Starting phenix.real_space_refine on Fri Mar 15 10:33:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpr_36487/03_2024/8jpr_36487_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpr_36487/03_2024/8jpr_36487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpr_36487/03_2024/8jpr_36487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpr_36487/03_2024/8jpr_36487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpr_36487/03_2024/8jpr_36487_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpr_36487/03_2024/8jpr_36487_updated.pdb" } resolution = 3.4 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= 0.007 sd= 0.058 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 72 5.16 5 Cl 4 4.86 5 C 7368 2.51 5 N 1910 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 670": "OE1" <-> "OE2" Residue "A GLU 733": "OE1" <-> "OE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "B GLU 733": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11396 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5664 Classifications: {'peptide': 730} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 30, 'TRANS': 699} Chain breaks: 4 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 5664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5664 Classifications: {'peptide': 730} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 30, 'TRANS': 699} Chain breaks: 4 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.55, per 1000 atoms: 0.57 Number of scatterers: 11396 At special positions: 0 Unit cell: (96.301, 92.9514, 113.886, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 72 16.00 P 6 15.00 Mg 2 11.99 O 2034 8.00 N 1910 7.00 C 7368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 125 " distance=2.02 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 430 " distance=2.04 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 125 " distance=2.02 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 430 " distance=2.04 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: 4.06 Conformation dependent library (CDL) restraints added in 2.1 seconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2684 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 4 sheets defined 58.4% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 59 through 67 Processing helix chain 'A' and resid 70 through 123 removed outlier: 3.660A pdb=" N GLN A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 150 removed outlier: 3.669A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 159 through 167 removed outlier: 3.859A pdb=" N CYS A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.687A pdb=" N LEU A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 215 removed outlier: 4.100A pdb=" N ILE A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 235 through 254 removed outlier: 4.001A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 298 removed outlier: 3.869A pdb=" N LYS A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 365 removed outlier: 3.729A pdb=" N GLY A 335 " --> pdb=" O MET A 332 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET A 340 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 343 " --> pdb=" O MET A 340 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 344 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 346 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LYS A 356 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS A 360 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET A 363 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 394 Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 462 through 479 removed outlier: 4.259A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 476 " --> pdb=" O TYR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 removed outlier: 3.719A pdb=" N CYS A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 533 Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 555 through 568 removed outlier: 3.833A pdb=" N VAL A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 582 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 601 through 604 No H-bonds generated for 'chain 'A' and resid 601 through 604' Processing helix chain 'A' and resid 618 through 627 Processing helix chain 'A' and resid 650 through 663 Processing helix chain 'A' and resid 667 through 676 Processing helix chain 'A' and resid 732 through 735 No H-bonds generated for 'chain 'A' and resid 732 through 735' Processing helix chain 'A' and resid 747 through 755 Processing helix chain 'A' and resid 774 through 777 No H-bonds generated for 'chain 'A' and resid 774 through 777' Processing helix chain 'A' and resid 820 through 829 Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 855 through 868 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 70 through 123 removed outlier: 3.651A pdb=" N GLN B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 150 removed outlier: 3.667A pdb=" N LEU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 159 through 167 removed outlier: 3.843A pdb=" N CYS B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 193 removed outlier: 3.690A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY B 193 " --> pdb=" O PHE B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 4.102A pdb=" N ILE B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Proline residue: B 215 - end of helix Processing helix chain 'B' and resid 235 through 254 removed outlier: 4.004A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 298 removed outlier: 3.846A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 365 removed outlier: 3.728A pdb=" N GLY B 335 " --> pdb=" O MET B 332 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET B 340 " --> pdb=" O PHE B 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE B 343 " --> pdb=" O MET B 340 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY B 344 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 346 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS B 356 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS B 360 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET B 363 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 394 Processing helix chain 'B' and resid 437 through 442 Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 451 through 455 Processing helix chain 'B' and resid 462 through 479 removed outlier: 4.229A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 476 " --> pdb=" O TYR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 509 removed outlier: 3.716A pdb=" N CYS B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 533 Processing helix chain 'B' and resid 539 through 548 Processing helix chain 