Starting phenix.real_space_refine on Fri Mar 15 22:17:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjo_32547/03_2024/7wjo_32547_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjo_32547/03_2024/7wjo_32547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjo_32547/03_2024/7wjo_32547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjo_32547/03_2024/7wjo_32547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjo_32547/03_2024/7wjo_32547_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjo_32547/03_2024/7wjo_32547_updated.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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 72 5.16 5 C 8394 2.51 5 N 2156 2.21 5 O 2310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12932 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6431 Classifications: {'peptide': 801} Link IDs: {'PTRANS': 30, 'TRANS': 770} Chain breaks: 1 Chain: "B" Number of atoms: 6431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6431 Classifications: {'peptide': 801} Link IDs: {'PTRANS': 30, 'TRANS': 770} Chain breaks: 1 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'BGI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'BGI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.88, per 1000 atoms: 0.53 Number of scatterers: 12932 At special positions: 0 Unit cell: (116.63, 114.49, 129.47, 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 72 16.00 O 2310 8.00 N 2156 7.00 C 8394 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: 4.64 Conformation dependent library (CDL) restraints added in 2.2 seconds 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 4 sheets defined 59.6% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 94 through 109 Processing helix chain 'A' and resid 113 through 133 removed outlier: 4.234A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 162 Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 243 through 261 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 358 through 373 Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 424 through 446 Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 481 through 484 No H-bonds generated for 'chain 'A' and resid 481 through 484' Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 495 through 504 removed outlier: 3.545A pdb=" N VAL A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 559 removed outlier: 3.782A pdb=" N LYS A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TRP A 539 " --> pdb=" O GLN A 535 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLY A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG A 556 " --> pdb=" O TRP A 552 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE A 557 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR A 558 " --> pdb=" O TRP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 586 Processing helix chain 'A' and resid 588 through 605 Processing helix chain 'A' and resid 620 through 646 removed outlier: 4.065A pdb=" N VAL A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 680 Processing helix chain 'A' and resid 685 through 705 removed outlier: 5.333A pdb=" N VAL A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 735 removed outlier: 5.265A pdb=" N THR A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N HIS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 721 " --> pdb=" O HIS A 717 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 722 " --> pdb=" O TYR A 718 " (cutoff:3.500A) Proline residue: A 723 - end of helix Processing helix chain 'A' and resid 765 through 818 Processing helix chain 'A' and resid 825 through 858 removed outlier: 5.049A pdb=" N GLY A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 113 through 133 removed outlier: 4.234A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 162 Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'B' and resid 243 through 261 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 358 through 373 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 424 through 446 Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 475 through 478 No H-bonds generated for 'chain 'B' and resid 475 through 478' Processing helix chain 'B' and resid 481 through 484 No H-bonds generated for 'chain 'B' and resid 481 through 484' Processing helix chain 'B' and resid 486 through 490 Processing