Starting phenix.real_space_refine on Tue Apr 9 23:19:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2x_23144/04_2024/7l2x_23144_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2x_23144/04_2024/7l2x_23144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2x_23144/04_2024/7l2x_23144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2x_23144/04_2024/7l2x_23144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2x_23144/04_2024/7l2x_23144_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2x_23144/04_2024/7l2x_23144_updated.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 C 11655 2.51 5 N 2817 2.21 5 O 3169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 600": "OE1" <-> "OE2" Residue "B PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "C GLU 600": "OE1" <-> "OE2" Residue "C TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17745 Number of models: 1 Model: "" Number of chains: 8 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: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'6EU': 1, '6IY': 1, 'XPJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'6EU': 1, '6IY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.46, per 1000 atoms: 0.48 Number of scatterers: 17745 At special positions: 0 Unit cell: (126.92, 127.755, 110.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 4 15.00 O 3169 8.00 N 2817 7.00 C 11655 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: 7.31 Conformation dependent library (CDL) restraints added in 3.1 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: 88 helices and 4 sheets defined 56.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 214 through 222 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 354 removed outlier: 3.535A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) 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 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' 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: 3.944A pdb=" N ASN A 551 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 598 removed outlier: 4.248A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (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 674 through 689 removed outlier: 3.650A pdb=" N ILE A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 711 removed outlier: 3.590A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 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: 3.995A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 598 removed outlier: 3.667A pdb=" N ARG D 575 " --> pdb=" O MET D 572 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP D 576 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU D 577 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS D 578 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET D 581 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE D 582 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D 589 " --> pdb=" O VAL D 586 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE D 591 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 593 " --> pdb=" O GLY D 590 " (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 689 Processing helix chain 'D' and resid 691 through 710 removed outlier: 4.602A pdb=" N LYS D 694 " --> pdb=" O GLN D 691 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP D 697 " --> 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 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' 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 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: 4.331A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 574 removed outlier: 3.766A pdb=" N ALA B 566 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 598 removed outlier: 4.488A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (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 689 removed outlier: 3.608A pdb=" N ILE B 689 " --> pdb=" O THR B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 711 removed outlier: 4.606A pdb=" N LYS B 694 " --> pdb=" O GLN B 691 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 711 " --> pdb=" O THR B 708 " (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 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: 3.959A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 598 removed outlier: 3.537A pdb=" N ALA C 566 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 575 " --> pdb=" O MET C 572 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP C 576 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU C 577 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N CYS C 578 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 582 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 589 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 591 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 593 " --> pdb=" O GLY C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 Processing helix chain 'C' and resid 656 through 671 Processing helix chain 'C' and resid 674 through 690 Processing helix chain 'C' and resid 693 through 710 removed outlier: 4.336A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 6.437A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.339A 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: 6.394A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.218A 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: 6.442A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.226A 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: 6.217A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) 869 hydrogen bonds defined for protein. 