Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 14:21:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2w_23143/04_2023/7l2w_23143_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2w_23143/04_2023/7l2w_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_23143/04_2023/7l2w_23143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2w_23143/04_2023/7l2w_23143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2w_23143/04_2023/7l2w_23143_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2w_23143/04_2023/7l2w_23143_updated.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 9.56, per 1000 atoms: 0.54 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: 7.26 Conformation dependent library (CDL) restraints added in 2.7 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: 1.64 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: 4.83 Time building geometry restraints manager: 7.82 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: 10390 28.24 - 56.49: 201 56.49 - 84.73: 47 84.73 - 112.98: 23 112.98 - 141.22: 3 Dihedral angle restraints: 10664 sinusoidal: 4344 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 10661 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.840 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 45.150 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.190 ------------------------------------------------------------------------------- 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 : 14.261 141.220 6608 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 % 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 *********************** 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 : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 0 residues processed: 541 average time/residue: 0.3414 time to fit residues: 265.0851 Evaluate side-chains 383 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 2.333 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 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: 0.9584 ------------------------------------------------------------------------------- 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 410 HIS 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 18168 Z= 0.171 Angle : 0.554 10.880 24616 Z= 0.289 Chirality : 0.037 0.138 2752 Planarity : 0.005 0.044 3020 Dihedral : 11.008 82.988 2536 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.63 % Favored : 95.32 % Rotamer Outliers : 1.58 % 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: 2.06 (0.14), residues: 1228 sheet: -0.16 (0.52), residues: 64 loop : -1.28 (0.22), residues: 844 *********************** 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 469 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 439 time to evaluate : 2.465 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 outliers start: 30 outliers final: 14 residues processed: 448 average time/residue: 0.3010 time to fit residues: 202.2461 Evaluate side-chains 393 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 379 time to evaluate : 2.238 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1718 time to fit residues: 7.2931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 160 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 192 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 191 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 700 GLN C 285 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS C 700 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2717 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= 0.167 Angle : 0.529 9.600 24616 Z= 0.271 Chirality : 0.037 0.168 2752 Planarity : 0.004 0.046 3020 Dihedral : 9.865 88.892 2536 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 1.69 % 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: 1232 sheet: 0.04 (0.50), residues: 64 loop : -1.27 (0.22), residues: 840 *********************** 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 446 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 414 time to evaluate : 2.170 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: symmetry clash outliers start: 32 outliers final: 14 residues processed: 427 average time/residue: 0.3025 time to fit residues: 194.2261 Evaluate side-chains 398 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 384 time to evaluate : 2.225 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2080 time to fit residues: 7.9294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 0.1980 chunk 129 optimal weight: 0.8980 chunk 193 optimal weight: 0.7980 chunk 204 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** 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 206 HIS C 285 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 18168 Z= 0.143 Angle : 0.510 9.244 24616 Z= 0.261 Chirality : 0.036 0.152 2752 Planarity : 0.004 0.042 3020 Dihedral : 9.162 87.737 2536 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 0.95 % 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: 1.19 (0.19), residues: 2136 helix: 2.11 (0.15), residues: 1236 sheet: 0.34 (0.52), residues: 64 loop : -1.28 (0.22), residues: 836 *********************** 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 424 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 406 time to evaluate : 4.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 412 average time/residue: 0.2912 time to fit residues: 183.8380 Evaluate side-chains 401 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 391 time to evaluate : 2.370 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1678 time to fit residues: 6.1863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 104 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 51 optimal weight: 30.