helix chain 'B' and resid 495 through 504 removed outlier: 3.545A pdb=" N VAL B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 559 removed outlier: 3.781A pdb=" N LYS B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TRP B 539 " --> pdb=" O GLN B 535 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLY B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG B 556 " --> pdb=" O TRP B 552 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE B 557 " --> pdb=" O ASN B 553 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR B 558 " --> pdb=" O TRP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 586 Processing helix chain 'B' and resid 588 through 605 Processing helix chain 'B' and resid 620 through 646 removed outlier: 4.065A pdb=" N VAL B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 680 Processing helix chain 'B' and resid 685 through 705 removed outlier: 5.333A pdb=" N VAL B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TYR B 698 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 735 removed outlier: 5.265A pdb=" N THR B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N HIS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU B 721 " --> pdb=" O HIS B 717 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 722 " --> pdb=" O TYR B 718 " (cutoff:3.500A) Proline residue: B 723 - end of helix Processing helix chain 'B' and resid 765 through 818 Processing helix chain 'B' and resid 825 through 858 removed outlier: 5.049A pdb=" N GLY B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU B 855 " --> pdb=" O HIS B 851 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG B 858 " --> pdb=" O GLY B 854 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 177 through 180 removed outlier: 8.024A pdb=" N ARG A 200 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N THR A 332 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN A 346 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 352 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A 232 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N CYS A 287 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 234 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL A 289 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 236 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR A 377 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N CYS A 235 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ALA A 379 " --> pdb=" O CYS A 235 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N THR A 237 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N MET A 381 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A 461 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY A 406 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR A 512 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA A 408 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS A 514 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 411 through 414 Processing sheet with id= C, first strand: chain 'B' and resid 177 through 180 removed outlier: 8.025A pdb=" N ARG B 200 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR B 332 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN B 346 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS B 352 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 232 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N CYS B 287 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE B 234 " --> pdb=" O CYS B 287 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL B 289 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 236 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR B 377 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N CYS B 235 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA B 379 " --> pdb=" O CYS B 235 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR B 237 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N MET B 381 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 461 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY B 406 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR B 512 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 408 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS B 514 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 411 through 414 742 hydrogen bonds defined for protein. 