2103 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: 6.14 Time building geometry restraints manager: 7.73 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: 2722 1.30 - 1.43: 5097 1.43 - 1.55: 10189 1.55 - 1.68: 8 1.68 - 1.81: 164 Bond restraints: 18180 Sorted by residual: bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C13 6IY B 902 " pdb=" O6 6IY B 902 " ideal model delta sigma weight residual 1.333 1.418 -0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 18175 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.21: 255 105.21 - 112.44: 9081 112.44 - 119.67: 6560 119.67 - 126.91: 8569 126.91 - 134.14: 166 Bond angle restraints: 24631 Sorted by residual: angle pdb=" O3 6IY B 902 " pdb=" P 6IY B 902 " pdb=" O4 6IY B 902 " ideal model delta sigma weight residual 123.06 99.29 23.77 3.00e+00 1.11e-01 6.28e+01 angle pdb=" O3 6IY A 903 " pdb=" P 6IY A 903 " pdb=" O4 6IY A 903 " ideal model delta sigma weight residual 123.06 100.73 22.33 3.00e+00 1.11e-01 5.54e+01 angle pdb=" O3 6IY D 902 " pdb=" P 6IY D 902 " pdb=" O4 6IY D 902 " ideal model delta sigma weight residual 123.06 100.88 22.18 3.00e+00 1.11e-01 5.46e+01 angle pdb=" O3 6IY A 902 " pdb=" P 6IY A 902 " pdb=" O4 6IY A 902 " ideal model delta sigma weight residual 123.06 102.23 20.83 3.00e+00 1.11e-01 4.82e+01 angle pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 ... (remaining 24626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 10498 21.45 - 42.90: 411 42.90 - 64.35: 80 64.35 - 85.80: 47 85.80 - 107.26: 13 Dihedral angle restraints: 11049 sinusoidal: 4729 harmonic: 6320 Sorted by residual: 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 -153.73 -26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA VAL D 415 " pdb=" C VAL D 415 " pdb=" N GLU D 416 " pdb=" CA GLU D 416 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA GLN D 561 " pdb=" C GLN D 561 " pdb=" N MET D 562 " pdb=" CA MET D 562 " ideal model delta harmonic sigma weight residual -180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 11046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2541 0.087 - 0.173: 207 0.173 - 0.260: 2 0.260 - 0.346: 1 0.346 - 0.433: 5 Chirality restraints: 2756 Sorted by residual: 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 4.69e+00 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 4.64e+00 chirality pdb=" CAO 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" CAR 6EU C 901 " pdb=" CAW 6EU C 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 2753 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 539 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" C ALA D 539 " -0.052 2.00e-02 2.50e+03 pdb=" O ALA D 539 " 0.019 2.00e-02 2.50e+03 pdb=" N SER D 540 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 569 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C ILE B 569 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE B 569 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 570 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 541 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.07e+00 pdb=" C MET A 541 " -0.049 2.00e-02 2.50e+03 pdb=" O MET A 541 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 542 " 0.017 2.00e-02 2.50e+03 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1354 2.72 - 3.27: 18254 3.27 - 3.81: 28180 3.81 - 4.36: 34334 4.36 - 4.90: 59424 Nonbonded interactions: 141546 Sorted by model distance: nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.179 2.440 nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.229 2.440 nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.233 2.440 nonbonded pdb=" O ALA C 719 " pdb=" NH1 ARG C 721 " model vdw 2.247 2.520 nonbonded pdb=" NH2 ARG C 557 " pdb=" OE1 GLU C 570 " model vdw 2.257 2.520 ... (remaining 141541 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 or resid 901)) selection = (chain 'B' and (resid 193 through 751 or resid 901)) selection = chain 'C' selection = (chain 'D' and (resid 193 through 751 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 12.760 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 54.960 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.130 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.010 0.124 18180 Z= 0.672 Angle : 1.058 23.766 24631 Z= 0.524 Chirality : 0.053 0.433 2756 Planarity : 0.006 0.042 3020 Dihedral : 13.940 107.256 6993 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 0.79 % Allowed : 1.58 % Favored : 97.63 % 