586 (m) cc_final: 0.9385 (m) outliers start: 37 outliers final: 24 residues processed: 404 average time/residue: 0.2704 time to fit residues: 168.1058 Evaluate side-chains 408 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 382 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 696 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 185 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 18168 Z= 0.158 Angle : 0.535 10.611 24616 Z= 0.267 Chirality : 0.036 0.175 2752 Planarity : 0.004 0.044 3020 Dihedral : 7.895 86.493 2904 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.37 % Allowed : 16.03 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.19), residues: 2136 helix: 2.00 (0.15), residues: 1236 sheet: 0.58 (0.60), residues: 64 loop : -1.25 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 372 HIS 0.013 0.001 HIS B 378 PHE 0.014 0.001 PHE A 712 TYR 0.025 0.001 TYR D 309 ARG 0.003 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 408 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 TYR cc_start: 0.6619 (m-80) cc_final: 0.5721 (m-80) REVERT: A 460 LEU cc_start: 0.8210 (mt) cc_final: 0.7979 (pp) REVERT: A 650 THR cc_start: 0.8920 (p) cc_final: 0.8709 (m) REVERT: D 389 THR cc_start: 0.8952 (m) cc_final: 0.8713 (p) REVERT: D 424 ASP cc_start: 0.8919 (t70) cc_final: 0.8377 (t0) REVERT: D 575 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7859 (mtp85) REVERT: D 740 TRP cc_start: 0.8443 (m100) cc_final: 0.7675 (m100) REVERT: B 206 HIS cc_start: 0.8545 (m90) cc_final: 0.8126 (m90) REVERT: B 260 GLN cc_start: 0.7056 (mt0) cc_final: 0.6670 (mt0) REVERT: B 371 GLU cc_start: 0.8218 (tp30) cc_final: 0.7692 (tt0) REVERT: B 389 THR cc_start: 0.8871 (m) cc_final: 0.8622 (p) REVERT: B 424 ASP cc_start: 0.9020 (t70) cc_final: 0.8602 (t70) REVERT: B 471 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7540 (t0) REVERT: B 740 TRP cc_start: 0.8401 (m100) cc_final: 0.8133 (m100) REVERT: C 211 ARG cc_start: 0.8496 (mmp80) cc_final: 0.8229 (mmm160) REVERT: C 288 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8655 (mt) REVERT: C 392 LYS cc_start: 0.8619 (mmtm) cc_final: 0.8281 (tptp) REVERT: C 424 ASP cc_start: 0.9054 (t70) cc_final: 0.8684 (t0) outliers start: 26 outliers final: 19 residues processed: 418 average time/residue: 0.2762 time to fit residues: 177.4834 Evaluate side-chains 416 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 395 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 4.9990 chunk 178 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 chunk 172 optimal weight: 0.1980 chunk 180 optimal weight: 0.7980 chunk 189 optimal weight: 0.5980 chunk 125 optimal weight: 8.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 18168 Z= 0.141 Angle : 0.531 10.691 24616 Z= 0.266 Chirality : 0.036 0.174 2752 Planarity : 0.004 0.043 3020 Dihedral : 7.539 86.183 2904 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.90 % Allowed : 16.72 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.15 (0.19), residues: 2136 helix: 2.02 (0.15), residues: 1236 sheet: 0.56 (0.61), residues: 64 loop : -1.21 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 372 HIS 0.012 0.001 HIS B 378 PHE 0.012 0.001 PHE A 712 TYR 0.022 0.001 TYR D 309 ARG 0.011 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 423 time to evaluate : 2.174 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 374 TYR cc_start: 0.6471 (m-80) cc_final: 0.5584 (m-80) REVERT: A 460 LEU cc_start: 0.8213 (mt) cc_final: 0.7999 (pp) REVERT: D 389 THR cc_start: 0.8962 (m) cc_final: 0.8754 (p) REVERT: D 424 ASP cc_start: 0.8930 (t70) cc_final: 0.8539 (t70) REVERT: D 575 ARG cc_start: 0.8109 (ttp-110) cc_final: 0.7845 (mtp85) REVERT: D 740 TRP cc_start: 0.8396 (m100) cc_final: 0.7818 (m100) REVERT: B 206 HIS cc_start: 0.8540 (m90) cc_final: 0.8163 (m90) REVERT: B 260 GLN cc_start: 0.7063 (mt0) cc_final: 0.6661 (mt0) REVERT: B 371 GLU cc_start: 0.8241 (tp30) cc_final: 0.7712 (tt0) REVERT: B 389 THR cc_start: 0.8897 (m) cc_final: 0.8662 (p) REVERT: