Starting phenix.real_space_refine on Tue Nov 19 09:16:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chr_45599/11_2024/9chr_45599.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chr_45599/11_2024/9chr_45599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chr_45599/11_2024/9chr_45599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chr_45599/11_2024/9chr_45599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chr_45599/11_2024/9chr_45599.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chr_45599/11_2024/9chr_45599.cif" } resolution = 3.5 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 6292 2.51 5 N 1568 2.21 5 O 1600 1.98 5 H 9596 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19104 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Chain: "B" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Chain: "C" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Chain: "D" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Time building chain proxies: 9.49, per 1000 atoms: 0.50 Number of scatterers: 19104 At special positions: 0 Unit cell: (123.9, 122.85, 96.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 1600 8.00 N 1568 7.00 C 6292 6.00 H 9596 1.00 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 - 3.00 Amino acid : True - 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: 4.74 Conformation dependent library (CDL) restraints added in 1.4 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 1 sheets defined 81.1% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 404 through 432 removed outlier: 3.688A pdb=" N LEU A 416 " --> pdb=" O TRP A 412 " (cutoff:3.500A) Proline residue: A 426 - end of helix removed outlier: 3.607A pdb=" N LEU A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 removed outlier: 3.546A pdb=" N LEU A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 495 removed outlier: 3.632A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 507 through 512 removed outlier: 4.339A pdb=" N ILE A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.726A pdb=" N LYS A 525 " --> pdb=" O ILE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 545 through 575 removed outlier: 3.548A pdb=" N GLU A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 593 removed outlier: 3.660A pdb=" N ASN A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 634 through 667 removed outlier: 3.823A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 687 Processing helix chain 'A' and resid 690 through 709 removed outlier: 4.000A pdb=" N ARG A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 431 removed outlier: 3.805A pdb=" N LEU B 416 " --> pdb=" O TRP B 412 " (cutoff:3.500A) Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 450 through 471 removed outlier: 3.622A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 495 removed outlier: 3.610A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 504 Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 517 through 525 removed outlier: 3.971A pdb=" N LYS B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 545 through 575 removed outlier: 3.516A pdb=" N GLU B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 593 removed outlier: 3.618A pdb=" N ASN B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 634 through 667 removed outlier: 4.011A pdb=" N PHE B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 688 Processing helix chain 'B' and resid 690 through 709 removed outlier: 3.926A pdb=" N ARG B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 432 removed outlier: 3.645A pdb=" N LEU C 416 " --> pdb=" O TRP C 412 " (cutoff:3.500A) Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 450 through 471 removed outlier: 4.219A pdb=" N ASP C 456 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 495 removed outlier: 3.549A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 507 through 512 removed outlier: 3.580A pdb=" N ILE C 512 " --> pdb=" O PHE C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 525 removed outlier: 3.877A pdb=" N LYS C 525 " --> pdb=" O ILE C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 