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: 0.61 (0.18), residues: 2136 helix: 1.51 (0.13), residues: 1248 sheet: -0.77 (0.55), residues: 76 loop : -1.25 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 372 HIS 0.008 0.002 HIS D 410 PHE 0.039 0.003 PHE B 304 TYR 0.030 0.003 TYR D 627 ARG 0.007 0.001 ARG B 455 *********************** 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 634 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 619 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.8809 (tp40) cc_final: 0.8466 (tp-100) REVERT: A 504 LYS cc_start: 0.8839 (mttt) cc_final: 0.8632 (mttm) REVERT: A 557 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8618 (mtt-85) REVERT: A 636 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7309 (tp30) REVERT: D 368 LYS cc_start: 0.8286 (tttt) cc_final: 0.7758 (tttp) REVERT: D 374 TYR cc_start: 0.6458 (m-80) cc_final: 0.5886 (m-10) REVERT: D 378 HIS cc_start: 0.7501 (p-80) cc_final: 0.6941 (p90) REVERT: D 410 HIS cc_start: 0.8477 (p-80) cc_final: 0.8209 (p90) REVERT: D 423 GLN cc_start: 0.8717 (tp40) cc_final: 0.8480 (tp-100) REVERT: D 571 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8192 (tptp) REVERT: D 581 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7321 (mmt) REVERT: B 211 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7965 (mmm160) REVERT: B 324 LYS cc_start: 0.8923 (mttt) cc_final: 0.8639 (mptt) REVERT: B 410 HIS cc_start: 0.7874 (m90) cc_final: 0.7639 (m-70) REVERT: B 416 GLU cc_start: 0.7553 (tp30) cc_final: 0.6926 (tp30) REVERT: B 420 ARG cc_start: 0.8478 (mmt180) cc_final: 0.8118 (mmm-85) REVERT: B 423 GLN cc_start: 0.8895 (tp40) cc_final: 0.8496 (tp-100) REVERT: B 703 ILE cc_start: 0.9621 (mt) cc_final: 0.9378 (mp) REVERT: C 343 SER cc_start: 0.9075 (m) cc_final: 0.8785 (p) REVERT: C 483 SER cc_start: 0.9483 (t) cc_final: 0.9278 (p) REVERT: C 636 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7963 (mm-30) outliers start: 15 outliers final: 4 residues processed: 629 average time/residue: 0.3589 time to fit residues: 323.0520 Evaluate side-chains 412 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 407 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 285 ASN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 289 HIS B 378 HIS C 228 GLN C 378 HIS C 393 ASN C 700 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18180 Z= 0.212 Angle : 0.568 6.872 24631 Z= 0.301 Chirality : 0.039 0.160 2756 Planarity : 0.005 0.058 3020 Dihedral : 11.531 105.856 2930 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 1.90 % Allowed : 8.86 % Favored : 89.24 % 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: 1.00 (0.18), residues: 2136 helix: 1.87 (0.14), residues: 1260 sheet: -1.16 (0.52), residues: 84 loop : -1.15 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 372 HIS 0.009 0.001 HIS B 378 PHE 0.049 0.001 PHE D 304 TYR 0.029 0.001 TYR A 309 ARG 0.007 0.001 ARG A 575 *********************** 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 486 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 450 time to evaluate : 2.066 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 REVERT: A 288 LEU cc_start: 0.8434 (mt) cc_final: 0.8225 (mt) REVERT: A 423 GLN cc_start: 0.8907 (tp40) cc_final: 0.8678 (tp-100) REVERT: A 504 LYS cc_start: 0.8857 (mttt) cc_final: 0.8647 (mtpp) REVERT: A 636 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7568 (tp30) REVERT: A 707 ASP cc_start: 0.8831 (m-30) cc_final: 0.8597 (m-30) REVERT: D 374 TYR cc_start: 0.6176 (m-80) cc_final: 0.5876 (m-10) REVERT: D 410 HIS cc_start: 0.8377 (p-80) cc_final: 0.7954 (p90) REVERT: B 324 LYS cc_start: 0.8948 (mttt) cc_final: 0.8610 (mptt) REVERT: B 410 HIS cc_start: 0.7871 (m90) cc_final: 0.7577 (m-70) REVERT: B 416 GLU cc_start: 0.7573 (tp30) cc_final: 0.7049 (tp30) REVERT: B 420 ARG cc_start: 0.8536 (mmt180) cc_final: 0.8199 (mmm-85) REVERT: B 653 TYR cc_start: 0.6178 (OUTLIER) cc_final: 0.5236 (p90) REVERT: B 724 LYS cc_start: 0.8684 (tmtt) cc_final: 0.8466 (tmtt) REVERT: C 313 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8908 (mt) REVERT: C 342 SER cc_start: 0.9166 (t) cc_final: 0.8820 (p) REVERT: C 343 SER cc_start: 0.9043 (m) cc_final: 0.8614 (p) REVERT: C 420 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8259 (mmm-85) REVERT: C 636 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7977 (mm-30) REVERT: C 700 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8675 (tp40) REVERT: C 716 MET cc_start: 0.4857 (ptm) cc_final: 0.4484 (ptp) REVERT: C 740 TRP cc_start: 0.8614 (m100) cc_final: 0.8266 (m100) REVERT: C 743 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.7541 (tpp80) outliers start: 36 outliers final: 21 residues processed: 467 average time/residue: 0.2883 time to fit residues: 204.4542 Evaluate side-chains 426 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 403 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 160 optimal weight: 0.0570 chunk 131 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 273 GLN B 285 ASN C 206 HIS C 285 ASN