2196 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: 3.85 Time building geometry restraints manager: 5.07 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: 2030 1.29 - 1.42: 3786 1.42 - 1.55: 7348 1.55 - 1.68: 8 1.68 - 1.81: 112 Bond restraints: 13284 Sorted by residual: bond pdb=" C25 BGI B1001 " pdb=" O26 BGI B1001 " ideal model delta sigma weight residual 1.216 1.433 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C25 BGI A1001 " pdb=" O26 BGI A1001 " ideal model delta sigma weight residual 1.216 1.433 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C17 BGI B1001 " pdb=" C18 BGI B1001 " ideal model delta sigma weight residual 1.532 1.332 0.200 2.00e-02 2.50e+03 9.96e+01 bond pdb=" C17 BGI A1001 " pdb=" C18 BGI A1001 " ideal model delta sigma weight residual 1.532 1.333 0.199 2.00e-02 2.50e+03 9.88e+01 bond pdb=" C17 BGI B1001 " pdb=" O21 BGI B1001 " ideal model delta sigma weight residual 1.433 1.606 -0.173 2.00e-02 2.50e+03 7.46e+01 ... (remaining 13279 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.80: 372 106.80 - 113.60: 7180 113.60 - 120.40: 5220 120.40 - 127.20: 5114 127.20 - 134.00: 156 Bond angle restraints: 18042 Sorted by residual: angle pdb=" N GLU B 463 " pdb=" CA GLU B 463 " pdb=" C GLU B 463 " ideal model delta sigma weight residual 114.62 108.77 5.85 1.14e+00 7.69e-01 2.64e+01 angle pdb=" N GLU A 463 " pdb=" CA GLU A 463 " pdb=" C GLU A 463 " ideal model delta sigma weight residual 114.62 108.78 5.84 1.14e+00 7.69e-01 2.63e+01 angle pdb=" CA GLU A 463 " pdb=" C GLU A 463 " pdb=" N ALA A 464 " ideal model delta sigma weight residual 119.71 116.14 3.57 1.17e+00 7.31e-01 9.31e+00 angle pdb=" CA GLU B 463 " pdb=" C GLU B 463 " pdb=" N ALA B 464 " ideal model delta sigma weight residual 119.71 116.18 3.53 1.17e+00 7.31e-01 9.09e+00 angle pdb=" C18 BGI B1001 " pdb=" C19 BGI B1001 " pdb=" O30 BGI B1001 " ideal model delta sigma weight residual 116.99 108.55 8.44 3.00e+00 1.11e-01 7.91e+00 ... (remaining 18037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 7327 17.32 - 34.63: 398 34.63 - 51.95: 57 51.95 - 69.27: 18 69.27 - 86.58: 14 Dihedral angle restraints: 7814 sinusoidal: 3122 harmonic: 4692 Sorted by residual: dihedral pdb=" CA TYR A 617 " pdb=" C TYR A 617 " pdb=" N SER A 618 " pdb=" CA SER A 618 " ideal model delta harmonic sigma weight residual 180.00 -163.72 -16.28 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA TYR B 617 " pdb=" C TYR B 617 " pdb=" N SER B 618 " pdb=" CA SER B 618 " ideal model delta harmonic sigma weight residual -180.00 -163.75 -16.25 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB ARG B 797 " pdb=" CG ARG B 797 " pdb=" CD ARG B 797 " pdb=" NE ARG B 797 " ideal model delta sinusoidal sigma weight residual 180.00 123.01 56.99 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 7811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1722 0.056 - 0.112: 237 0.112 - 0.168: 23 0.168 - 0.223: 0 0.223 - 0.279: 2 Chirality restraints: 1984 Sorted by residual: chirality pdb=" C18 BGI A1001 " pdb=" C17 BGI A1001 " pdb=" C19 BGI A1001 " pdb=" O31 BGI A1001 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C18 BGI B1001 " pdb=" C17 BGI B1001 " pdb=" C19 BGI B1001 " pdb=" O31 BGI B1001 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C19 BGI B1001 " pdb=" C18 BGI B1001 " pdb=" C20 BGI B1001 " pdb=" O30 BGI B1001 " both_signs ideal model delta sigma weight residual False 2.48 2.63 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 1981 not shown) Planarity restraints: 2278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 598 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C PHE B 598 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE B 598 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE B 599 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 598 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C PHE A 598 " 0.037 2.00e-02 2.50e+03 pdb=" O PHE A 598 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 599 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 599 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C ILE B 599 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE B 599 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 600 " 0.012 2.00e-02 2.50e+03 ... (remaining 2275 