531 Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 545 through 575 Processing helix chain 'C' and resid 584 through 593 removed outlier: 3.641A pdb=" N ASN C 588 " --> pdb=" O GLY C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 623 Processing helix chain 'C' and resid 634 through 667 removed outlier: 4.095A pdb=" N PHE C 656 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 688 Processing helix chain 'C' and resid 690 through 709 removed outlier: 4.370A pdb=" N ARG C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 431 removed outlier: 3.846A pdb=" N LEU D 416 " --> pdb=" O TRP D 412 " (cutoff:3.500A) Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 450 through 471 removed outlier: 4.046A pdb=" N ASP D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 496 removed outlier: 3.745A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 504 Processing helix chain 'D' and resid 507 through 512 removed outlier: 3.849A pdb=" N ILE D 512 " --> pdb=" O PHE D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 525 removed outlier: 3.801A pdb=" N LYS D 525 " --> pdb=" O ILE D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 531 Processing helix chain 'D' and resid 532 through 537 removed outlier: 3.536A pdb=" N ALA D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 545 through 575 removed outlier: 3.537A pdb=" N PHE D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 593 removed outlier: 3.667A pdb=" N ASN D 588 " --> pdb=" O GLY D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 623 Processing helix chain 'D' and resid 634 through 653 Processing helix chain 'D' and resid 654 through 667 removed outlier: 3.560A pdb=" N SER D 660 " --> pdb=" O PHE D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 688 Processing helix chain 'D' and resid 690 through 709 removed outlier: 4.501A pdb=" N ARG D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN D 702 " --> pdb=" O GLU D 698 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 597 through 598 removed outlier: 3.751A pdb=" N LEU C 602 " --> pdb=" O ASN C 598 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.06 Time building geometry restraints manager: 5.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 9580 1.13 - 1.30: 1520 1.30 - 1.48: 4059 1.48 - 1.65: 4133 1.65 - 1.82: 80 Bond restraints: 19372 Sorted by residual: bond pdb=" CD1 PHE B 551 " pdb=" HD1 PHE B 551 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASP B 509 " pdb=" H ASP B 509 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE2 GLN A 592 " pdb="HE21 GLN A 592 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ALA A 653 " pdb=" H ALA A 653 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH2 ARG B 672 " pdb="HH21 ARG B 672 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 19367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 29601 2.51 - 5.02: 4093 5.02 - 7.52: 1148 7.52 - 10.03: 54 10.03 - 12.54: 16 Bond angle restraints: 34912 Sorted by residual: angle pdb=" C GLY C 604 " pdb=" N PRO C 605 " pdb=" CA PRO C 605 " ideal model delta sigma weight residual 119.76 125.05 -5.29 1.03e+00 9.43e-01 2.64e+01 angle pdb=" CB HIS D 587 " pdb=" CG HIS D 587 " pdb=" CD2 HIS D 587 " ideal model delta sigma weight residual 131.20 124.66 6.54 1.30e+00 5.92e-01 2.53e+01 angle pdb=" CB HIS C 587 " pdb=" CG HIS C 587 " pdb=" CD2 HIS C 587 " ideal model delta sigma weight residual 131.20 124.72 6.48 1.30e+00 5.92e-01 2.48e+01 angle pdb=" C GLY B 604 " pdb=" N PRO B 605 " pdb=" CA PRO B 605 " ideal model delta sigma weight residual 119.78 124.79 -5.01 1.03e+00 9.43e-01 2.37e+01 angle pdb=" CB HIS A 587 " pdb=" CG HIS A 587 " pdb=" CD2 HIS A 587 " ideal model delta sigma weight residual 131.20 124.91 6.29 1.30e+00 5.92e-01 2.34e+01 ... (remaining 34907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 8479 16.53 - 33.06: 419 33.06 - 49.58: 137 49.58 - 66.11: 84 66.11 - 82.64: 5 Dihedral angle restraints: 9124 sinusoidal: 4760 harmonic: 4364 Sorted by residual: dihedral pdb=" CA HIS A 578 " pdb=" C HIS A 578 " pdb=" N MET A 579 " pdb=" CA