C 378 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18180 Z= 0.220 Angle : 0.532 7.296 24631 Z= 0.280 Chirality : 0.038 0.154 2756 Planarity : 0.004 0.043 3020 Dihedral : 9.973 88.641 2924 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.27 % Rotamer: Outliers : 2.00 % Allowed : 11.81 % Favored : 86.18 % 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: 0.99 (0.18), residues: 2136 helix: 1.96 (0.15), residues: 1236 sheet: -0.60 (0.57), residues: 76 loop : -1.30 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 372 HIS 0.009 0.001 HIS C 378 PHE 0.045 0.001 PHE D 304 TYR 0.015 0.001 TYR A 584 ARG 0.008 0.001 ARG B 211 *********************** 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 453 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 415 time to evaluate : 2.022 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 revert: symmetry clash revert: symmetry clash REVERT: A 504 LYS cc_start: 0.8846 (mttt) cc_final: 0.8629 (mtpp) REVERT: A 636 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7614 (tp30) REVERT: A 700 GLN cc_start: 0.8995 (tp-100) cc_final: 0.8667 (tp40) REVERT: D 354 GLN cc_start: 0.8719 (mt0) cc_final: 0.8371 (mt0) REVERT: D 410 HIS cc_start: 0.8366 (p-80) cc_final: 0.7891 (p90) REVERT: D 416 GLU cc_start: 0.7608 (tp30) cc_final: 0.7331 (tp30) REVERT: D 653 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.5443 (p90) REVERT: D 700 GLN cc_start: 0.9001 (tp40) cc_final: 0.8565 (tp-100) REVERT: B 206 HIS cc_start: 0.8433 (m90) cc_final: 0.8062 (m-70) REVERT: B 324 LYS cc_start: 0.8955 (mttt) cc_final: 0.8619 (mptt) REVERT: B 410 HIS cc_start: 0.7928 (m90) cc_final: 0.7624 (m-70) REVERT: B 416 GLU cc_start: 0.7598 (tp30) cc_final: 0.7148 (tp30) REVERT: B 420 ARG cc_start: 0.8525 (mmt180) cc_final: 0.8214 (mmm-85) REVERT: B 483 SER cc_start: 0.9254 (t) cc_final: 0.9018 (p) REVERT: B 653 TYR cc_start: 0.6258 (OUTLIER) cc_final: 0.5366 (p90) REVERT: B 724 LYS cc_start: 0.8591 (tmtt) cc_final: 0.8346 (tmtt) REVERT: C 342 SER cc_start: 0.9125 (t) cc_final: 0.8833 (p) REVERT: C 343 SER cc_start: 0.8964 (m) cc_final: 0.8498 (p) REVERT: C 420 ARG cc_start: 0.8583 (mmm-85) cc_final: 0.8232 (mmm-85) REVERT: C 503 LEU cc_start: 0.8611 (mp) cc_final: 0.8409 (mt) REVERT: C 700 GLN cc_start: 0.8925 (tp-100) cc_final: 0.8575 (tp-100) REVERT: C 716 MET cc_start: 0.4960 (ptm) cc_final: 0.4448 (ptp) REVERT: C 740 TRP cc_start: 0.8618 (m100) cc_final: 0.8309 (m100) REVERT: C 743 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.7556 (tpp80) outliers start: 38 outliers final: 28 residues processed: 438 average time/residue: 0.2818 time to fit residues: 189.9369 Evaluate side-chains 423 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 393 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 ASN B 378 HIS C 206 HIS C 285 ASN C 378 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18180 Z= 0.223 Angle : 0.521 6.992 24631 Z= 0.272 Chirality : 0.037 0.196 2756 Planarity : 0.004 0.054 3020 Dihedral : 9.397 89.362 2923 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.48 % Allowed : 12.76 % Favored : 84.76 % 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: 1.01 (0.19), residues: 2136 helix: 1.98 (0.15), residues: 1236 sheet: -0.62 (0.57), residues: 76 loop : -1.31 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 372 HIS 0.013 0.001 HIS B 378 PHE 0.045 0.001 PHE D 304 TYR 0.022 0.001 TYR C 309 ARG 0.004 0.000 ARG D 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 452 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 405 time to evaluate : 1.895 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 REVERT: A 584 TYR cc_start: 0.8606 (t80) cc_final: 0.8404 (t80) REVERT: A 700 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8459 (tp-100) REVERT: A 707 ASP cc_start: 0.8818 (m-30) cc_final: 0.8573 (m-30) REVERT: A 745 ASP cc_start: 0.8212 (m-30) cc_final: 0.7585 (p0) REVERT: D 354 GLN cc_start: 0.8723 (mt0) cc_final: 0.8356 (mp10) REVERT: D 410 HIS cc_start: 0.8369 (p-80) cc_final: 0.7869 (p90) REVERT: D 416 GLU cc_start: 0.7623 (tp30) cc_final: 0.7337 (tp30) REVERT: D 424 ASP cc_start: 0.9056 (t70) cc_final: 0.8718 (t70) REVERT: D 653 TYR cc_start: 0.6925 (OUTLIER) cc_final: 0.5429 (p90) REVERT: D 700 GLN cc_start: 0.9006 (tp40) cc_final: 0.8564 (tp-100) REVERT: B 206 HIS cc_start: 0.8490 (m90) cc_final: 0.8132 (m-70) REVERT: B 324 LYS cc_start: 0.8949 (mttt) cc_final: 0.8585 (mptt) REVERT: B 416 GLU cc_start: 0.7538 (tp30) cc_final: 0.7066 (tp30) REVERT: B 420 ARG cc_start: 0.8525 (mmt180) cc_final: 0.8216 (mmm-85) REVERT: B 653 TYR cc_start: 0.6243 (OUTLIER) cc_final: 0.5350 (p90) REVERT: B 724 LYS cc_start: 0.8604 (tmtt) cc_final: 0.8368 (tmtt) REVERT: C 342 SER cc_start: 0.9130 (t) cc_final: 0.8827 (p) REVERT: C 343 SER cc_start: 0.8936 (m) cc_final: 0.8471 (p) REVERT: C 397 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7610 (mt-10) REVERT: C 420 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8199 (mmm-85) REVERT: C 503 LEU cc_start: 0.8588 (mp) cc_final: 0.8380 (mt) REVERT: C 648 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7532 (mm-30) REVERT: C 700 GLN cc_start: 0.8927 (tp-100) cc_final: 0.8622 (tp-100) REVERT: C 716 MET cc_start: 0.4918 (ptm) cc_final: 0.4391 (ptp) REVERT: C 740 TRP cc_start: 0.8601 (m100) cc_final: 0.8298 (m100) REVERT: C 743 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.7599 (tpp80) outliers start: 47 outliers final: 27 residues processed: 429 average time/residue: 0.2761 time to fit residues: 183.1893 Evaluate side-chains 414 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 385 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 104 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 423 GLN A 498 GLN D 285 ASN B 273 GLN B 628 ASN C 206 HIS C 285 ASN C 378 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18180 Z= 0.333 Angle : 0.574 7.077 24631 Z= 0.296 Chirality : 0.039 0.251 2756 Planarity : 0.004 0.043 3020 Dihedral : 9.204 86.330 2923 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.80 % Allowed : 13.40 % Favored : 83.81 % 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: 0.88 (0.19), residues: 2136 helix: 1.85 (0.15), residues: 1256 sheet: -0.78 (0.57), residues: 76 loop : -1.37 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 372 HIS 0.007 0.001 HIS C 378 PHE 0.047 0.001 PHE D 304 TYR 0.029 0.001 TYR A 309 ARG 0.012 0.001 ARG D 331 *********************** 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 444 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 391 time to evaluate : 2.099 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 revert: symmetry clash REVERT: A 423 GLN cc_start: 0.8969 (tp40) cc_final: 0.8765 (tp-100) REVERT: A 584 TYR cc_start: 0.8665 (t80) cc_final: 0.8423 (t80) REVERT: A 700 GLN cc_start: 0.9043 (tp-100) cc_final: 0.8487 (tp-100) REVERT: A 707 ASP cc_start: 0.8853 (m-30) cc_final: 0.8596 (m-30) REVERT: A 745 ASP cc_start: 0.8278 (m-30) cc_final: 0.7689 (p0) REVERT: D 354 GLN cc_start: 0.8701 (mt0) cc_final: 0.8345 (mp10) REVERT: D 410 HIS cc_start: 0.8398 (p-80) cc_final: 0.7873 (p90) REVERT: D 424 ASP cc_start: 0.9040 (t70) cc_final: 0.8717 (t70) REVERT: D 653 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.5613 (p90) REVERT: D 700 GLN cc_start: 0.8984 (tp40) cc_final: 0.8516 (tp-100) REVERT: B 206 HIS cc_start: 0.8450 (m90) cc_final: 0.8133 (m-70) REVERT: B 324 LYS cc_start: 0.8925 (mttt) cc_final: 0.8526 (mptt) REVERT: B 416 GLU cc_start: 0.7538 (tp30) cc_final: 0.7264 (tp30) REVERT: B 653 TYR cc_start: 0.6310 (OUTLIER) cc_final: 0.5461 (p90) REVERT: C 342 SER cc_start: 0.9131 (t) cc_final: 0.8820 (p) REVERT: C 343 SER cc_start: 0.8906 (m) cc_final: 0.8412 (p) REVERT: C 397 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7644 (mt-10) REVERT: C 420 ARG cc_start: 0.8557 (mmm-85) cc_final: 0.8198 (mmm-85) REVERT: C 648 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7482 (mm-30) REVERT: C 700 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8637 (tp-100) REVERT: C 716 MET cc_start: 0.5048 (ptm) cc_final: 0.4548 (ptp) REVERT: C 743 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.7677 (tpp80) outliers start: 53 outliers final: 37 residues processed: 419 average time/residue: 0.2950 time to fit residues: 193.1555 Evaluate side-chains 415 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 376 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 694 LYS Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 741 CYS Chi-restraints excluded: chain C residue 745 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 285 ASN B 410 HIS C 206 HIS C 285 ASN C 378 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18180 Z= 0.216 Angle : 0.530 11.993 24631 Z= 0.273 Chirality : 0.038 0.418 2756 Planarity : 0.004 0.042 3020 Dihedral : 8.748 86.062 2923 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.43 % Allowed : 14.24 % Favored : 83.33 % 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: 0.98 (0.19), residues: 2136 helix: 1.98 (0.15), residues: 1236 sheet: -0.71 (0.58), residues: 76 loop : -1.35 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 272 HIS 0.006 0.001 HIS C 378 PHE 0.045 0.001 PHE D 304 TYR 0.018 0.001 TYR C 309 ARG 0.003 0.000 ARG D 331 *********************** 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 441 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 395 time to evaluate : 2.124 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 584 TYR cc_start: 0.8527 (t80) cc_final: 0.8202 (t80) REVERT: A 636 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: A 700 GLN cc_start: 0.9033 (tp-100) cc_final: 0.8466 (tp-100) REVERT: A 707 ASP cc_start: 0.8855 (m-30) cc_final: 0.8586 (m-30) REVERT: A 745 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7684 (p0) REVERT: D 354 GLN cc_start: 0.8711 (mt0) cc_final: 0.8329 (mp10) REVERT: D 410 HIS cc_start: 0.8386 (p-80) cc_final: 0.7844 (p90) REVERT: D 424 ASP cc_start: 0.9032 (t70) cc_final: 0.8701 (t70) REVERT: D 653 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.5631 (p90) REVERT: D 700 GLN cc_start: 