Starting phenix.real_space_refine on Mon Apr 8 19:07:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2l_23132/04_2024/7l2l_23132_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2l_23132/04_2024/7l2l_23132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2l_23132/04_2024/7l2l_23132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2l_23132/04_2024/7l2l_23132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2l_23132/04_2024/7l2l_23132_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2l_23132/04_2024/7l2l_23132_updated.pdb" } resolution = 3.42 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= 0.003 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 9420 2.51 5 N 2244 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 367": "NH1" <-> "NH2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "C ARG 367": "NH1" <-> "NH2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D ARG 367": "NH1" <-> "NH2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B ARG 367": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14252 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3517 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 418} Chain breaks: 2 Chain: "C" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3517 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 418} Chain breaks: 2 Chain: "D" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3517 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 418} Chain breaks: 2 Chain: "B" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3517 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 418} Chain breaks: 2 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 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} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" 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: 7.53, per 1000 atoms: 0.53 Number of scatterers: 14252 At special positions: 0 Unit cell: (121.776, 122.808, 101.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2496 8.00 N 2244 7.00 C 9420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.94 Conformation dependent library (CDL) restraints added in 2.5 seconds 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 4 sheets defined 62.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 287 through 293 removed outlier: 3.529A pdb=" N VAL A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 354 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 409 through 414 removed outlier: 4.197A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 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: 4.315A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP A 549 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 598 removed outlier: 3.826A pdb=" N TYR A 565 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 566 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 567 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 572 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 573 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 575 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP A 576 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU A 577 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N CYS A 578 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 579 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 584 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 588 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 591 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 596 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 638 Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 673 through 711 removed outlier: 6.062A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) 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 409 through 414 removed outlier: 3.977A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 409 through 414' Processing helix chain 'C' and resid 416 through 428 Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 4.082A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP C 549 " --> pdb=" O ALA C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 598 removed outlier: 3.780A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 638 Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 673 through 711 removed outlier: 5.960A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 299 through 319 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 409 through 414 removed outlier: 4.176A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 409 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 503 through 505 No H-bonds generated for 'chain 'D' and resid 503 through 505' Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 4.121A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 575 Processing helix chain 'D' and resid 577 through 598 Processing helix chain 'D' and resid 630 through 638 Processing helix chain 'D' and resid 656 through 669 Processing helix chain 'D' and resid 673 through 711 removed outlier: 6.202A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 409 through 414 removed outlier: 4.132A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 409 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: 4.265A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 547 " --> pdb=" O SER B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 575 Processing helix chain 'B' and resid 577 through 598 Processing helix chain 'B' and resid 630 through 638 Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 711 removed outlier: 6.360A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 741 through 746 removed outlier: 3.723A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASP A 383 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS A 368 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 368 through 370 Processing sheet with id= C, first strand: chain 'D' and resid 368 through 370 Processing sheet with id= D, first strand: chain 'B' and resid 742 through 746 removed outlier: 3.720A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2106 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: 3.84 