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1252 2.74 - 3.28: 12292 3.28 - 3.82: 21062 3.82 - 4.36: 22786 4.36 - 4.90: 43376 Nonbonded interactions: 100768 Sorted by model distance: nonbonded pdb=" OH TYR A 88 " pdb=" OD1 ASP B 115 " model vdw 2.203 2.440 nonbonded pdb=" OH TYR A 52 " pdb=" OE2 GLU B 225 " model vdw 2.207 2.440 nonbonded pdb=" O LYS A 269 " pdb=" OH TYR A 393 " model vdw 2.277 2.440 nonbonded pdb=" O LYS B 269 " pdb=" OH TYR B 393 " model vdw 2.277 2.440 nonbonded pdb=" OE2 GLU A 225 " pdb=" OH TYR B 52 " model vdw 2.284 2.440 ... (remaining 100763 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 6.010 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 34.820 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.006 0.217 13284 Z= 0.364 Angle : 0.554 8.440 18042 Z= 0.282 Chirality : 0.040 0.279 1984 Planarity : 0.004 0.031 2278 Dihedral : 11.696 86.583 4802 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.29 % Allowed : 6.02 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.22), residues: 1594 helix: 2.59 (0.17), residues: 982 sheet: 0.13 (0.43), residues: 170 loop : -1.37 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 804 HIS 0.005 0.001 HIS A 403 PHE 0.016 0.001 PHE B 601 TYR 0.011 0.001 TYR A 365 ARG 0.002 0.000 ARG B 608 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 230 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ARG cc_start: 0.7539 (mtt180) cc_final: 0.5958 (mtt90) REVERT: A 264 MET cc_start: 0.7999 (tpp) cc_final: 0.7763 (ttt) REVERT: A 552 TRP cc_start: 0.7187 (t-100) cc_final: 0.6802 (m-10) REVERT: A 850 ILE cc_start: 0.8256 (tt) cc_final: 0.8026 (tt) REVERT: B 187 ASP cc_start: 0.7188 (p0) cc_final: 0.6596 (p0) REVERT: B 305 GLU cc_start: 0.7831 (tt0) cc_final: 0.7572 (tt0) REVERT: B 645 LEU cc_start: 0.8575 (tp) cc_final: 0.8364 (tt) REVERT: B 790 LYS cc_start: 0.7486 (mttt) cc_final: 0.7261 (mptt) REVERT: B 820 SER cc_start: 0.7917 (m) cc_final: 0.7712 (p) REVERT: B 850 ILE cc_start: 0.8487 (tt) cc_final: 0.8249 (tt) outliers start: 4 outliers final: 2 residues processed: 232 average time/residue: 0.2948 time to fit residues: 93.2900 Evaluate side-chains 144 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 326 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.0070 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 0.0050 chunk 93 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.5414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13284 Z= 0.159 Angle : 0.486 6.986 18042 Z= 0.251 Chirality : 0.038 0.157 1984 Planarity : 0.004 0.030 2278 Dihedral : 6.347 43.623 1852 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.18 % Allowed : 9.43 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.22), residues: 1594 helix: 2.57 (0.17), residues: 982 sheet: 0.08 (0.43), residues: 170 loop : -1.37 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 804 HIS 0.002 0.001 HIS A 394 PHE 0.016 0.001 PHE A 457 TYR 0.019 0.001 TYR A 732 ARG 0.003 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7781 (mp) REVERT: A 238 MET cc_start: 0.7708 (ttm) cc_final: 0.7445 (ttm) REVERT: A 552 TRP cc_start: 0.7190 (t-100) cc_final: 0.6839 (m-10) REVERT: A 730 THR cc_start: 0.8398 (m) cc_final: 0.8103 (p) REVERT: A 794 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6591 (mm-30) REVERT: A 850 ILE cc_start: 0.8260 (tt) cc_final: 0.8029 (tt) REVERT: B 187 ASP cc_start: 0.7238 (p0) cc_final: 0.6692 (p0) REVERT: B 305 GLU cc_start: 0.7762 (tt0) cc_final: 0.7531 (tt0) REVERT: B 850 ILE cc_start: 0.8519 (tt) cc_final: 0.8241 (tt) outliers start: 30 outliers final: 16 residues processed: 167 average time/residue: 0.2839 time to fit residues: 67.4288 Evaluate side-chains 148 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 684 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13284 Z= 0.254 Angle : 0.521 8.286 18042 Z= 0.274 Chirality : 0.040 0.131 1984 Planarity : 0.004 0.051 2278 Dihedral : 4.894 30.032 1850 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.61 % Allowed : 10.52 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.22), residues: 1594 helix: 2.44 (0.17), residues: 950 sheet: -0.25 (0.42), residues: 174 loop : -1.41 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 804 HIS 0.005 0.001 HIS A 578 PHE 0.017 0.001 PHE A 601 TYR 0.020 0.001 TYR A 732 ARG 0.006 0.001 