0.9000 (tp40) cc_final: 0.8549 (tp-100) REVERT: B 206 HIS cc_start: 0.8468 (m90) cc_final: 0.8161 (m-70) REVERT: B 324 LYS cc_start: 0.8903 (mttt) cc_final: 0.8454 (mmtt) REVERT: B 416 GLU cc_start: 0.7459 (tp30) cc_final: 0.7098 (tp30) REVERT: B 420 ARG cc_start: 0.8772 (tpp80) cc_final: 0.8518 (tpp80) REVERT: B 423 GLN cc_start: 0.9113 (tp-100) cc_final: 0.8665 (tp-100) REVERT: B 653 TYR cc_start: 0.6301 (OUTLIER) cc_final: 0.5350 (p90) REVERT: B 663 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9218 (mt) REVERT: B 724 LYS cc_start: 0.8544 (tmtt) cc_final: 0.8321 (tmtt) REVERT: C 342 SER cc_start: 0.9130 (t) cc_final: 0.8835 (p) REVERT: C 343 SER cc_start: 0.8893 (m) cc_final: 0.8404 (p) REVERT: C 397 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7672 (mt-10) REVERT: C 420 ARG cc_start: 0.8576 (mmm-85) cc_final: 0.8221 (mmm-85) REVERT: C 653 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.5154 (p90) REVERT: C 700 GLN cc_start: 0.8925 (tp-100) cc_final: 0.8635 (tp-100) REVERT: C 716 MET cc_start: 0.4997 (ptm) cc_final: 0.4616 (ptp) outliers start: 46 outliers final: 34 residues processed: 422 average time/residue: 0.2754 time to fit residues: 180.4590 Evaluate side-chains 420 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 380 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 741 CYS Chi-restraints excluded: chain C residue 745 ASP 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: 4.9990 chunk 116 optimal weight: 0.3980 chunk 149 optimal weight: 9.9990 chunk 172 optimal weight: 0.7980 chunk 114 optimal weight: 20.0000 chunk 204 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 423 GLN B 410 HIS C 206 HIS C 285 ASN C 378 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18180 Z= 0.165 Angle : 0.503 8.172 24631 Z= 0.260 Chirality : 0.037 0.259 2756 Planarity : 0.004 0.043 3020 Dihedral : 8.352 86.204 2923 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.22 % Allowed : 15.24 % Favored : 82.54 % 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: 1.04 (0.19), residues: 2136 helix: 2.03 (0.15), residues: 1240 sheet: -0.73 (0.58), residues: 76 loop : -1.34 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 372 HIS 0.006 0.001 HIS C 378 PHE 0.043 0.001 PHE D 304 TYR 0.019 0.001 TYR C 309 ARG 0.003 0.000 ARG D 331 *********************** 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 443 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 401 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8096 (mt-10) REVERT: A 354 GLN cc_start: 0.8722 (mt0) cc_final: 0.8346 (mp10) REVERT: A 584 TYR cc_start: 0.8496 (t80) cc_final: 0.8149 (t80) REVERT: A 636 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: A 700 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8448 (tp-100) REVERT: A 707 ASP cc_start: 0.8857 (m-30) cc_final: 0.8569 (m-30) REVERT: A 745 ASP cc_start: 0.8172 (m-30) cc_final: 0.7686 (p0) REVERT: D 354 GLN cc_start: 0.8748 (mt0) cc_final: 0.8399 (mp10) REVERT: D 410 HIS cc_start: 0.8376 (p-80) cc_final: 0.7868 (p90) REVERT: D 424 ASP cc_start: 0.9044 (t70) cc_final: 0.8686 (t70) REVERT: D 653 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.5542 (p90) REVERT: D 700 GLN cc_start: 0.8958 (tp40) cc_final: 0.8518 (tp-100) REVERT: B 206 HIS cc_start: 0.8464 (m90) cc_final: 0.8182 (m-70) REVERT: B 324 LYS cc_start: 0.8894 (mttt) cc_final: 0.8459 (mmtt) REVERT: B 416 GLU cc_start: 0.7394 (tp30) cc_final: 0.7097 (tp30) REVERT: B 420 ARG cc_start: 0.8761 (tpp80) cc_final: 0.8392 (mmt90) REVERT: B 423 GLN cc_start: 0.9099 (tp-100) cc_final: 0.8648 (tp-100) REVERT: B 653 TYR cc_start: 0.6341 (OUTLIER) cc_final: 0.5391 (p90) REVERT: B 724 LYS cc_start: 0.8522 (tmtt) cc_final: 0.8309 (tmtt) REVERT: C 342 SER cc_start: 0.9091 (t) cc_final: 0.8802 (p) REVERT: C 343 SER cc_start: 0.8854 (m) cc_final: 0.8378 (p) REVERT: C 397 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7651 (mt-10) REVERT: C 420 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.8215 (mmm-85) REVERT: C 653 TYR cc_start: 0.6582 (OUTLIER) cc_final: 0.5070 (p90) REVERT: C 700 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8622 (tp40) REVERT: C 716 MET cc_start: 0.4966 (ptm) cc_final: 0.4572 (ptp) REVERT: C 724 LYS cc_start: 0.7993 (tmtt) cc_final: 0.7537 (tmtt) outliers start: 42 outliers final: 32 residues processed: 424 average time/residue: 0.2843 time to fit residues: 186.9909 Evaluate side-chains 419 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 383 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 741 CYS 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: 9.