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2163 1.29 - 1.42: 4101 1.42 - 1.55: 8168 1.55 - 1.68: 24 1.68 - 1.81: 152 Bond restraints: 14608 Sorted by residual: bond pdb=" CAM 6EU B 901 " pdb=" OAC 6EU B 901 " ideal model delta sigma weight residual 1.422 1.166 0.256 2.00e-02 2.50e+03 1.63e+02 bond pdb=" CAM 6EU A 901 " pdb=" OAC 6EU A 901 " ideal model delta sigma weight residual 1.422 1.167 0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" CAM 6EU C 901 " pdb=" OAC 6EU C 901 " ideal model delta sigma weight residual 1.422 1.167 0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" CAM 6EU D 901 " pdb=" OAC 6EU D 901 " ideal model delta sigma weight residual 1.422 1.171 0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" CAV 6EU D 901 " pdb=" CBB 6EU D 901 " ideal model delta sigma weight residual 1.330 1.514 -0.184 2.00e-02 2.50e+03 8.43e+01 ... (remaining 14603 not shown) Histogram of bond angle deviations from ideal: 94.36 - 102.30: 56 102.30 - 110.24: 3370 110.24 - 118.18: 7566 118.18 - 126.12: 8646 126.12 - 134.06: 162 Bond angle restraints: 19800 Sorted by residual: angle pdb=" CAN 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAO 6EU B 901 " ideal model delta sigma weight residual 115.38 131.01 -15.63 3.00e+00 1.11e-01 2.71e+01 angle pdb=" CAN 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" OAA 6EU C 901 " ideal model delta sigma weight residual 110.99 95.68 15.31 3.00e+00 1.11e-01 2.60e+01 angle pdb=" CAN 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" CAO 6EU C 901 " ideal model delta sigma weight residual 115.38 130.55 -15.17 3.00e+00 1.11e-01 2.56e+01 angle pdb=" CAN 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" OAA 6EU B 901 " ideal model delta sigma weight residual 110.99 96.09 14.90 3.00e+00 1.11e-01 2.47e+01 angle pdb=" CAN 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" OAA 6EU A 901 " ideal model delta sigma weight residual 110.99 96.11 14.88 3.00e+00 1.11e-01 2.46e+01 ... (remaining 19795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 8111 17.73 - 35.47: 634 35.47 - 53.20: 72 53.20 - 70.94: 32 70.94 - 88.67: 11 Dihedral angle restraints: 8860 sinusoidal: 3776 harmonic: 5084 Sorted by residual: dihedral pdb=" CA LEU C 647 " pdb=" C LEU C 647 " pdb=" N GLU C 648 " pdb=" CA GLU C 648 " ideal model delta harmonic sigma weight residual 180.00 153.05 26.95 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA LEU B 647 " pdb=" C LEU B 647 " pdb=" N GLU B 648 " pdb=" CA GLU B 648 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA LEU A 647 " pdb=" C LEU A 647 " pdb=" N GLU A 648 " pdb=" CA GLU A 648 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 8857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 2197 0.143 - 0.285: 31 0.285 - 0.427: 1 0.427 - 0.570: 7 0.570 - 0.712: 4 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CAJ 6EU B 901 " pdb=" CAK 6EU B 901 " pdb=" CAN 6EU B 901 " pdb=" CAO 6EU B 901 " both_signs ideal model delta sigma weight residual False 2.66 1.94 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CAJ 6EU C 901 " pdb=" CAK 6EU C 901 " pdb=" CAN 6EU C 901 " pdb=" CAO 6EU C 901 " both_signs ideal model delta sigma weight residual False 2.66 1.95 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CAJ 6EU A 901 " pdb=" CAK 6EU A 901 " pdb=" CAN 6EU A 901 " pdb=" CAO 6EU A 901 " both_signs ideal model delta sigma weight residual False 2.66 2.02 0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 2237 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM 6EU D 901 " -0.118 2.00e-02 2.50e+03 2.07e-01 4.30e+02 pdb=" CAV 6EU D 901 " 0.359 2.00e-02 2.50e+03 pdb=" CBB 6EU D 901 " -0.123 2.00e-02 2.50e+03 pdb=" CBD 6EU D 901 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU B 901 " 0.118 2.00e-02 2.50e+03 2.07e-01 4.30e+02 pdb=" CAV 6EU B 901 " -0.359 2.00e-02 2.50e+03 pdb=" CBB 6EU B 901 " 0.123 2.00e-02 2.50e+03 pdb=" CBD 6EU B 901 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM 6EU A 901 " 0.118 2.00e-02 2.50e+03 2.07e-01 4.29e+02 pdb=" CAV 6EU A 901 " -0.359 2.00e-02 2.50e+03 pdb=" CBB 6EU A 901 " 0.124 2.00e-02 2.50e+03 pdb=" CBD 6EU A 901 " 0.117 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 140 2.55 - 3.14: 12673 3.14 - 3.72: 22643 3.72 - 4.31: 31787 4.31 - 4.90: 52715 Nonbonded interactions: 119958 Sorted by model distance: nonbonded pdb=" O LEU A 588 " pdb=" OG SER A 592 " model vdw 1.961 2.440 nonbonded pdb=" O LEU C 588 " pdb=" OG SER C 592 " model vdw 1.972 2.440 nonbonded pdb=" O LEU D 588 " pdb=" OG SER D 592 " model vdw 1.984 2.440 nonbonded pdb=" OG SER C 512 " pdb=" OAI 6EU C 901 " model vdw 2.075 2.440 nonbonded pdb=" OG SER D 512 " pdb=" OAI 6EU D 901 " model vdw 2.076 2.440 ... (remaining 119953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.990 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: 5.950 Check model and map are aligned: 0.190 Set scattering table: 0.140 Process input model: 39.460 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 0.016 0.256 14608 Z= 1.042 Angle : 1.142 15.627 19800 Z= 0.577 Chirality : 0.069 0.712 2240 Planarity : 0.010 0.207 2400 Dihedral : 13.071 88.671 5588 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.19), residues: 1692 helix: 0.33 (0.14), residues: 1124 sheet: -1.23 (0.65), residues: 68 loop : -1.70 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 740 HIS 0.008 0.002 HIS A 358 PHE 0.029 0.003 PHE A 659 TYR 0.019 0.003 TYR C 441 ARG 0.005 0.001 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 646 time to evaluate : 1.723 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 475 VAL cc_start: 0.9208 (p) cc_final: 0.8721 (t) REVERT: A 478 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7410 (mt-10) REVERT: A 494 GLN cc_start: 0.8210 (mt0) cc_final: 0.7990 (tt0) REVERT: A 551 ASN cc_start: 0.9081 (m-40) cc_final: 0.8740 (m-40) REVERT: A 561 GLN cc_start: 0.8079 (tt0) cc_final: 0.6898 (pm20) REVERT: A 568 MET cc_start: 0.7729 (mtp) cc_final: 0.7513 (mtp) REVERT: A 577 LEU cc_start: 0.9166 (tp) cc_final: 0.8945 (tt) REVERT: A 629 SER cc_start: 0.8544 (p) cc_final: 0.8180 (m) REVERT: A 681 LEU cc_start: 0.8403 (mt) cc_final: 0.7767 (mt) REVERT: C 345 LYS