MET A 579 " ideal model delta harmonic sigma weight residual -180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA HIS B 578 " pdb=" C HIS B 578 " pdb=" N MET B 579 " pdb=" CA MET B 579 " ideal model delta harmonic sigma weight residual 180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA HIS C 578 " pdb=" C HIS C 578 " pdb=" N MET C 579 " pdb=" CA MET C 579 " ideal model delta harmonic sigma weight residual 180.00 -151.16 -28.84 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 9121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 971 0.083 - 0.166: 447 0.166 - 0.249: 55 0.249 - 0.332: 18 0.332 - 0.415: 5 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA SER C 624 " pdb=" N SER C 624 " pdb=" C SER C 624 " pdb=" CB SER C 624 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA SER D 624 " pdb=" N SER D 624 " pdb=" C SER D 624 " pdb=" CB SER D 624 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA SER B 624 " pdb=" N SER B 624 " pdb=" C SER B 624 " pdb=" CB SER B 624 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.71e+00 ... (remaining 1493 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 652 " -0.213 2.00e-02 2.50e+03 8.80e-02 2.32e+02 pdb=" CG TYR B 652 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 652 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 TYR B 652 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR B 652 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR B 652 " 0.053 2.00e-02 2.50e+03 pdb=" CZ TYR B 652 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR B 652 " -0.164 2.00e-02 2.50e+03 pdb=" HD1 TYR B 652 " 0.070 2.00e-02 2.50e+03 pdb=" HD2 TYR B 652 " 0.037 2.00e-02 2.50e+03 pdb=" HE1 TYR B 652 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR B 652 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 652 " -0.209 2.00e-02 2.50e+03 8.53e-02 2.18e+02 pdb=" CG TYR C 652 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR C 652 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TYR C 652 " 0.060 2.00e-02 2.50e+03 pdb=" CE1 TYR C 652 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR C 652 " 0.051 2.00e-02 2.50e+03 pdb=" CZ TYR C 652 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR C 652 " -0.154 2.00e-02 2.50e+03 pdb=" HD1 TYR C 652 " 0.072 2.00e-02 2.50e+03 pdb=" HD2 TYR C 652 " 0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR C 652 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR C 652 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 652 " -0.192 2.00e-02 2.50e+03 7.97e-02 1.91e+02 pdb=" CG TYR D 652 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR D 652 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR D 652 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR D 652 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR D 652 " 0.050 2.00e-02 2.50e+03 pdb=" CZ TYR D 652 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR D 652 " -0.150 2.00e-02 2.50e+03 pdb=" HD1 TYR D 652 " 0.065 2.00e-02 2.50e+03 pdb=" HD2 TYR D 652 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR D 652 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR D 652 " 0.032 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 953 2.20 - 2.80: 34043 2.80 - 3.40: 52130 3.40 - 4.00: 68372 4.00 - 4.60: 97650 Nonbonded interactions: 253148 Sorted by model distance: nonbonded pdb=" OE2 GLU D 575 " pdb=" HG SER D 636 " model vdw 1.602 2.450 nonbonded pdb=" OE2 GLU C 575 " pdb=" HG SER C 636 " model vdw 1.602 2.450 nonbonded pdb=" OE2 GLU B 575 " pdb=" HG SER B 636 " model vdw 1.604 2.450 nonbonded pdb=" OE2 GLU A 575 " pdb=" HG SER A 636 " model vdw 1.608 2.450 nonbonded pdb=" HH TYR C 420 " pdb=" OD1 ASP C 456 " model vdw 1.620 2.450 ... (remaining 253143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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 group one per residue 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: 4.950 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 39.670 Find NCS groups from input model: 0.420 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 : 0.013 0.045 9776 