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 393 ASN A 700 GLN ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN C 206 HIS ** 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: 0.8502 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.105 18168 Z= 0.437 Angle : 0.641 15.641 24616 Z= 0.322 Chirality : 0.041 0.159 2752 Planarity : 0.005 0.046 3020 Dihedral : 9.520 89.598 2536 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.62 % Favored : 94.34 % Rotamer Outliers : 1.79 % 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: 0.91 (0.19), residues: 2136 helix: 1.94 (0.15), residues: 1224 sheet: 0.54 (0.55), residues: 56 loop : -1.47 (0.22), residues: 856 *********************** 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 420 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 386 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 23 residues processed: 405 average time/residue: 0.3059 time to fit residues: 188.7631 Evaluate side-chains 392 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 369 time to evaluate : 2.194 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1755 time to fit residues: 10.3114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 18168 Z= 0.188 Angle : 0.548 11.354 24616 Z= 0.273 Chirality : 0.037 0.213 2752 Planarity : 0.004 0.045 3020 Dihedral : 8.954 89.505 2536 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.47 % 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: 1.03 (0.19), residues: 2136 helix: 2.00 (0.15), residues: 1224 sheet: 0.38 (0.55), residues: 64 loop : -1.34 (0.22), residues: 848 *********************** 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 408 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 399 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 402 average time/residue: 0.2904 time to fit residues: 177.5896 Evaluate side-chains 387 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 383 time to evaluate : 2.196 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3394 time to fit residues: 4.9291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 204 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 126 optimal weight: 0.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 HIS ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS ** 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: 0.8447 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 18168 Z= 0.192 Angle : 0.549 13.502 24616 Z= 0.271 Chirality : 0.037 0.163 2752 Planarity : 0.004 0.043 3020 Dihedral : 8.555 87.502 2536 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 0.95 % 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: 1.98 (0.15), residues: 1228 sheet: 0.43 (0.57), residues: 64 loop : -1.29 (0.22), residues: 844 *********************** 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 422 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 404 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 413 average time/residue: 0.2833 time to fit residues: 179.2518 Evaluate side-chains 394 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 385 time to evaluate : 2.223 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1627 time to fit residues: 5.7780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 0.0030 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.090 18168 Z= 0.149 Angle : 0.546 12.573 24616 Z= 0.268 Chirality : 0.036 0.171 2752 Planarity : 0.004 0.042 3020 Dihedral : 8.081 89.946 2536 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.26 % 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: 1.08 (0.19), residues: 2136 helix: 1.97 (0.15), residues: 1236 sheet: 0.51 (0.58), residues: 64 loop : -1.25 (0.22), residues: 836 *********************** 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 427 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 422 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 423 average time/residue: 0.2858 time to fit residues: 186.1939 Evaluate side-chains 410 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 407 time to evaluate : 2.448 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1621 time to fit residues: 4.0564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 190 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** D 494 GLN D 700 GLN ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 18168 Z= 0.383 Angle : 0.627 11.931 24616 Z= 0.313 Chirality : 0.040 0.195 2752 Planarity : 0.004 0.041 3020 Dihedral : 8.191 88.158 2536 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.58 % 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: 0.91 (0.19), residues: 2136 helix: 1.87 (0.15), residues: 1224 sheet: 0.37 (0.58), residues: 64 loop : -1.34 (0.22), residues: 848 *********************** 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 401 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 390 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 11 residues processed: 394 average time/residue: 0.3048 time to fit residues: 186.6254 Evaluate side-chains 391 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 380 time to evaluate : 2.170 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1966 time to fit residues: 6.8559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 139 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 168 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN C 206 HIS ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 18168 Z= 0.208 Angle : 0.588 12.429 24616 Z= 0.288 Chirality : 0.038 0.187 2752 Planarity : 0.004 0.045 3020 Dihedral : 7.743 87.254 2536 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.05 % 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: 0.96 (0.19), residues: 2136 helix: 1.90 (0.15), residues: 1224 sheet: 0.47 (0.59), residues: 64 loop : -1.31 (0.22), residues: 848 ********************** 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 404 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 403 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 404 average time/residue: 0.2771 time to fit residues: 174.2788 Evaluate side-chains 393 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.097878 restraints weight = 29259.083| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.64 r_work: 0.2938 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 18168 Z= 0.256 Angle : 0.592 12.060 24616 Z= 0.292 Chirality : 0.038 0.187 2752 Planarity : 0.004 0.041 3020 Dihedral : 7.580 87.797 2536 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 0.16 % 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: 1.88 (0.15), residues: 1224 sheet: 0.40 (0.59), residues: 64 loop : -1.34 (0.22), residues: 848 =============================================================================== Job complete usr+sys time: 4334.40 seconds wall clock time: 79 minutes 4.79 seconds (4744.79 seconds total)