cc_start: 0.8506 (mmtm) cc_final: 0.8213 (mmmm) REVERT: C 397 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7835 (mt-10) REVERT: C 425 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8740 (mtmt) REVERT: C 431 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8709 (ttpt) REVERT: C 474 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.6128 (mpt180) REVERT: C 478 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7690 (mt-10) REVERT: C 551 ASN cc_start: 0.8982 (m-40) cc_final: 0.8562 (m-40) REVERT: C 569 ILE cc_start: 0.9214 (mt) cc_final: 0.9009 (mt) REVERT: C 570 GLU cc_start: 0.8138 (tt0) cc_final: 0.7873 (tt0) REVERT: C 629 SER cc_start: 0.8550 (p) cc_final: 0.8237 (m) REVERT: C 673 LEU cc_start: 0.8348 (tp) cc_final: 0.8118 (tp) REVERT: D 401 TYR cc_start: 0.7300 (m-80) cc_final: 0.7011 (m-80) REVERT: D 432 ARG cc_start: 0.7684 (mmt180) cc_final: 0.7380 (mmt180) REVERT: D 478 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7357 (mt-10) REVERT: D 551 ASN cc_start: 0.8992 (m-40) cc_final: 0.8699 (m-40) REVERT: D 577 LEU cc_start: 0.9156 (tp) cc_final: 0.8910 (tt) REVERT: D 629 SER cc_start: 0.8545 (p) cc_final: 0.8198 (m) REVERT: D 672 ILE cc_start: 0.7743 (mm) cc_final: 0.7282 (mt) REVERT: D 696 ILE cc_start: 0.8577 (tt) cc_final: 0.8364 (mt) REVERT: D 740 TRP cc_start: 0.7012 (m100) cc_final: 0.6747 (m-10) REVERT: B 304 PHE cc_start: 0.7674 (t80) cc_final: 0.7458 (t80) REVERT: B 368 LYS cc_start: 0.7176 (pptt) cc_final: 0.6962 (pttt) REVERT: B 425 LYS cc_start: 0.8732 (mtpt) cc_final: 0.7779 (mtmt) REVERT: B 429 PHE cc_start: 0.7569 (p90) cc_final: 0.6679 (t80) REVERT: B 431 LYS cc_start: 0.8904 (ttmt) cc_final: 0.8686 (ttpt) REVERT: B 466 LYS cc_start: 0.7993 (mmtm) cc_final: 0.7545 (tptt) REVERT: B 474 ARG cc_start: 0.7844 (ttp-110) cc_final: 0.6200 (mmt180) REVERT: B 478 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7760 (mt-10) REVERT: B 551 ASN cc_start: 0.9180 (m-40) cc_final: 0.8733 (m110) REVERT: B 629 SER cc_start: 0.8521 (p) cc_final: 0.8224 (m) REVERT: B 681 LEU cc_start: 0.8507 (mt) cc_final: 0.7465 (mt) outliers start: 1 outliers final: 1 residues processed: 647 average time/residue: 0.3056 time to fit residues: 273.5696 Evaluate side-chains 476 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 475 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN C 297 ASN C 310 ASN C 320 HIS C 498 GLN D 297 ASN D 533 GLN D 687 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14608 Z= 0.214 Angle : 0.610 7.523 19800 Z= 0.324 Chirality : 0.039 0.215 2240 Planarity : 0.004 0.032 2400 Dihedral : 7.512 76.367 2274 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.84 % Allowed : 13.05 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1692 helix: 0.91 (0.15), residues: 1112 sheet: -1.38 (0.60), residues: 68 loop : -1.64 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 697 HIS 0.004 0.001 HIS C 320 PHE 0.023 0.002 PHE C 659 TYR 0.020 0.002 TYR D 351 ARG 0.006 0.000 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 593 time to evaluate : 1.577 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: symmetry clash REVERT: A 387 ILE cc_start: 0.8604 (mm) cc_final: 0.8337 (mm) REVERT: A 431 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8763 (tttt) REVERT: A 475 VAL cc_start: 0.9221 (p) cc_final: 0.8753 (t) REVERT: A 480 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8577 (mt) REVERT: A 551 ASN cc_start: 0.8966 (m-40) cc_final: 0.8568 (m110) REVERT: A 555 TYR cc_start: 0.9029 (m-80) cc_final: 0.8413 (m-80) REVERT: A 561 GLN cc_start: 0.7721 (tt0) cc_final: 0.6643 (pm20) REVERT: A 629 SER cc_start: 0.8281 (p) cc_final: 0.8059 (m) REVERT: A 681 LEU cc_start: 0.8204 (mt) cc_final: 0.7807 (mt) REVERT: A 700 GLN cc_start: 0.8434 (tp40) cc_final: 0.7536 (tm-30) REVERT: A 743 ARG cc_start: 0.7608 (mtp85) cc_final: 0.6939 (mpt180) REVERT: C 364 HIS cc_start: 0.6556 (p-80) cc_final: 0.5937 (m90) REVERT: C 480 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8608 (mp) REVERT: C 551 ASN cc_start: 0.8890 (m-40) cc_final: 0.8353 (m-40) REVERT: C 555 TYR cc_start: 0.9168 (m-80) cc_final: 0.8915 (m-80) REVERT: C 629 SER cc_start: 0.8277 (p) cc_final: 0.8041 (m) REVERT: C 695 ASN cc_start: 0.6928 (m-40) cc_final: 0.6400 (m-40) REVERT: D 401 TYR cc_start: 0.7273 (m-80) cc_final: 0.6877 (m-80) REVERT: D 412 MET cc_start: 0.8673 (ttm) cc_final: 0.8297 (ttm) REVERT: D 426 TRP cc_start: 0.8914 (t-100) cc_final: 0.8559 (t-100) REVERT: D 432 ARG cc_start: 0.7441 (mmt180) cc_final: 0.7177 (mmt180) REVERT: D 478 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7405 (mt-10) REVERT: D 480 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8609 (mp) REVERT: D 494 GLN cc_start: 0.8644 (tt0) cc_final: 0.8349 (tm-30) REVERT: D 550 THR cc_start: 0.9160 (p) cc_final: 0.8960 (p) REVERT: D 551 ASN cc_start: 0.8781 (m-40) cc_final: 0.8325 (m-40) REVERT: D 555 TYR cc_start: 0.8999 (m-80) cc_final: 0.8635 (m-80) REVERT: D 557 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8382 (mtp180) REVERT: D 570 GLU cc_start: 0.8074 (tt0) cc_final: 0.7870 (tt0) REVERT: D 629 SER cc_start: 0.8257 (p) cc_final: 0.7950 (m) REVERT: D 653 TYR cc_start: 0.7787 (p90) cc_final: 0.7569 (p90) REVERT: D 696 ILE cc_start: 0.8330 (tt) cc_final: 0.8124 (mt) REVERT: B 426 TRP cc_start: 0.8967 (t-100) cc_final: 0.8610 (t-100) REVERT: B 466 LYS cc_start: 0.7913 (mmtm) cc_final: 0.7506 (tptt) REVERT: B 551 ASN cc_start: 0.8983 (m-40) cc_final: 0.8540 (m110) REVERT: B 568 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7691 (mtp) REVERT: B 629 SER cc_start: 0.8269 (p) cc_final: 0.7994 (m) REVERT: B 637 LEU cc_start: 0.9066 (mp) cc_final: 0.8792 (mp) REVERT: B 662 LEU cc_start: 0.8834 (mt) cc_final: 0.8474 (mt) REVERT: B 687 ASN cc_start: 0.6507 (OUTLIER) cc_final: 0.6234 (m-40) REVERT: B 689 ILE cc_start: 0.7449 (mm) cc_final: 0.7191 (mm) REVERT: B 695 ASN cc_start: 0.7449 (m-40) cc_final: 0.6866 (m-40) REVERT: B 700 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7140 (tm-30) REVERT: B 701 ARG cc_start: 0.8642 (tpp80) cc_final: 0.8431 (mmm-85) outliers start: 44 outliers final: 17 residues processed: 611 average time/residue: 0.2642 time