Z= 0.827 Angle : 1.699 8.247 13288 Z= 1.177 Chirality : 0.091 0.415 1496 Planarity : 0.016 0.169 1620 Dihedral : 11.424 82.638 3420 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.87 (0.23), residues: 1140 helix: -0.72 (0.15), residues: 868 sheet: None (None), residues: 0 loop : 0.63 (0.45), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.122 0.016 TRP B 705 HIS 0.013 0.003 HIS A 587 PHE 0.086 0.012 PHE D 701 TYR 0.184 0.022 TYR B 652 ARG 0.008 0.001 ARG D 531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.435 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: symmetry clash REVERT: A 461 ILE cc_start: 0.7911 (mm) cc_final: 0.7649 (mt) REVERT: A 688 GLN cc_start: 0.8191 (mt0) cc_final: 0.7960 (tm-30) REVERT: A 707 TYR cc_start: 0.7726 (t80) cc_final: 0.7475 (t80) REVERT: B 398 TRP cc_start: 0.6067 (m-90) cc_final: 0.5723 (m100) REVERT: B 468 LEU cc_start: 0.7761 (mt) cc_final: 0.7556 (mt) REVERT: B 472 ARG cc_start: 0.6638 (mmt180) cc_final: 0.6425 (mmm160) REVERT: B 578 HIS cc_start: 0.5045 (t-170) cc_final: 0.3686 (m170) REVERT: B 583 ILE cc_start: 0.8712 (mm) cc_final: 0.8478 (mt) REVERT: C 574 MET cc_start: 0.7535 (mtt) cc_final: 0.7331 (mtp) REVERT: C 591 ASP cc_start: 0.7814 (m-30) cc_final: 0.7215 (m-30) REVERT: C 677 MET cc_start: 0.8348 (tpp) cc_final: 0.8115 (tpt) REVERT: D 578 HIS cc_start: 0.6452 (t-170) cc_final: 0.5725 (t70) REVERT: D 673 TYR cc_start: 0.8452 (t80) cc_final: 0.8168 (t80) REVERT: D 682 GLU cc_start: 0.8304 (tt0) cc_final: 0.7913 (tt0) REVERT: D 696 ARG cc_start: 0.8301 (mtp180) cc_final: 0.8059 (mtm-85) REVERT: D 702 GLN cc_start: 0.7913 (mt0) cc_final: 0.7703 (mt0) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.6675 time to fit residues: 217.4678 Evaluate side-chains 177 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN A 576 GLN B 674 HIS C 470 ASN C 578 HIS C 674 HIS C 702 GLN D 703 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9776 Z= 0.199 Angle : 0.554 4.695 13288 Z= 0.310 Chirality : 0.040 0.147 1496 Planarity : 0.005 0.061 1620 Dihedral : 5.011 25.624 1280 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.08 % Allowed : 4.22 % Favored : 94.71 % 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: 1.16 (0.25), residues: 1140 helix: 0.77 (0.16), residues: 888 sheet: None (None), residues: 0 loop : 1.28 (0.49), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 585 HIS 0.014 0.002 HIS C 578 PHE 0.018 0.002 PHE B 701 TYR 0.015 0.002 TYR D 700 ARG 0.008 0.001 ARG C 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 1.603 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: B 673 TYR cc_start: 0.8201 (t80) cc_final: 0.7983 (t80) REVERT: B 681 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.7622 (mtm-85) REVERT: D 578 HIS cc_start: 0.6173 (t-170) cc_final: 0.5355 (t70) REVERT: D 673 TYR cc_start: 0.8291 (t80) cc_final: 0.7999 (t80) outliers start: 11 outliers final: 8 residues processed: 185 average time/residue: 0.5021 time to fit residues: 129.7139 Evaluate side-chains 160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 703 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 105 optimal weight: 0.0470 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN B 687 HIS D 702 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9776 Z= 0.248 Angle : 0.521 4.829 13288 Z= 0.290 Chirality : 0.039 0.156 1496 Planarity : 0.004 0.053 1620 Dihedral : 4.609 25.112 1280 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.18 % Allowed : 4.90 % Favored : 93.92 % 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: 1.64 (0.25), residues: 1140 helix: 1.08 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 1.58 (0.48), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 585 HIS 0.012 0.001 HIS D 703 PHE 0.016 0.001 PHE B 701 TYR 0.014 0.002 TYR D 700 ARG 0.006 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 578 HIS cc_start: 0.5126 (t-170) cc_final: 0.3464 (m90) REVERT: B 673 TYR cc_start: 0.8297 (t80) cc_final: 0.7980 (t80) REVERT: B 681 ARG cc_start: 0.7912 (ttp-170) cc_final: 0.7659 (mtm-85) REVERT: C 677 MET cc_start: 