B 424 ASP cc_start: 0.9022 (t70) cc_final: 0.8613 (t70) REVERT: B 471 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7495 (t0) REVERT: B 739 ARG cc_start: 0.7037 (mtt180) cc_final: 0.6740 (mtt180) REVERT: B 740 TRP cc_start: 0.8332 (m100) cc_final: 0.8089 (m100) REVERT: C 310 ASN cc_start: 0.8897 (m-40) cc_final: 0.8693 (m-40) REVERT: C 392 LYS cc_start: 0.8604 (mmtm) cc_final: 0.8267 (tptp) REVERT: C 424 ASP cc_start: 0.9038 (t70) cc_final: 0.8720 (t70) REVERT: C 740 TRP cc_start: 0.8447 (m100) cc_final: 0.8246 (m100) outliers start: 17 outliers final: 15 residues processed: 430 average time/residue: 0.2890 time to fit residues: 192.0086 Evaluate side-chains 429 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 413 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 632 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 211 optimal weight: 10.0000 chunk 194 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 GLN ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18168 Z= 0.189 Angle : 0.562 11.705 24616 Z= 0.281 Chirality : 0.037 0.231 2752 Planarity : 0.004 0.045 3020 Dihedral : 7.518 87.893 2904 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.95 % Allowed : 16.77 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.19), residues: 2136 helix: 1.98 (0.15), residues: 1232 sheet: 0.53 (0.61), residues: 64 loop : -1.20 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 372 HIS 0.013 0.001 HIS B 378 PHE 0.012 0.001 PHE A 712 TYR 0.020 0.001 TYR D 309 ARG 0.007 0.000 ARG A 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 412 time to evaluate : 2.032 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 374 TYR cc_start: 0.6516 (m-80) cc_final: 0.5649 (m-80) REVERT: D 424 ASP cc_start: 0.8928 (t70) cc_final: 0.8423 (t0) REVERT: D 575 ARG cc_start: 0.8135 (ttp-110) cc_final: 0.7879 (mtp85) REVERT: D 740 TRP cc_start: 0.8395 (m100) cc_final: 0.7797 (m100) REVERT: B 206 HIS cc_start: 0.8532 (m90) cc_final: 0.8135 (m90) REVERT: B 260 GLN cc_start: 0.6997 (mt0) cc_final: 0.6756 (mt0) REVERT: B 371 GLU cc_start: 0.8237 (tp30) cc_final: 0.7680 (tt0) REVERT: B 389 THR cc_start: 0.8889 (m) cc_final: 0.8652 (p) REVERT: B 424 ASP cc_start: 0.9006 (t70) cc_final: 0.8607 (t70) REVERT: B 471 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7555 (t0) REVERT: B 739 ARG cc_start: 0.6995 (mtt180) cc_final: 0.6713 (mtt180) REVERT: B 740 TRP cc_start: 0.8365 (m100) cc_final: 0.8093 (m100) REVERT: C 392 LYS cc_start: 0.8667 (mmtm) cc_final: 0.8321 (tptp) REVERT: C 424 ASP cc_start: 0.9044 (t70) cc_final: 0.8705 (t0) REVERT: C 740 TRP cc_start: 0.8452 (m100) cc_final: 0.8251 (m100) outliers start: 18 outliers final: 16 residues processed: 418 average time/residue: 0.2737 time to fit residues: 176.1894 Evaluate side-chains 425 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 408 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 632 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.4980 chunk 51 optimal weight: 0.2980 chunk 155 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN C 206 HIS ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.150864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.099026 restraints weight = 29380.823| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.68 r_work: 0.2958 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18168 Z= 0.207 Angle : 0.573 16.032 24616 Z= 0.283 Chirality : 0.038 0.220 2752 Planarity : 0.004 0.042 3020 Dihedral : 7.427 89.234 2904 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.16 % Allowed : 16.88 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.19), residues: 2136 helix: 1.95 (0.15), residues: 1228 sheet: 0.50 (0.60), residues: 64 loop : -1.23 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 372 HIS 0.013 0.001 HIS B 378 PHE 0.012 0.001 PHE A 712 TYR 0.021 0.001 TYR B 738 ARG 0.007 0.000 ARG A 499 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4447.56 seconds wall clock time: 81 minutes 1.41 seconds (4861.41 seconds total)