to fit residues: 232.6847 Evaluate side-chains 542 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 520 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 310 ASN C 498 GLN D 297 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 HIS B 498 GLN B 560 GLN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14608 Z= 0.294 Angle : 0.601 7.208 19800 Z= 0.323 Chirality : 0.040 0.155 2240 Planarity : 0.004 0.032 2400 Dihedral : 7.473 71.600 2274 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.97 % Allowed : 17.83 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1692 helix: 0.83 (0.15), residues: 1112 sheet: -1.36 (0.61), residues: 68 loop : -1.53 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 697 HIS 0.004 0.001 HIS B 364 PHE 0.026 0.002 PHE B 438 TYR 0.021 0.002 TYR D 511 ARG 0.005 0.000 ARG D 721 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 548 time to evaluate : 1.447 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 432 ARG cc_start: 0.7449 (mmt180) cc_final: 0.7157 (mmt180) REVERT: A 551 ASN cc_start: 0.9063 (m-40) cc_final: 0.8671 (m110) REVERT: A 555 TYR cc_start: 0.8996 (m-80) cc_final: 0.8352 (m-80) REVERT: A 561 GLN cc_start: 0.7709 (tt0) cc_final: 0.6607 (pm20) REVERT: A 629 SER cc_start: 0.8344 (p) cc_final: 0.8136 (m) REVERT: A 653 TYR cc_start: 0.7879 (p90) cc_final: 0.7589 (p90) REVERT: A 681 LEU cc_start: 0.8252 (mt) cc_final: 0.7832 (mt) REVERT: A 694 LYS cc_start: 0.8899 (tptt) cc_final: 0.8675 (ptmt) REVERT: A 695 ASN cc_start: 0.7387 (m-40) cc_final: 0.6945 (m-40) REVERT: A 698 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8237 (mptt) REVERT: A 700 GLN cc_start: 0.8406 (tp40) cc_final: 0.7546 (tm-30) REVERT: A 706 LEU cc_start: 0.9169 (mp) cc_final: 0.8946 (mp) REVERT: A 720 PHE cc_start: 0.5717 (m-80) cc_final: 0.5374 (p90) REVERT: A 743 ARG cc_start: 0.7712 (mtp85) cc_final: 0.7011 (mpt180) REVERT: C 364 HIS cc_start: 0.6704 (p-80) cc_final: 0.6039 (m90) REVERT: C 474 ARG cc_start: 0.7790 (ttp-110) cc_final: 0.6405 (mpt180) REVERT: C 551 ASN cc_start: 0.8979 (m-40) cc_final: 0.8464 (m110) REVERT: C 570 GLU cc_start: 0.8081 (tt0) cc_final: 0.7876 (tt0) REVERT: C 579 ARG cc_start: 0.7488 (ptp-170) cc_final: 0.6943 (mtm-85) REVERT: D 297 ASN cc_start: 0.7404 (m-40) cc_final: 0.7106 (m-40) REVERT: D 397 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7794 (mt-10) REVERT: D 401 TYR cc_start: 0.7312 (m-80) cc_final: 0.6925 (m-80) REVERT: D 412 MET cc_start: 0.8569 (ttm) cc_final: 0.8318 (ttm) REVERT: D 425 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8593 (mtpt) REVERT: D 429 PHE cc_start: 0.7440 (p90) cc_final: 0.6983 (t80) REVERT: D 432 ARG cc_start: 0.7414 (mmt180) cc_final: 0.7165 (mmt180) REVERT: D 478 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7242 (mt-10) REVERT: D 480 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8734 (mp) REVERT: D 550 THR cc_start: 0.9158 (p) cc_final: 0.8956 (p) REVERT: D 551 ASN cc_start: 0.8809 (m-40) cc_final: 0.8410 (m110) REVERT: D 557 ARG cc_start: 0.8614 (mtp85) cc_final: 0.8390 (mtp180) REVERT: D 570 GLU cc_start: 0.8174 (tt0) cc_final: 0.7952 (tt0) REVERT: D 653 TYR cc_start: 0.7849 (p90) cc_final: 0.7629 (p90) REVERT: B 429 PHE cc_start: 0.7379 (p90) cc_final: 0.7021 (t80) REVERT: B 466 LYS cc_start: 0.7945 (mmtm) cc_final: 0.7473 (tptt) REVERT: B 474 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.6348 (mpt180) REVERT: B 498 GLN cc_start: 0.7763 (pt0) cc_final: 0.7470 (pt0) REVERT: B 551 ASN cc_start: 0.9032 (m-40) cc_final: 0.8632 (m110) REVERT: B 568 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7466 (mtp) REVERT: B 572 MET cc_start: 0.8133 (ttp) cc_final: 0.7429 (ttp) REVERT: B 662 LEU cc_start: 0.8891 (mt) cc_final: 0.8517 (mt) REVERT: B 687 ASN cc_start: 0.6506 (OUTLIER) cc_final: 0.6131 (m-40) REVERT: B 689 ILE cc_start: 0.7541 (mm) cc_final: 0.7011 (mt) REVERT: B 694 LYS cc_start: 0.8513 (ptmt) cc_final: 0.8290 (pptt) REVERT: B 695 ASN cc_start: 0.7444 (m-40) cc_final: 0.6731 (m-40) REVERT: B 700 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7120 (tm-30) outliers start: 46 outliers final: 27 residues processed: 564 average time/residue: 0.2731 time to fit residues: 219.9750 Evaluate side-chains 520 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 490 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 498 GLN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 560 GLN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14608 Z= 0.187 Angle : 0.558 7.654 19800 Z= 0.301 Chirality : 0.038 0.185 2240 Planarity : 0.003 0.028 2400 Dihedral : 7.100 61.942 2274 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.17 % Allowed : 18.54 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1692 helix: 1.12 (0.15), residues: 1100 sheet: -1.33 (0.61), residues: 68 loop : -1.39 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 697 HIS 0.003 0.001 HIS A 358 PHE 0.016 0.001 PHE C 438 TYR 0.022 0.001 TYR D 351 ARG 0.005 0.000 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 552 time to evaluate : 1.570 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 387 ILE cc_start: 0.8604 (mm) cc_final: 0.8158 (mm) REVERT: A 432 ARG cc_start: 0.7430 (mmt180) cc_final: 0.7119 (mmt180) REVERT: A 533 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7247 (mm-40) REVERT: A 547 MET cc_start: 0.8118 (mtp) cc_final: 0.7877 (mtp) REVERT: A 551 ASN cc_start: 0.8979 (m-40) cc_final: 0.8503 (m110) REVERT: A 555 TYR cc_start: 0.8895 (m-80) cc_final: 0.8238 (m-80) REVERT: A 561 GLN cc_start: 0.7492 (tt0) cc_final: 0.6410 (pm20) REVERT: A 637 LEU cc_start: 0.9007 (mp) cc_final: 0.8767 (mm) REVERT: A 647 LEU cc_start: 0.8993 (tp) cc_final: 0.8732 (mt) REVERT: A 653 TYR cc_start: 0.7704 (p90) cc_final: 0.7414 (p90) REVERT: A 681 LEU cc_start: 0.8127 (mt) cc_final: 0.7688 (mt) REVERT: A 694 LYS cc_start: 0.8879 (tptt) cc_final: 0.8398 (ptmt) REVERT: A 695 ASN cc_start: 0.7326 (m-40) cc_final: 0.6697 (m-40) REVERT: A 697 TRP cc_start: 0.8154 (t60) cc_final: 0.7751 (t60) REVERT: A 698 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8037 (mtmt) REVERT: A 700 GLN cc_start: 0.8291 (tp40) cc_final: 0.7456 (tm-30) REVERT: A 