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7838 (mp) REVERT: A 199 ARG cc_start: 0.7548 (mtt180) cc_final: 0.7293 (mtt-85) REVERT: A 552 TRP cc_start: 0.7277 (t-100) cc_final: 0.6712 (m-10) REVERT: A 730 THR cc_start: 0.8520 (m) cc_final: 0.8180 (p) REVERT: A 850 ILE cc_start: 0.8438 (tt) cc_final: 0.8171 (tt) REVERT: B 187 ASP cc_start: 0.7440 (p0) cc_final: 0.6810 (p0) REVERT: B 195 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7662 (tp30) REVERT: B 305 GLU cc_start: 0.7830 (tt0) cc_final: 0.7609 (tt0) REVERT: B 785 ARG cc_start: 0.7089 (mtt180) cc_final: 0.6743 (ptp-170) REVERT: B 850 ILE cc_start: 0.8568 (tt) cc_final: 0.8264 (tt) outliers start: 36 outliers final: 26 residues processed: 173 average time/residue: 0.2745 time to fit residues: 67.1894 Evaluate side-chains 160 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain B residue 820 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13284 Z= 0.279 Angle : 0.521 7.316 18042 Z= 0.276 Chirality : 0.040 0.135 1984 Planarity : 0.004 0.030 2278 Dihedral : 4.969 30.930 1850 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.12 % Allowed : 11.39 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.22), residues: 1594 helix: 2.34 (0.17), residues: 950 sheet: -0.29 (0.42), residues: 174 loop : -1.48 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 804 HIS 0.004 0.001 HIS B 578 PHE 0.015 0.001 PHE A 601 TYR 0.018 0.001 TYR A 732 ARG 0.003 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7854 (mp) REVERT: A 199 ARG cc_start: 0.7487 (mtt180) cc_final: 0.7209 (mtt-85) REVERT: A 552 TRP cc_start: 0.7297 (t-100) cc_final: 0.6836 (m-10) REVERT: A 730 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8211 (p) REVERT: A 850 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8318 (tt) REVERT: B 187 ASP cc_start: 0.7585 (p0) cc_final: 0.6854 (p0) REVERT: B 318 ASN cc_start: 0.9275 (OUTLIER) cc_final: 0.8987 (m-40) REVERT: B 451 SER cc_start: 0.8863 (t) cc_final: 0.8539 (p) REVERT: B 785 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6734 (ptp-170) REVERT: B 850 ILE cc_start: 0.8615 (tt) cc_final: 0.8272 (tt) outliers start: 43 outliers final: 25 residues processed: 159 average time/residue: 0.2747 time to fit residues: 61.7970 Evaluate side-chains 151 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 647 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13284 Z= 0.209 Angle : 0.490 7.256 18042 Z= 0.258 Chirality : 0.039 0.133 1984 Planarity : 0.004 0.030 2278 Dihedral : 4.782 28.489 1850 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.83 % Allowed : 12.26 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1594 helix: 2.43 (0.17), residues: 950 sheet: -0.29 (0.43), residues: 174 loop : -1.43 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 804 HIS 0.003 0.001 HIS A 578 PHE 0.015 0.001 PHE B 601 TYR 0.016 0.001 TYR A 732 ARG 0.005 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 131 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7799 (mp) REVERT: A 199 ARG cc_start: 0.7500 (mtt180) cc_final: 0.7219 (mtt-85) REVERT: A 318 ASN cc_start: 0.9267 (OUTLIER) cc_final: 0.8988 (m-40) REVERT: A 552 TRP cc_start: 0.7288 (OUTLIER) cc_final: 0.6825 (m-10) REVERT: A 730 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 850 ILE cc_start: 0.8485 (tt) cc_final: 0.8235 (tt) REVERT: B 318 ASN cc_start: 0.9282 (OUTLIER) cc_final: 0.8994 (m-40) REVERT: B 371 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7368 (mm-30) REVERT: B 451 SER cc_start: 0.8820 (t) cc_final: 0.8542 (p) REVERT: B 538 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6868 (mtt180) REVERT: B 785 ARG cc_start: 0.7072 (mtt180) cc_final: 0.6724 (ptp-170) REVERT: B 850 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8264 (tt) outliers start: 39 outliers final: 24 residues processed: 157 average time/residue: 0.2666 time to fit residues: 59.6100 Evaluate side-chains 158 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13284 Z= 0.399 Angle : 0.579 8.157 18042 Z= 0.305 Chirality : 0.042 0.149 1984 Planarity : 0.004 0.031 2278 Dihedral : 5.299 33.002 1850 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.83 % Allowed : 13.57 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1594 helix: 2.11 (0.17), residues: 950 sheet: -0.47 (0.42), residues: 172 loop : -1.52 