0.8750 (tpp) cc_final: 0.8382 (tpt) REVERT: D 578 HIS cc_start: 0.6403 (t-170) cc_final: 0.5468 (t70) REVERT: D 673 TYR cc_start: 0.8371 (t80) cc_final: 0.8043 (t80) REVERT: D 688 GLN cc_start: 0.8787 (mt0) cc_final: 0.8396 (mm-40) REVERT: D 699 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7944 (mt-10) outliers start: 12 outliers final: 9 residues processed: 167 average time/residue: 0.4296 time to fit residues: 103.1170 Evaluate side-chains 163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 703 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 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 587 HIS A 635 ASN D 703 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9776 Z= 0.275 Angle : 0.517 5.286 13288 Z= 0.286 Chirality : 0.039 0.156 1496 Planarity : 0.004 0.049 1620 Dihedral : 4.455 23.019 1280 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.08 % Allowed : 6.37 % Favored : 92.55 % 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: 1.65 (0.25), residues: 1140 helix: 1.13 (0.17), residues: 880 sheet: None (None), residues: 0 loop : 1.41 (0.48), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 585 HIS 0.009 0.001 HIS C 578 PHE 0.014 0.002 PHE B 494 TYR 0.015 0.002 TYR B 616 ARG 0.004 0.000 ARG B 534 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 578 HIS cc_start: 0.5156 (t-170) cc_final: 0.3488 (m90) REVERT: B 681 ARG cc_start: 0.7975 (ttp-170) cc_final: 0.7735 (mtm-85) REVERT: C 677 MET cc_start: 0.8791 (tpp) cc_final: 0.8310 (tpt) REVERT: C 695 GLN cc_start: 0.7546 (tt0) cc_final: 0.7196 (tt0) REVERT: C 699 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7150 (mt-10) REVERT: D 578 HIS cc_start: 0.6485 (t-170) cc_final: 0.5525 (t70) REVERT: D 673 TYR cc_start: 0.8422 (t80) cc_final: 0.8051 (t80) REVERT: D 688 GLN cc_start: 0.8725 (mt0) cc_final: 0.8331 (mm-40) outliers start: 11 outliers final: 9 residues processed: 159 average time/residue: 0.4225 time to fit residues: 98.1123 Evaluate side-chains 160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 703 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN A 635 ASN C 578 HIS D 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 9776 Z= 0.318 Angle : 0.531 7.243 13288 Z= 0.294 Chirality : 0.040 0.158 1496 Planarity : 0.004 0.049 1620 Dihedral : 4.425 21.356 1280 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.57 % Allowed : 7.75 % Favored : 90.69 % 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: 1.54 (0.25), residues: 1140 helix: 1.07 (0.17), residues: 880 sheet: None (None), residues: 0 loop : 1.30 (0.47), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 585 HIS 0.009 0.001 HIS D 703 PHE 0.014 0.002 PHE C 656 TYR 0.016 0.002 TYR B 616 ARG 0.003 0.000 ARG B 534 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8097 (mp) REVERT: A 652 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.6777 (m-80) REVERT: B 578 HIS cc_start: 0.5238 (t-170) cc_final: 0.3648 (m90) REVERT: C 677 MET cc_start: 0.8769 (tpp) cc_final: 0.8278 (tpt) REVERT: C 695 GLN cc_start: 0.7756 (tt0) cc_final: 0.7383 (tt0) REVERT: C 699 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7182 (mt-10) REVERT: D 578 HIS cc_start: 0.6648 (t-170) cc_final: 0.5631 (t70) REVERT: D 579 MET cc_start: 0.6443 (mtp) cc_final: 0.6105 (mtp) REVERT: D 673 TYR cc_start: 0.8438 (t80) cc_final: 0.8012 (t80) REVERT: D 688 GLN cc_start: 0.8697 (mt0) cc_final: 0.8327 (mm-40) REVERT: D 698 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6611 (mt-10) REVERT: D 699 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8124 (mt-10) outliers start: 16 outliers final: 11 residues processed: 162 average time/residue: 0.4188 time to fit residues: 100.5254 Evaluate side-chains 168 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 652 TYR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 703 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN D 703 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 9776 Z= 0.227 Angle : 0.484 7.820 13288 Z= 0.263 Chirality : 0.038 0.153 1496 Planarity : 0.004 0.046 1620 Dihedral : 4.259 