706 LEU cc_start: 0.9188 (mp) cc_final: 0.8931 (mp) REVERT: A 720 PHE cc_start: 0.5595 (m-80) cc_final: 0.5249 (p90) REVERT: C 364 HIS cc_start: 0.6673 (p-80) cc_final: 0.6002 (m90) REVERT: C 425 LYS cc_start: 0.8965 (mtmt) cc_final: 0.8623 (mtpp) REVERT: C 428 ARG cc_start: 0.7911 (tmt170) cc_final: 0.7629 (tmt170) REVERT: C 474 ARG cc_start: 0.7772 (ttp-110) cc_final: 0.6480 (mpt180) REVERT: C 551 ASN cc_start: 0.8962 (m-40) cc_final: 0.8415 (m110) REVERT: C 579 ARG cc_start: 0.7421 (ptp-170) cc_final: 0.6773 (mtm180) REVERT: C 653 TYR cc_start: 0.7634 (p90) cc_final: 0.7351 (p90) REVERT: C 695 ASN cc_start: 0.6873 (m-40) cc_final: 0.6633 (m-40) REVERT: C 706 LEU cc_start: 0.9199 (mp) cc_final: 0.8975 (mp) REVERT: D 297 ASN cc_start: 0.7288 (m-40) cc_final: 0.6980 (m-40) REVERT: D 397 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7749 (mt-10) REVERT: D 412 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8181 (ttm) REVERT: D 432 ARG cc_start: 0.7325 (mmt180) cc_final: 0.7096 (mmt180) REVERT: D 480 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8740 (mp) REVERT: D 551 ASN cc_start: 0.8694 (m-40) cc_final: 0.8284 (m-40) REVERT: D 653 TYR cc_start: 0.7715 (p90) cc_final: 0.7495 (p90) REVERT: D 720 PHE cc_start: 0.5528 (m-10) cc_final: 0.5274 (m-10) REVERT: D 740 TRP cc_start: 0.6512 (m-10) cc_final: 0.6302 (m-10) REVERT: B 466 LYS cc_start: 0.7906 (mmtm) cc_final: 0.7436 (tptt) REVERT: B 474 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.6443 (mpt180) REVERT: B 551 ASN cc_start: 0.8984 (m-40) cc_final: 0.8532 (m110) REVERT: B 568 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7705 (mtp) REVERT: B 687 ASN cc_start: 0.6438 (OUTLIER) cc_final: 0.5984 (m-40) REVERT: B 695 ASN cc_start: 0.7357 (m-40) cc_final: 0.6652 (m-40) REVERT: B 706 LEU cc_start: 0.9219 (mp) cc_final: 0.8975 (mp) outliers start: 49 outliers final: 25 residues processed: 566 average time/residue: 0.2754 time to fit residues: 222.4282 Evaluate side-chains 533 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 503 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 498 GLN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 310 ASN B 560 GLN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14608 Z= 0.301 Angle : 0.599 8.820 19800 Z= 0.321 Chirality : 0.040 0.163 2240 Planarity : 0.004 0.029 2400 Dihedral : 7.250 63.650 2274 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.55 % Allowed : 19.06 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1692 helix: 1.05 (0.15), residues: 1096 sheet: -1.23 (0.63), residues: 68 loop : -1.48 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 697 HIS 0.005 0.001 HIS D 358 PHE 0.016 0.002 PHE C 438 TYR 0.018 0.002 TYR C 441 ARG 0.007 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 506 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 ARG cc_start: 0.7370 (mmt180) cc_final: 0.7085 (mmt180) REVERT: A 551 ASN cc_start: 0.9056 (m-40) cc_final: 0.8670 (m110) REVERT: A 555 TYR cc_start: 0.9008 (m-80) cc_final: 0.8308 (m-80) REVERT: A 561 GLN cc_start: 0.7715 (tt0) cc_final: 0.6539 (pm20) REVERT: A 681 LEU cc_start: 0.8283 (mt) cc_final: 0.7885 (mt) REVERT: A 695 ASN cc_start: 0.7359 (m-40) cc_final: 0.6910 (m-40) REVERT: A 697 TRP cc_start: 0.8315 (t60) cc_final: 0.8093 (t60) REVERT: A 698 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8055 (mtmt) REVERT: A 700 GLN cc_start: 0.8257 (tp40) cc_final: 0.7360 (tm-30) REVERT: A 706 LEU cc_start: 0.9194 (mp) cc_final: 0.8889 (mp) REVERT: A 720 PHE cc_start: 0.5567 (m-80) cc_final: 0.5246 (p90) REVERT: A 743 ARG cc_start: 0.7798 (mtp85) cc_final: 0.7038 (mpt180) REVERT: C 364 HIS cc_start: 0.6706 (p-80) cc_final: 0.6060 (m90) REVERT: C 428 ARG cc_start: 0.7927 (tmt170) cc_final: 0.7516 (tmt170) REVERT: C 474 ARG cc_start: 0.7904 (ttp-110) cc_final: 0.5807 (mpt180) REVERT: C 498 GLN cc_start: 0.7692 (pt0) cc_final: 0.7467 (pt0) REVERT: C 551 ASN cc_start: 0.9023 (m-40) cc_final: 0.8516 (m110) REVERT: C 570 GLU cc_start: 0.8073 (tt0) cc_final: 0.7787 (tt0) REVERT: C 579 ARG cc_start: 0.7498 (ptp-170) cc_final: 0.6900 (mtm-85) REVERT: D 297 ASN cc_start: 0.7233 (m-40) cc_final: 0.6913 (m-40) REVERT: D 397 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7779 (mt-10) REVERT: D 425 LYS cc_start: 0.8506 (mttt) cc_final: 0.8071 (mmmt) REVERT: D 432 ARG cc_start: 0.7383 (mmt180) cc_final: 0.7144 (mmt180) REVERT: D 480 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8794 (mp) REVERT: D 551 ASN cc_start: 0.8722 (m-40) cc_final: 0.8368 (m110) REVERT: D 570 GLU cc_start: 0.8163 (tt0) cc_final: 0.7939 (tt0) REVERT: D 653 TYR cc_start: 0.7821 (p90) cc_final: 0.7616 (p90) REVERT: B 466 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7447 (tptt) REVERT: B 474 ARG cc_start: 0.7877 (ttp-110) cc_final: 0.5752 (mpt180) REVERT: B 551 ASN cc_start: 0.9038 (m-40) cc_final: 0.8688 (m110) REVERT: B 568 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7468 (mtp) REVERT: B 572 MET cc_start: 0.8161 (ttp) cc_final: 0.7878 (ttp) REVERT: B 700 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7182 (tm-30) outliers start: 55 outliers final: 39 residues processed: 520 average time/residue: 0.2642 time to fit residues: 198.0024 Evaluate side-chains 510 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 469 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 557 ARG Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 310 ASN B 498 GLN B 560 GLN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14608 Z= 0.202 Angle : 0.574 9.384 19800 Z= 0.308 Chirality : 0.039 0.250 2240 Planarity : 0.003 0.028 2400 Dihedral : 7.000 60.780 2274 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.65 % Allowed : 19.83 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1692 helix: 1.11 (0.15), residues: 1100 sheet: -1.24 (0.62), residues: 68 loop : -1.44 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 697 HIS 0.003 0.001 HIS D 358 PHE 0.027 0.001 PHE C 438 TYR 0.025 0.001 TYR C 351 ARG 0.007 0.000 ARG D 721 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 526 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8104 (tmt170) cc_final: 0.7790 (tmt170) REVERT: A 432 ARG