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 423 GLN D 270 ASN B 206 HIS B 285 ASN B 410 HIS B 628 ASN C 206 HIS C 285 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 18180 Z= 0.154 Angle : 0.503 8.395 24631 Z= 0.261 Chirality : 0.036 0.171 2756 Planarity : 0.004 0.043 3020 Dihedral : 8.036 86.746 2923 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.22 % Allowed : 15.82 % 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: 1.04 (0.19), residues: 2136 helix: 1.96 (0.15), residues: 1264 sheet: -0.66 (0.58), residues: 76 loop : -1.31 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 697 HIS 0.004 0.001 HIS A 378 PHE 0.046 0.001 PHE D 304 TYR 0.021 0.001 TYR C 309 ARG 0.003 0.000 ARG D 331 *********************** 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 446 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 404 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8013 (mt-10) REVERT: A 354 GLN cc_start: 0.8707 (mt0) cc_final: 0.8324 (mp10) REVERT: A 423 GLN cc_start: 0.8791 (tp40) cc_final: 0.8568 (tp-100) REVERT: A 584 TYR cc_start: 0.8474 (t80) cc_final: 0.8141 (t80) REVERT: A 636 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: A 700 GLN cc_start: 0.9033 (tp-100) cc_final: 0.8441 (tp-100) REVERT: A 707 ASP cc_start: 0.8859 (m-30) cc_final: 0.8569 (m-30) REVERT: A 745 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7662 (p0) REVERT: D 210 GLU cc_start: 0.8285 (tt0) cc_final: 0.7734 (mt-10) REVERT: D 270 ASN cc_start: 0.5975 (OUTLIER) cc_final: 0.5622 (p0) REVERT: D 354 GLN cc_start: 0.8770 (mt0) cc_final: 0.8413 (mp10) REVERT: D 410 HIS cc_start: 0.8391 (p-80) cc_final: 0.7887 (p90) REVERT: D 424 ASP cc_start: 0.8953 (t70) cc_final: 0.8606 (t70) REVERT: D 653 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.5554 (p90) REVERT: D 700 GLN cc_start: 0.8963 (tp40) cc_final: 0.8524 (tp-100) REVERT: B 324 LYS cc_start: 0.8918 (mttt) cc_final: 0.8481 (mmtt) REVERT: B 420 ARG cc_start: 0.8756 (tpp80) cc_final: 0.8507 (mmt90) REVERT: B 423 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8660 (tp-100) REVERT: B 653 TYR cc_start: 0.6319 (OUTLIER) cc_final: 0.5371 (p90) REVERT: B 724 LYS cc_start: 0.8485 (tmtt) cc_final: 0.8279 (tmtt) REVERT: C 342 SER cc_start: 0.9099 (t) cc_final: 0.8811 (p) REVERT: C 343 SER cc_start: 0.8871 (m) cc_final: 0.8388 (p) REVERT: C 378 HIS cc_start: 0.7250 (p90) cc_final: 0.6490 (p-80) REVERT: C 397 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7651 (mt-10) REVERT: C 420 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8205 (mmm-85) REVERT: C 653 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.5032 (p90) REVERT: C 700 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8639 (tp40) REVERT: C 716 MET cc_start: 0.4968 (ptm) cc_final: 0.4560 (ptp) REVERT: C 724 LYS cc_start: 0.8009 (tmtt) cc_final: 0.7582 (tmtt) REVERT: C 748 ASN cc_start: 0.8358 (t0) cc_final: 0.7981 (t0) outliers start: 42 outliers final: 32 residues processed: 427 average time/residue: 0.2596 time to fit residues: 174.3158 Evaluate side-chains 425 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 387 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 172 optimal weight: 0.4980 chunk 180 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 378 HIS D 206 HIS B 285 ASN B 410 HIS B 628 ASN C 206 HIS C 285 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18180 Z= 0.351 Angle : 0.587 9.636 24631 Z= 0.302 Chirality : 0.040 0.276 2756 Planarity : 0.004 0.043 3020 Dihedral : 8.414 87.962 2923 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.48 % Allowed : 16.30 % Favored : 81.22 % 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: 0.90 (0.19), residues: 2136 helix: 1.87 (0.15), residues: 1260 sheet: -0.77 (0.58), residues: 76 loop : -1.41 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 697 HIS 0.003 0.001 HIS A 358 PHE 0.050 0.001 PHE D 304 TYR 0.045 0.001 TYR C 309 ARG 0.003 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 428 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 381 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 TYR cc_start: 0.8689 (t80) cc_final: 0.8379 (t80) REVERT: A 636 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: A 700 GLN cc_start: 0.9055 (tp-100) cc_final: 0.8481 (tp-100) REVERT: A 707 ASP cc_start: 0.8872 (m-30) cc_final: 0.8571 (m-30) REVERT: A 745 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7538 (p0) REVERT: D 210 GLU cc_start: 0.8337 (tt0) cc_final: 0.7855 (mt-10) REVERT: D 354 GLN cc_start: 0.8738 (mt0) cc_final: 0.8330 (mp10) REVERT: D 410 HIS cc_start: 0.8390 (p-80) cc_final: 0.7843 (p90) REVERT: D 424 ASP cc_start: 0.9042 (t70) cc_final: 0.8655 (t70) REVERT: D 653 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.5639 (p90) REVERT: B 324 LYS cc_start: 0.8927 (mttt) cc_final: 0.8489 (mmtt) REVERT: B 416 GLU cc_start: 0.7365 (tp30) cc_final: 0.6917 (tp30) REVERT: B 653 TYR cc_start: 0.6376 (OUTLIER) cc_final: 0.5484 (p90) REVERT: C 313 LEU cc_start: 0.9183 (mt) cc_final: 0.8745 (mt) REVERT: C 342 SER cc_start: 0.9111 (t) cc_final: 0.8801 (p) REVERT: C 343 SER cc_start: 0.8870 (m) cc_final: 0.8370 (p) REVERT: C 389 THR cc_start: 0.8850 (m) cc_final: 0.8561 (p) REVERT: C 397 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7709 (mt-10) REVERT: C 420 ARG cc_start: 0.8583 (mmm-85) cc_final: 0.8223 (mmm-85) REVERT: C 653 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.5240 (p90) REVERT: C 700 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8641 (tp-100) REVERT: C 716 MET cc_start: 0.4961 (ptm) cc_final: 0.4545 (ptp) REVERT: C 724 LYS cc_start: 0.8196 (tmtt) cc_final: 0.7927 (tmtt) outliers start: 47 outliers final: 38 residues processed: 411 average time/residue: 0.2704 time to fit residues: 174.1149 Evaluate side-chains 415 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 372 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 741 CYS 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: 0.7980 chunk 95 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 378 HIS A 423 GLN D 206 HIS D 270 ASN B 410 HIS C 206 HIS C 285 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18180 Z= 0.177 Angle : 0.530 8.083 24631 Z= 0.274 Chirality : 0.037 0.192 2756 Planarity : 0.004 0.043 3020 Dihedral : 8.024 88.740 2923 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.11 % Allowed : 17.09 % Favored : 80.80 % 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: 0.98 (0.19), residues: 2136 helix: 2.00 (0.15), residues: 1236 sheet: -0.79 (0.58), residues: 76 loop : -1.37 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 697 HIS 0.002 0.001 HIS A 289 PHE 0.041 0.001 PHE D 304 TYR 0.013 0.001 TYR B 584 ARG 0.003 0.000 ARG A 331 ********************** 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: 40 poor density : 390 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 584 TYR cc_start: 0.8493 (t80) cc_final: 0.8150 (t80) REVERT: A 636 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: A 700 GLN cc_start: 0.9043 (tp-100) cc_final: 0.8463 (tp-100) REVERT: A 707 ASP cc_start: 0.8870 (m-30) cc_final: 0.8566 (m-30) REVERT: A 745 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7486 (p0) REVERT: D 210 GLU cc_start: 0.8267 (tt0) cc_final: 0.7834 (mt-10) REVERT: D 270 ASN cc_start: 0.5541 (OUTLIER) cc_final: 0.5122 (p0) REVERT: D 354 GLN cc_start: 0.8768 (mt0) cc_final: 0.8419 (mp10) REVERT: D 410 HIS cc_start: 0.8422 (p-80) cc_final: 0.7896 (p90) REVERT: D 424 ASP cc_start: 0.9026 (t70) cc_final: 0.8670 (t70) REVERT: D 653 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.5529 (p90) REVERT: D 700 GLN cc_start: 0.8970 (tp40) cc_final: 0.8518 (tp-100) REVERT: B 253 SER cc_start: 0.9046 (m) cc_final: 0.8832 (p) REVERT: B 266 PHE cc_start: 0.8745 (t80) cc_final: 0.8528 (t80) REVERT: B 324 LYS cc_start: 0.8890 (mttt) cc_final: 0.8464 (mmtt) REVERT: B 416 GLU cc_start: 0.7420 (tp30) cc_final: 0.6633 (tp30) REVERT: B 420 ARG cc_start: 0.8897 (tpp80) cc_final: 0.8505 (mmm-85) REVERT: B 423 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8691 (tp-100) REVERT: B 653 TYR cc_start: 0.6409 (OUTLIER) cc_final: 0.5447 (p90) REVERT: C 313 LEU cc_start: 0.9149 (mt) cc_final: 0.8869 (mt) REVERT: C 342 SER cc_start: 0.9122 (t) cc_final: 0.8803 (p) REVERT: C 343 SER cc_start: 0.8866 (m) cc_final: 0.8389 (p) REVERT: C 383 ASP cc_start: 0.7908 (t0) cc_final: 0.7360 (t0) REVERT: C 385 SER cc_start: 0.8931 (t) cc_final: 0.8366 (m) REVERT: C 389 THR cc_start: 0.8811 (m) cc_final: 0.8532 (p) REVERT: C 397 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7664 (mt-10) REVERT: C 420 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.8262 (mmm-85) REVERT: C 653 TYR cc_start: 0.6726 (OUTLIER) cc_final: 0.5310 (p90) REVERT: C 700 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8712 (tp-100) REVERT: C 716 MET cc_start: 0.4854 (ptm) cc_final: 0.4498 (ptp) REVERT: C 724 LYS cc_start: 0.8153 (tmtt) cc_final: 0.7681 (tmtt) outliers start: 40 outliers final: 32 residues processed: 412 average time/residue: 0.2633 time to fit residues: 169.9398 Evaluate side-chains 423 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 385 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 733 ASP Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 4.9990 chunk 51 optimal weight: 0.0570 chunk 155 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 0.0270 chunk 70 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 overall best weight: 1.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 378 HIS D 206 HIS B 410 HIS C 206 HIS C 285 ASN C 378 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.151916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101675 restraints weight = 28953.193| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.64 r_work: 0.3004 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.239 18180 Z= 0.250 Angle : 0.724 59.189 24631 Z= 0.416 Chirality : 0.039 0.698 2756 Planarity : 0.004 0.043 3020 Dihedral : 8.047 88.750 2923 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.16 % Allowed : 16.98 % Favored : 80.85 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.97 (0.19), residues: 2136 helix: 1.99 (0.15), residues: 1236 sheet: -0.80 (0.58), residues: 76 loop : -1.37 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 697 HIS 0.002 0.001 HIS A 289 PHE 0.042 0.001 PHE D 304 TYR 0.013 0.001 TYR B 584 ARG 0.002 0.000 ARG A 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4426.99 seconds wall clock time: 81 minutes 31.63 seconds (4891.63 seconds total)