20.396 1280 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.37 % Allowed : 8.73 % Favored : 89.90 % 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: 1.78 (0.26), residues: 1140 helix: 1.24 (0.17), residues: 880 sheet: None (None), residues: 0 loop : 1.40 (0.48), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 585 HIS 0.005 0.001 HIS D 703 PHE 0.013 0.001 PHE C 656 TYR 0.015 0.001 TYR B 616 ARG 0.003 0.000 ARG C 537 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 524 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8109 (mp) REVERT: A 652 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.6587 (m-80) REVERT: A 678 LEU cc_start: 0.8690 (tp) cc_final: 0.8464 (tt) REVERT: B 578 HIS cc_start: 0.5240 (t-170) cc_final: 0.3697 (m90) REVERT: C 695 GLN cc_start: 0.7695 (tt0) cc_final: 0.7246 (tt0) REVERT: C 699 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7144 (mt-10) REVERT: D 578 HIS cc_start: 0.6640 (t-170) cc_final: 0.5640 (t70) REVERT: D 579 MET cc_start: 0.6272 (mtp) cc_final: 0.5888 (mtp) REVERT: D 673 TYR cc_start: 0.8427 (t80) cc_final: 0.7991 (t80) REVERT: D 688 GLN cc_start: 0.8669 (mt0) cc_final: 0.8333 (mm-40) outliers start: 14 outliers final: 8 residues processed: 156 average time/residue: 0.4155 time to fit residues: 94.8144 Evaluate side-chains 161 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 652 TYR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 703 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN C 635 ASN D 702 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9776 Z= 0.197 Angle : 0.470 8.137 13288 Z= 0.255 Chirality : 0.037 0.153 1496 Planarity : 0.004 0.046 1620 Dihedral : 4.123 19.763 1280 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.27 % Allowed : 8.63 % Favored : 90.10 % 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: 2.02 (0.26), residues: 1140 helix: 1.43 (0.17), residues: 872 sheet: None (None), residues: 0 loop : 1.43 (0.47), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.009 0.001 HIS D 703 PHE 0.014 0.001 PHE D 701 TYR 0.014 0.001 TYR B 616 ARG 0.002 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 524 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8122 (mp) REVERT: A 652 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: B 578 HIS cc_start: 0.5201 (t-170) cc_final: 0.3685 (m90) REVERT: D 578 HIS cc_start: 0.6535 (t-170) cc_final: 0.5560 (t70) REVERT: D 673 TYR cc_start: 0.8411 (t80) cc_final: 0.7978 (t80) REVERT: D 688 GLN cc_start: 0.8662 (mt0) cc_final: 0.8348 (mm-40) outliers start: 13 outliers final: 8 residues processed: 158 average time/residue: 0.4415 time to fit residues: 100.2544 Evaluate side-chains 163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 652 TYR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 703 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN C 635 ASN D 703 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9776 Z= 0.196 Angle : 0.471 8.626 13288 Z= 0.253 Chirality : 0.037 0.152 1496 Planarity : 0.004 0.044 1620 Dihedral : 4.069 19.475 1280 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.08 % Allowed : 9.22 % Favored : 89.71 % 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: 2.10 (0.26), residues: 1140 helix: 1.48 (0.17), residues: 872 sheet: None (None), residues: 0 loop : 1.45 (0.47), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 568 HIS 0.009 0.001 HIS D 703 PHE 0.022 0.001 PHE D 701 TYR 0.014 0.001 TYR B 616 ARG 0.002 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 524 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8119 (mp) REVERT: A 652 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6467 (m-80) REVERT: B 578 HIS cc_start: 0.5120 (t-170) cc_final: 0.3856 (m90) REVERT: D 578 HIS cc_start: 0.6554 (t-170) cc_final: 0.5600 (t70) REVERT: D 673 TYR cc_start: 0.8411 (t80) cc_final: 0.7893 (t80) REVERT: D 688 GLN cc_start: 0.8663 (mt0) cc_final: 0.8362 (mm-40) outliers start: 11 outliers final: 8 residues processed: 159 average time/residue: 0.4449 time to fit residues: 102.3197 Evaluate side-chains 