cc_start: 0.7378 (mmt180) cc_final: 0.7089 (mmt180) REVERT: A 551 ASN cc_start: 0.8973 (m-40) cc_final: 0.8563 (m110) REVERT: A 555 TYR cc_start: 0.9011 (m-80) cc_final: 0.8488 (m-80) REVERT: A 561 GLN cc_start: 0.7597 (tt0) cc_final: 0.6463 (pm20) REVERT: A 637 LEU cc_start: 0.9025 (mp) cc_final: 0.8655 (mm) REVERT: A 653 TYR cc_start: 0.7753 (p90) cc_final: 0.7465 (p90) REVERT: A 681 LEU cc_start: 0.8226 (mt) cc_final: 0.7798 (mt) REVERT: A 694 LYS cc_start: 0.9029 (tptt) cc_final: 0.8803 (tptt) REVERT: A 695 ASN cc_start: 0.7267 (m-40) cc_final: 0.6624 (m-40) REVERT: A 697 TRP cc_start: 0.8351 (t60) cc_final: 0.8092 (t60) REVERT: A 698 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8021 (mtmt) REVERT: A 700 GLN cc_start: 0.8292 (tp40) cc_final: 0.7373 (tm-30) REVERT: A 743 ARG cc_start: 0.7752 (mtp85) cc_final: 0.6897 (mpt180) REVERT: C 364 HIS cc_start: 0.6705 (p-80) cc_final: 0.6050 (m90) REVERT: C 412 MET cc_start: 0.8532 (ttm) cc_final: 0.7913 (ttm) REVERT: C 474 ARG cc_start: 0.7716 (ttp-110) cc_final: 0.6168 (mpt180) REVERT: C 478 GLU cc_start: 0.8156 (mp0) cc_final: 0.7809 (mp0) REVERT: C 551 ASN cc_start: 0.9000 (m-40) cc_final: 0.8482 (m110) REVERT: C 570 GLU cc_start: 0.7994 (tt0) cc_final: 0.7736 (tt0) REVERT: C 653 TYR cc_start: 0.7643 (p90) cc_final: 0.7411 (p90) REVERT: D 297 ASN cc_start: 0.7267 (m-40) cc_final: 0.6956 (m-40) REVERT: D 397 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7776 (mt-10) REVERT: D 425 LYS cc_start: 0.8440 (mttt) cc_final: 0.8173 (mmmt) REVERT: D 432 ARG cc_start: 0.7368 (mmt180) cc_final: 0.7134 (mmt180) REVERT: D 551 ASN cc_start: 0.8625 (m-40) cc_final: 0.8320 (m-40) REVERT: D 653 TYR cc_start: 0.7682 (p90) cc_final: 0.7476 (p90) REVERT: B 408 ASN cc_start: 0.7700 (m110) cc_final: 0.6924 (t0) REVERT: B 466 LYS cc_start: 0.7891 (mmtm) cc_final: 0.7442 (tptt) REVERT: B 474 ARG cc_start: 0.7723 (ttp-110) cc_final: 0.6159 (mpt180) REVERT: B 478 GLU cc_start: 0.8195 (mp0) cc_final: 0.7871 (mp0) REVERT: B 480 LEU cc_start: 0.9135 (mt) cc_final: 0.8905 (mm) REVERT: B 551 ASN cc_start: 0.9003 (m-40) cc_final: 0.8628 (m110) REVERT: B 568 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7539 (mtp) REVERT: B 694 LYS cc_start: 0.8453 (pptt) cc_final: 0.8220 (tmtt) outliers start: 41 outliers final: 32 residues processed: 537 average time/residue: 0.2931 time to fit residues: 228.5552 Evaluate side-chains 519 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 486 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 101 optimal weight: 0.0270 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 310 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14608 Z= 0.190 Angle : 0.570 9.967 19800 Z= 0.305 Chirality : 0.039 0.210 2240 Planarity : 0.003 0.028 2400 Dihedral : 6.959 60.644 2274 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.04 % Allowed : 19.90 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1692 helix: 1.15 (0.15), residues: 1096 sheet: -1.22 (0.63), residues: 68 loop : -1.45 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 740 HIS 0.002 0.001 HIS D 358 PHE 0.031 0.001 PHE B 438 TYR 0.021 0.001 TYR D 511 ARG 0.007 0.000 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 512 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ASN cc_start: 0.7439 (m110) cc_final: 0.7090 (t0) REVERT: A 412 MET cc_start: 0.8265 (ttm) cc_final: 0.7764 (ttm) REVERT: A 551 ASN cc_start: 0.9000 (m-40) cc_final: 0.8574 (m110) REVERT: A 555 TYR cc_start: 0.8968 (m-80) cc_final: 0.8419 (m-80) REVERT: A 561 GLN cc_start: 0.7551 (tt0) cc_final: 0.6379 (pm20) REVERT: A 637 LEU cc_start: 0.8996 (mp) cc_final: 0.8690 (mm) REVERT: A 653 TYR cc_start: 0.7693 (p90) cc_final: 0.7420 (p90) REVERT: A 695 ASN cc_start: 0.7282 (m-40) cc_final: 0.6657 (m-40) REVERT: A 700 GLN cc_start: 0.8286 (tp40) cc_final: 0.7399 (tm-30) REVERT: A 706 LEU cc_start: 0.9184 (mp) cc_final: 0.8847 (mp) REVERT: A 720 PHE cc_start: 0.5601 (m-10) cc_final: 0.5397 (p90) REVERT: A 743 ARG cc_start: 0.7786 (mtp85) cc_final: 0.6916 (mpt180) REVERT: C 364 HIS cc_start: 0.6699 (p-80) cc_final: 0.6049 (m90) REVERT: C 412 MET cc_start: 0.8558 (ttm) cc_final: 0.8006 (ttm) REVERT: C 474 ARG cc_start: 0.7686 (ttp-110) cc_final: 0.5705 (mpt180) REVERT: C 478 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: C 498 GLN cc_start: 0.7785 (pt0) cc_final: 0.7166 (pt0) REVERT: C 551 ASN cc_start: 0.9016 (m-40) cc_final: 0.8514 (m110) REVERT: C 570 GLU cc_start: 0.8052 (tt0) cc_final: 0.7763 (tt0) REVERT: C 647 LEU cc_start: 0.9039 (tp) cc_final: 0.8683 (tp) REVERT: D 297 ASN cc_start: 0.7240 (m-40) cc_final: 0.6937 (m-40) REVERT: D 397 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7848 (mt-10) REVERT: D 425 LYS cc_start: 0.8491 (mttt) cc_final: 0.8248 (mmmt) REVERT: D 432 ARG cc_start: 0.7328 (mmt180) cc_final: 0.7093 (mmt180) REVERT: D 551 ASN cc_start: 0.8626 (m-40) cc_final: 0.8277 (m-40) REVERT: B 408 ASN cc_start: 0.7641 (m110) cc_final: 0.6898 (t0) REVERT: B 466 LYS cc_start: 0.7913 (mmtm) cc_final: 0.7374 (tptt) REVERT: B 472 TYR cc_start: 0.6972 (m-80) cc_final: 0.6770 (m-10) REVERT: B 474 ARG cc_start: 0.7669 (ttp-110) cc_final: 0.6071 (mpt180) REVERT: B 478 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: B 480 LEU cc_start: 0.9136 (mt) cc_final: 0.8893 (mm) REVERT: B 551 ASN cc_start: 0.9011 (m-40) cc_final: 0.8643 (m110) REVERT: B 568 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7804 (mtp) REVERT: B 694 LYS cc_start: 0.8459 (pptt) cc_final: 0.8224 (tmtt) REVERT: B 700 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7168 (tm-30) outliers start: 47 outliers final: 37 residues processed: 526 average time/residue: 0.2618 time to fit residues: 200.5164 Evaluate side-chains 533 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 493 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 110 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14608 Z= 0.191 Angle : 0.601 11.870 19800 Z= 0.317 Chirality : 0.039 0.278 2240 Planarity : 0.003 0.027 2400 Dihedral : 6.915 60.987 2274 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.84 % Allowed : 20.61 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1692 helix: 