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 202 HIS 0.005 0.001 HIS A 578 PHE 0.017 0.002 PHE B 214 TYR 0.020 0.002 TYR A 365 ARG 0.004 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7902 (mp) REVERT: A 318 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.9006 (m-40) REVERT: A 730 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8355 (p) REVERT: A 850 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8488 (tt) REVERT: B 318 ASN cc_start: 0.9299 (OUTLIER) cc_final: 0.9019 (m-40) REVERT: B 371 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7391 (mm-30) REVERT: B 451 SER cc_start: 0.8869 (t) cc_final: 0.8562 (p) REVERT: B 785 ARG cc_start: 0.7066 (mtt180) cc_final: 0.6750 (ptp-170) REVERT: B 850 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8466 (tt) outliers start: 39 outliers final: 26 residues processed: 159 average time/residue: 0.2730 time to fit residues: 61.6400 Evaluate side-chains 158 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 154 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13284 Z= 0.193 Angle : 0.488 8.689 18042 Z= 0.257 Chirality : 0.038 0.128 1984 Planarity : 0.004 0.032 2278 Dihedral : 4.783 27.902 1850 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.76 % Allowed : 14.15 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.22), residues: 1594 helix: 2.36 (0.17), residues: 948 sheet: -0.40 (0.42), residues: 172 loop : -1.48 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 804 HIS 0.003 0.001 HIS B 563 PHE 0.014 0.001 PHE A 545 TYR 0.010 0.001 TYR A 492 ARG 0.004 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 133 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7825 (mp) REVERT: A 318 ASN cc_start: 0.9277 (OUTLIER) cc_final: 0.9005 (m-40) REVERT: A 552 TRP cc_start: 0.7387 (OUTLIER) cc_final: 0.6884 (m-10) REVERT: A 730 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8242 (p) REVERT: A 850 ILE cc_start: 0.8479 (tt) cc_final: 0.8200 (tt) REVERT: B 318 ASN cc_start: 0.9283 (OUTLIER) cc_final: 0.9009 (m-40) REVERT: B 371 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 538 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6818 (mtt180) REVERT: B 552 TRP cc_start: 0.7428 (OUTLIER) cc_final: 0.7033 (t-100) REVERT: B 785 ARG cc_start: 0.7168 (mtt180) cc_final: 0.6804 (ptp-170) REVERT: B 850 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8273 (tt) outliers start: 38 outliers final: 24 residues processed: 159 average time/residue: 0.2785 time to fit residues: 62.7946 Evaluate side-chains 157 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 552 TRP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 92 optimal weight: 8.9990 chunk 46 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13284 Z= 0.207 Angle : 0.496 8.663 18042 Z= 0.260 Chirality : 0.039 0.128 1984 Planarity : 0.004 0.032 2278 Dihedral : 4.736 27.818 1850 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.05 % Allowed : 14.30 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1594 helix: 2.34 (0.17), residues: 950 sheet: -0.43 (0.42), residues: 172 loop : -1.45 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 202 HIS 0.003 0.001 HIS B 578 PHE 0.014 0.001 PHE B 601 TYR 0.010 0.001 TYR A 365 ARG 0.003 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 126 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7855 (mp) REVERT: A 199 ARG cc_start: 0.7554 (mtt180) cc_final: 0.7352 (mtt-85) REVERT: A 318 ASN cc_start: 0.9303 (OUTLIER) cc_final: 0.9025 (m-40) REVERT: A 552 TRP cc_start: 0.7388 (OUTLIER) cc_final: 0.6884 (m-10) REVERT: A 730 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 850 ILE cc_start: 0.8480 (tt) cc_final: 0.8233 (tt) REVERT: B 318 ASN cc_start: 0.9298 (OUTLIER) cc_final: 0.9024 (m-40) REVERT: B 371 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7251 (mm-30) REVERT: B 513 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7259 (mtp) REVERT: B 538 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6831 (mtt180) REVERT: B 552 TRP cc_start: 0.7425 (OUTLIER) cc_final: 0.7038 (t-100) REVERT: B 785 ARG cc_start: 0.7146 (mtt180) cc_final: 0.6834 (ptp-170) REVERT: B 850 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8321 (tt) outliers start: 42 outliers final: 26 residues processed: 155 average time/residue: 0.2778 time to fit residues: 60.9514 Evaluate