163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 652 TYR Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 703 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN C 635 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 9776 Z= 0.297 Angle : 0.518 8.888 13288 Z= 0.284 Chirality : 0.039 0.155 1496 Planarity : 0.004 0.046 1620 Dihedral : 4.188 20.530 1280 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.18 % Allowed : 9.31 % Favored : 89.51 % 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: 1.85 (0.26), residues: 1140 helix: 1.31 (0.17), residues: 872 sheet: None (None), residues: 0 loop : 1.31 (0.46), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 568 HIS 0.006 0.001 HIS D 703 PHE 0.016 0.002 PHE C 656 TYR 0.016 0.002 TYR A 616 ARG 0.002 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 652 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6703 (m-80) REVERT: B 578 HIS cc_start: 0.5191 (t-170) cc_final: 0.4007 (m90) REVERT: D 501 ASP cc_start: 0.8127 (m-30) cc_final: 0.7804 (m-30) REVERT: D 578 HIS cc_start: 0.6561 (t-170) cc_final: 0.5622 (t70) REVERT: D 673 TYR cc_start: 0.8406 (t80) cc_final: 0.7920 (t80) REVERT: D 688 GLN cc_start: 0.8634 (mt0) cc_final: 0.8328 (mm-40) outliers start: 12 outliers final: 10 residues processed: 159 average time/residue: 0.4627 time to fit residues: 106.4586 Evaluate side-chains 164 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 652 TYR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 703 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 0.0040 chunk 115 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN C 635 ASN D 703 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9776 Z= 0.195 Angle : 0.470 9.477 13288 Z= 0.252 Chirality : 0.037 0.151 1496 Planarity : 0.004 0.044 1620 Dihedral : 4.058 19.343 1280 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.98 % Allowed : 9.41 % Favored : 89.61 % 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: 2.15 (0.26), residues: 1140 helix: 1.54 (0.17), residues: 868 sheet: None (None), residues: 0 loop : 1.37 (0.46), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 585 HIS 0.006 0.001 HIS D 703 PHE 0.012 0.001 PHE C 656 TYR 0.014 0.001 TYR B 616 ARG 0.002 0.000 ARG C 679 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 578 HIS cc_start: 0.5388 (t-170) cc_final: 0.4331 (m-70) REVERT: A 652 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.6426 (m-80) REVERT: B 578 HIS cc_start: 0.5155 (t-170) cc_final: 0.3994 (m90) REVERT: D 578 HIS cc_start: 0.6527 (t-170) cc_final: 0.5597 (t70) REVERT: D 673 TYR cc_start: 0.8361 (t80) cc_final: 0.7932 (t80) REVERT: D 688 GLN cc_start: 0.8631 (mt0) cc_final: 0.8343 (mm-40) outliers start: 10 outliers final: 9 residues processed: 159 average time/residue: 0.4410 time to fit residues: 99.9589 Evaluate side-chains 163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 652 TYR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 703 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN C 635 ASN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.153520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.103366 restraints weight = 31931.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.106479 restraints weight = 22108.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.108467 restraints weight = 18095.646| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9776 Z= 0.247 Angle : 0.495 9.077 13288 Z= 0.268 Chirality : 0.038 0.153 1496 Planarity : 0.004 0.045 1620 Dihedral : 4.085 19.909 1280 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.98 % Allowed : 9.61 % Favored : 89.41 % 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: 2.04 (0.26), residues: 1140 helix: 1.47 (0.17), residues: 868 sheet: None (None), residues: 0 loop : 1.32 (0.46), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 568 HIS 0.003 0.001 HIS D 687 PHE 0.015 0.001 PHE C 656 TYR 0.015 0.002 TYR B 616 ARG 0.002 0.000 ARG A 528 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3853.44 seconds wall clock time: 70 minutes 11.79 seconds (4211.79 seconds total)