1.14 (0.15), residues: 1096 sheet: -1.26 (0.63), residues: 68 loop : -1.45 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 697 HIS 0.002 0.001 HIS A 410 PHE 0.028 0.001 PHE C 438 TYR 0.019 0.001 TYR C 511 ARG 0.010 0.000 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 507 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ILE cc_start: 0.8483 (mm) cc_final: 0.8054 (mm) REVERT: A 408 ASN cc_start: 0.7310 (m110) cc_final: 0.7015 (t0) REVERT: A 412 MET cc_start: 0.8281 (ttm) cc_final: 0.7897 (ttm) REVERT: A 435 TYR cc_start: 0.8393 (m-80) cc_final: 0.8098 (m-80) REVERT: A 480 LEU cc_start: 0.9171 (mm) cc_final: 0.8741 (mm) REVERT: A 551 ASN cc_start: 0.8969 (m-40) cc_final: 0.8597 (m110) REVERT: A 555 TYR cc_start: 0.8940 (m-80) cc_final: 0.8544 (m-80) REVERT: A 561 GLN cc_start: 0.7230 (tt0) cc_final: 0.6714 (tm-30) REVERT: A 562 MET cc_start: 0.7604 (mtm) cc_final: 0.7205 (mtt) REVERT: A 637 LEU cc_start: 0.8985 (mp) cc_final: 0.8747 (mm) REVERT: A 653 TYR cc_start: 0.7652 (p90) cc_final: 0.7389 (p90) REVERT: A 695 ASN cc_start: 0.7234 (m-40) cc_final: 0.6473 (m-40) REVERT: A 698 LYS cc_start: 0.8373 (mtmm) cc_final: 0.8089 (mtmt) REVERT: A 700 GLN cc_start: 0.8298 (tp40) cc_final: 0.7427 (tm-30) REVERT: A 706 LEU cc_start: 0.9189 (mp) cc_final: 0.8846 (mp) REVERT: C 364 HIS cc_start: 0.6690 (p-80) cc_final: 0.6045 (m90) REVERT: C 412 MET cc_start: 0.8514 (ttm) cc_final: 0.7998 (ttm) REVERT: C 425 LYS cc_start: 0.8837 (ttmt) cc_final: 0.7777 (tptt) REVERT: C 474 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.5725 (mpt180) REVERT: C 478 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: C 551 ASN cc_start: 0.8964 (m-40) cc_final: 0.8502 (m110) REVERT: C 570 GLU cc_start: 0.8035 (tt0) cc_final: 0.7746 (tt0) REVERT: C 579 ARG cc_start: 0.7440 (ptp-170) cc_final: 0.6782 (mtm180) REVERT: C 647 LEU cc_start: 0.9000 (tp) cc_final: 0.8633 (tp) REVERT: C 651 GLU cc_start: 0.7479 (mp0) cc_final: 0.7267 (mm-30) REVERT: D 297 ASN cc_start: 0.7280 (m-40) cc_final: 0.6977 (m-40) REVERT: D 397 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7913 (mt-10) REVERT: D 412 MET cc_start: 0.8292 (ttm) cc_final: 0.7776 (ttm) REVERT: D 425 LYS cc_start: 0.8497 (mttt) cc_final: 0.8270 (mmmt) REVERT: D 551 ASN cc_start: 0.8616 (m-40) cc_final: 0.8295 (m-40) REVERT: D 740 TRP cc_start: 0.6336 (m-10) cc_final: 0.6040 (m-10) REVERT: B 397 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7852 (pt0) REVERT: B 408 ASN cc_start: 0.7620 (m110) cc_final: 0.6892 (t0) REVERT: B 466 LYS cc_start: 0.7880 (mmtm) cc_final: 0.7357 (tptt) REVERT: B 474 ARG cc_start: 0.7703 (ttp-110) cc_final: 0.5704 (mpt180) REVERT: B 478 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: B 480 LEU cc_start: 0.9173 (mt) cc_final: 0.8922 (mm) REVERT: B 551 ASN cc_start: 0.9002 (m-40) cc_final: 0.8653 (m110) REVERT: B 568 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7791 (mtp) REVERT: B 647 LEU cc_start: 0.9017 (tp) cc_final: 0.8700 (tp) REVERT: B 694 LYS cc_start: 0.8475 (pptt) cc_final: 0.8234 (tmtt) REVERT: B 700 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7229 (tm-30) REVERT: B 715 CYS cc_start: 0.5111 (m) cc_final: 0.4782 (m) outliers start: 44 outliers final: 33 residues processed: 521 average time/residue: 0.2543 time to fit residues: 193.6243 Evaluate side-chains 525 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 488 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 142 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 159 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14608 Z= 0.192 Angle : 0.628 12.372 19800 Z= 0.330 Chirality : 0.041 0.489 2240 Planarity : 0.003 0.027 2400 Dihedral : 6.903 61.692 2274 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.52 % Allowed : 21.51 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1692 helix: 1.12 (0.15), residues: 1092 sheet: -1.32 (0.63), residues: 68 loop : -1.48 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 697 HIS 0.002 0.001 HIS A 358 PHE 0.028 0.001 PHE B 438 TYR 0.023 0.001 TYR D 511 ARG 0.005 0.000 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 506 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ILE cc_start: 0.8473 (mm) cc_final: 0.8044 (mm) REVERT: A 408 ASN cc_start: 0.7340 (OUTLIER) cc_final: 0.7111 (t0) REVERT: A 412 MET cc_start: 0.8241 (ttm) cc_final: 0.7889 (ttm) REVERT: A 478 GLU cc_start: 0.8081 (mp0) cc_final: 0.7811 (mp0) REVERT: A 480 LEU cc_start: 0.9170 (mm) cc_final: 0.8742 (mm) REVERT: A 551 ASN cc_start: 0.8969 (m-40) cc_final: 0.8572 (m110) REVERT: A 555 TYR cc_start: 0.8941 (m-80) cc_final: 0.8594 (m-80) REVERT: A 561 GLN cc_start: 0.6939 (tt0) cc_final: 0.6046 (pm20) REVERT: A 562 MET cc_start: 0.7334 (mtm) cc_final: 0.7033 (mtt) REVERT: A 637 LEU cc_start: 0.8946 (mp) cc_final: 0.8718 (mm) REVERT: A 653 TYR cc_start: 0.7614 (p90) cc_final: 0.7346 (p90) REVERT: A 695 ASN cc_start: 0.7217 (m-40) cc_final: 0.6649 (m-40) REVERT: A 700 GLN cc_start: 0.8309 (tp40) cc_final: 0.7409 (tm-30) REVERT: A 706 LEU cc_start: 0.9174 (mp) cc_final: 0.8778 (mp) REVERT: C 364 HIS cc_start: 0.6734 (p-80) cc_final: 0.6019 (m90) REVERT: C 412 MET cc_start: 0.8417 (ttm) cc_final: 0.7948 (ttm) REVERT: C 425 LYS cc_start: 0.8815 (ttmt) cc_final: 0.7755 (tptt) REVERT: C 474 ARG cc_start: 0.7723 (ttp-110) cc_final: 0.5734 (mpt180) REVERT: C 478 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: C 551 ASN cc_start: 0.8953 (m-40) cc_final: 0.8506 (m110) REVERT: C 564 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.7132 (pt) REVERT: C 570 GLU cc_start: 0.8026 (tt0) cc_final: 0.7784 (tt0) REVERT: C 572 MET cc_start: 0.7591 (mtt) cc_final: 0.5872 (mtt) REVERT: C 579 ARG cc_start: 0.7445 (ptp-170) cc_final: 0.6774 (mtm180) REVERT: C 647 LEU cc_start: 0.8965 (tp) cc_final: 0.8617 (tp) REVERT: C 651 GLU cc_start: 0.7463 (mp0) cc_final: 0.7262 (mm-30) REVERT: D 297 ASN cc_start: 0.7204 (m-40) cc_final: 0.6917 (m-40) REVERT: D 397 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7956 (mt-10) REVERT: D 425 LYS cc_start: 0.8486 (mttt) cc_final: 0.8283 (mmmt) REVERT: D 432 ARG cc_start: 0.7364 (mmt180) cc_final: 0.7134 (mmt180) REVERT: D 551 ASN cc_start: 