side-chains 159 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 552 TRP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13284 Z= 0.206 Angle : 0.496 9.759 18042 Z= 0.260 Chirality : 0.039 0.128 1984 Planarity : 0.004 0.032 2278 Dihedral : 4.708 28.078 1850 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.61 % Allowed : 14.88 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.22), residues: 1594 helix: 2.37 (0.17), residues: 948 sheet: -0.42 (0.42), residues: 172 loop : -1.45 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 202 HIS 0.003 0.001 HIS B 578 PHE 0.015 0.001 PHE A 545 TYR 0.010 0.001 TYR A 207 ARG 0.003 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7841 (mp) REVERT: A 318 ASN cc_start: 0.9302 (OUTLIER) cc_final: 0.9028 (m-40) REVERT: A 552 TRP cc_start: 0.7413 (OUTLIER) cc_final: 0.6880 (m-10) REVERT: A 730 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8228 (p) REVERT: A 850 ILE cc_start: 0.8476 (tt) cc_final: 0.8229 (tt) REVERT: B 318 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.9019 (m-40) REVERT: B 371 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7277 (mm-30) REVERT: B 538 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6829 (mtt180) REVERT: B 552 TRP cc_start: 0.7429 (OUTLIER) cc_final: 0.7044 (t-100) REVERT: B 785 ARG cc_start: 0.7139 (mtt180) cc_final: 0.6830 (ptp-170) REVERT: B 850 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8313 (tt) outliers start: 36 outliers final: 27 residues processed: 152 average time/residue: 0.2747 time to fit residues: 58.6928 Evaluate side-chains 157 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 552 TRP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13284 Z= 0.249 Angle : 0.512 10.248 18042 Z= 0.269 Chirality : 0.039 0.131 1984 Planarity : 0.004 0.031 2278 Dihedral : 4.825 29.413 1850 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.76 % Allowed : 14.95 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1594 helix: 2.29 (0.17), residues: 948 sheet: -0.48 (0.42), residues: 172 loop : -1.46 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.003 0.001 HIS B 578 PHE 0.016 0.001 PHE B 601 TYR 0.012 0.001 TYR A 365 ARG 0.003 0.000 ARG B 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 122 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7828 (mp) REVERT: A 199 ARG cc_start: 0.7373 (mtt-85) cc_final: 0.7027 (mtt-85) REVERT: A 318 ASN cc_start: 0.9309 (OUTLIER) cc_final: 0.9027 (m-40) REVERT: A 552 TRP cc_start: 0.7406 (OUTLIER) cc_final: 0.6817 (m-10) REVERT: A 730 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8271 (p) REVERT: A 850 ILE cc_start: 0.8551 (tt) cc_final: 0.8309 (tt) REVERT: B 318 ASN cc_start: 0.9324 (OUTLIER) cc_final: 0.9039 (m-40) REVERT: B 371 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7303 (mm-30) REVERT: B 538 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6814 (mtt180) REVERT: B 785 ARG cc_start: 0.7150 (mtt180) cc_final: 0.6841 (ptp-170) REVERT: B 850 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8366 (tt) outliers start: 38 outliers final: 30 residues processed: 149 average time/residue: 0.2864 time to fit residues: 60.1610 Evaluate side-chains 158 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 527 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 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 = 0.3665 r_free = 0.3665 target = 0.140929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107675 restraints weight = 15392.425| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.18 r_work: 0.3107 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13284 Z= 0.189 Angle : 0.489 10.074 18042 Z= 0.257 Chirality : 0.038 0.146 1984 Planarity : 0.004 0.031 2278 Dihedral : 4.668 27.696 1850 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.69 % Allowed : 15.09 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.22), residues: 1594 helix: 2.39 (0.17), residues: 946 sheet: -0.46 (0.42), residues: 172 loop : -1.43 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 184 HIS 0.002 0.001 HIS B 563 PHE 0.016 0.001 PHE A 545 TYR 0.009 0.001 TYR A 492 ARG 0.002 0.000 ARG B 199 =============================================================================== Job complete usr+sys time: 2752.47 seconds wall clock time: 50 minutes 27.65 seconds (3027.65 seconds total)