0.8637 (m-40) cc_final: 0.8325 (m-40) REVERT: D 740 TRP cc_start: 0.6223 (m-10) cc_final: 0.5999 (m-10) REVERT: B 397 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7797 (pt0) REVERT: B 408 ASN cc_start: 0.7601 (m110) cc_final: 0.6900 (t0) REVERT: B 435 TYR cc_start: 0.8333 (m-80) cc_final: 0.8093 (m-80) REVERT: B 466 LYS cc_start: 0.7879 (mmtm) cc_final: 0.7343 (tptt) REVERT: B 474 ARG cc_start: 0.7710 (ttp-110) cc_final: 0.5675 (mpt180) REVERT: B 478 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: B 480 LEU cc_start: 0.9164 (mt) cc_final: 0.8922 (mm) REVERT: B 547 MET cc_start: 0.8122 (mtp) cc_final: 0.7921 (tpp) REVERT: B 551 ASN cc_start: 0.9011 (m-40) cc_final: 0.8665 (m110) REVERT: B 568 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7808 (mtp) REVERT: B 647 LEU cc_start: 0.8995 (tp) cc_final: 0.8716 (tp) REVERT: B 662 LEU cc_start: 0.8842 (mt) cc_final: 0.8598 (mt) REVERT: B 694 LYS cc_start: 0.8570 (pptt) cc_final: 0.8300 (tmtt) REVERT: B 700 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7238 (tm-30) REVERT: B 715 CYS cc_start: 0.4905 (m) cc_final: 0.4559 (m) outliers start: 39 outliers final: 31 residues processed: 516 average time/residue: 0.2557 time to fit residues: 191.9782 Evaluate side-chains 539 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 502 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 133 optimal weight: 0.0050 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14608 Z= 0.201 Angle : 0.646 19.499 19800 Z= 0.337 Chirality : 0.042 0.389 2240 Planarity : 0.003 0.027 2400 Dihedral : 6.879 62.159 2274 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.33 % Allowed : 22.42 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1692 helix: 1.11 (0.16), residues: 1088 sheet: -1.33 (0.63), residues: 68 loop : -1.49 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 697 HIS 0.002 0.001 HIS D 358 PHE 0.026 0.001 PHE C 438 TYR 0.024 0.001 TYR D 511 ARG 0.006 0.000 ARG C 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 505 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ILE cc_start: 0.8470 (mm) cc_final: 0.8043 (mm) REVERT: A 408 ASN cc_start: 0.7368 (OUTLIER) cc_final: 0.7144 (t0) REVERT: A 412 MET cc_start: 0.8226 (ttm) cc_final: 0.7887 (ttm) REVERT: A 478 GLU cc_start: 0.7984 (mp0) cc_final: 0.7777 (mp0) REVERT: A 551 ASN cc_start: 0.8981 (m-40) cc_final: 0.8624 (m110) REVERT: A 555 TYR cc_start: 0.8922 (m-80) cc_final: 0.8590 (m-80) REVERT: A 561 GLN cc_start: 0.6869 (tt0) cc_final: 0.6004 (pm20) REVERT: A 562 MET cc_start: 0.7329 (mtm) cc_final: 0.7059 (mtt) REVERT: A 637 LEU cc_start: 0.8941 (mp) cc_final: 0.8711 (mm) REVERT: A 653 TYR cc_start: 0.7609 (p90) cc_final: 0.7344 (p90) REVERT: A 694 LYS cc_start: 0.9044 (tptt) cc_final: 0.8387 (ptmt) REVERT: A 695 ASN cc_start: 0.7307 (m-40) cc_final: 0.6434 (m-40) REVERT: A 700 GLN cc_start: 0.8285 (tp40) cc_final: 0.7375 (tm-30) REVERT: A 706 LEU cc_start: 0.9160 (mp) cc_final: 0.8746 (mp) REVERT: C 364 HIS cc_start: 0.6734 (p-80) cc_final: 0.6012 (m90) REVERT: C 382 TYR cc_start: 0.7059 (m-80) cc_final: 0.6179 (m-80) REVERT: C 425 LYS cc_start: 0.8819 (ttmt) cc_final: 0.7766 (tptt) REVERT: C 474 ARG cc_start: 0.7736 (ttp-110) cc_final: 0.5751 (mpt180) REVERT: C 478 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: C 499 ARG cc_start: 0.7323 (mmp80) cc_final: 0.7112 (mmp80) REVERT: C 551 ASN cc_start: 0.8962 (m-40) cc_final: 0.8552 (m110) REVERT: C 564 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7057 (pt) REVERT: C 579 ARG cc_start: 0.7436 (ptp-170) cc_final: 0.6712 (mtm180) REVERT: C 647 LEU cc_start: 0.8940 (tp) cc_final: 0.8587 (tp) REVERT: D 297 ASN cc_start: 0.7021 (m-40) cc_final: 0.6755 (m-40) REVERT: D 397 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7911 (mt-10) REVERT: D 412 MET cc_start: 0.8105 (ttm) cc_final: 0.7790 (ttm) REVERT: D 425 LYS cc_start: 0.8521 (mttt) cc_final: 0.8303 (mmmt) REVERT: D 432 ARG cc_start: 0.7373 (mmt180) cc_final: 0.7147 (mmt180) REVERT: D 551 ASN cc_start: 0.8640 (m-40) cc_final: 0.8309 (m110) REVERT: D 647 LEU cc_start: 0.8953 (tp) cc_final: 0.8673 (tp) REVERT: B 397 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7666 (pt0) REVERT: B 408 ASN cc_start: 0.7622 (m110) cc_final: 0.6868 (t0) REVERT: B 466 LYS cc_start: 0.7880 (mmtm) cc_final: 0.7381 (tptt) REVERT: B 474 ARG cc_start: 0.7722 (ttp-110) cc_final: 0.5701 (mpt180) REVERT: B 478 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: B 480 LEU cc_start: 0.9164 (mt) cc_final: 0.8906 (mm) REVERT: B 551 ASN cc_start: 0.9030 (m-40) cc_final: 0.8686 (m110) REVERT: B 568 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7718 (mtp) REVERT: B 647 LEU cc_start: 0.8971 (tp) cc_final: 0.8665 (tp) REVERT: B 662 LEU cc_start: 0.8845 (mt) cc_final: 0.8600 (mt) REVERT: B 694 LYS cc_start: 0.8598 (pptt) cc_final: 0.8337 (tmtt) REVERT: B 700 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7241 (tm-30) REVERT: B 706 LEU cc_start: 0.9109 (mp) cc_final: 0.8679 (mp) outliers start: 36 outliers final: 27 residues processed: 513 average time/residue: 0.2608 time to fit residues: 194.3404 Evaluate side-chains 517 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 484 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 687 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.178702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.137577 restraints weight = 22580.248| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.90 r_work: 0.3531 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14608 Z= 0.238 Angle : 0.671 19.182 19800 Z= 0.348 Chirality : 0.041 0.237 2240 Planarity : 0.003 0.028 2400 Dihedral : 6.916 63.939 2274 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.20 % Allowed : 22.87 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1692 helix: 1.01 (0.16), residues: 1100 sheet: -1.27 (0.65), residues: 68 loop : -1.41 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 697 HIS 0.002 0.001 HIS A 358 PHE 0.031 0.001 PHE B 438 TYR 0.029 0.001 TYR D 511 ARG 0.005 0.000 ARG D 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4068.65 seconds wall clock time: 78 minutes 40.00 seconds (4720.00 seconds total)