'B' and resid 555 through 568 removed outlier: 3.503A pdb=" N THR B 560 " --> pdb=" O PRO B 556 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 582 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 601 through 604 No H-bonds generated for 'chain 'B' and resid 601 through 604' Processing helix chain 'B' and resid 618 through 627 Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 667 through 676 Processing helix chain 'B' and resid 732 through 735 No H-bonds generated for 'chain 'B' and resid 732 through 735' Processing helix chain 'B' and resid 747 through 755 Processing helix chain 'B' and resid 774 through 777 No H-bonds generated for 'chain 'B' and resid 774 through 777' Processing helix chain 'B' and resid 820 through 829 Processing helix chain 'B' and resid 850 through 852 No H-bonds generated for 'chain 'B' and resid 850 through 852' Processing helix chain 'B' and resid 855 through 868 Processing sheet with id= A, first strand: chain 'A' and resid 632 through 638 removed outlier: 6.470A pdb=" N THR A 637 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N PHE A 741 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 835 through 838 Processing sheet with id= C, first strand: chain 'B' and resid 632 through 638 removed outlier: 6.466A pdb=" N THR B 637 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N PHE B 741 " --> pdb=" O THR B 637 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 835 through 838 569 hydrogen bonds defined for protein. 1557 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: 3.05 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3595 1.35 - 1.47: 2936 1.47 - 1.60: 5003 1.60 - 1.72: 0 1.72 - 1.85: 112 Bond restraints: 11646 Sorted by residual: bond pdb=" C TYR A 781 " pdb=" N PRO A 782 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.73e+00 bond pdb=" C TYR B 781 " pdb=" N PRO B 782 " ideal model delta sigma weight residual 1.335 1.353 -0.017 1.36e-02 5.41e+03 1.61e+00 bond pdb=" CA VAL B 758 " pdb=" CB VAL B 758 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.38e+00 bond pdb=" CB CYS A 125 " pdb=" SG CYS A 125 " ideal model delta sigma weight residual 1.808 1.845 -0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CA VAL A 758 " pdb=" CB VAL A 758 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.23e+00 ... (remaining 11641 not shown) Histogram of bond angle deviations from ideal: 99.34 - 107.43: 401 107.43 - 115.52: 7083 115.52 - 123.61: 8056 123.61 - 131.69: 244 131.69 - 139.78: 20 Bond angle restraints: 15804 Sorted by residual: angle pdb=" N VAL A 169 " pdb=" CA VAL A 169 " pdb=" C VAL A 169 " ideal model delta sigma weight residual 112.96 109.14 3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" N VAL B 169 " pdb=" CA VAL B 169 " pdb=" C VAL B 169 " ideal model delta sigma weight residual 112.96 109.17 3.79 1.00e+00 1.00e+00 1.44e+01 angle pdb=" CA CYS B 125 " pdb=" CB CYS B 125 " pdb=" SG CYS B 125 " ideal model delta sigma weight residual 114.40 122.48 -8.08 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CA CYS A 125 " pdb=" CB CYS A 125 " pdb=" SG CYS A 125 " ideal model delta sigma weight residual 114.40 122.41 -8.01 2.30e+00 1.89e-01 1.21e+01 angle pdb=" N VAL B 148 " pdb=" CA VAL B 148 " pdb=" C VAL B 148 " ideal model delta sigma weight residual 112.35 108.61 3.74 1.41e+00 5.03e-01 7.03e+00 ... (remaining 15799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 6274 17.30 - 34.59: 491 34.59 - 51.89: 110 51.89 - 69.19: 10 69.19 - 86.49: 17 Dihedral angle restraints: 6902 sinusoidal: 2726 harmonic: 4176 Sorted by residual: dihedral pdb=" CB CYS B 399 " pdb=" SG CYS B 399 " pdb=" SG CYS B 430 " pdb=" CB CYS B 430 " ideal model delta sinusoidal sigma weight residual 93.00 165.01 -72.01 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CB CYS B 120 " pdb=" SG CYS B 120 " pdb=" SG CYS B 125 " pdb=" CB CYS B 125 " ideal model delta sinusoidal sigma weight residual -86.00 -152.44 66.44 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS A 399 " pdb=" SG CYS A 399 " pdb=" SG CYS A 430 " pdb=" CB CYS A 430 " ideal model delta sinusoidal sigma weight residual 93.00 158.88 -65.88 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 6899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1264 0.034 - 0.068: 419 0.068 - 0.102: 98 0.102 - 0.137: 47 0.137 - 0.171: 4 Chirality restraints: 1832 Sorted by residual: chirality pdb=" CA PHE B 101 " pdb=" N PHE B 101 " pdb=" C PHE B 101 " pdb=" CB PHE B 101 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA PHE A 101 " pdb=" N PHE A 101 " pdb=" C PHE A 101 " pdb=" CB PHE A 101 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA VAL B 171 " pdb=" N VAL B 171 " pdb=" C VAL B 171 " pdb=" CB VAL B 171 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1829 not shown) Planarity restraints: 1976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 351 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C PHE A 351 " 0.028 2.00e-02 2.50e+03 pdb=" O PHE A 351 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 352 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 835 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO B 836 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 836 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 836 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 835 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 836 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 836 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 836 " 0.021 5.00e-02 4.00e+02 ... (remaining 1973 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 122 2.67 - 3.23: 11260 3.23 - 3.78: 17384 3.78 - 4.34: 23707 4.34 - 4.90: 40288 Nonbonded interactions: 92761 Sorted by model distance: nonbonded pdb=" OD1 ASP A 235 " pdb=" OH TYR A 781 " model vdw 2.111 2.440 nonbonded pdb=" OD1 ASP B 235 " pdb=" OH TYR B 781 " model vdw 2.111 2.440 nonbonded pdb=" O PRO B 431 " pdb=" OG1 THR B 434 " model vdw 2.150 2.440 nonbonded pdb=" O PRO A 431 " pdb=" OG1 THR A 434 " model vdw 2.162 2.440 nonbonded pdb=" O PHE B 428 " pdb=" ND2 ASN B 436 " model vdw 2.230 2.520 ... (remaining 92756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 869 or resid 902 or resid 904)) selection = (chain 'B' and (resid 46 through 869 or resid 902 or resid 904)) } 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.300 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.960 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.060 ------------------------------------------------------------------------------- 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 : 0.003 0.037 11646 Z= 0.182 Angle : 0.556 8.080 15804 Z= 0.310 Chirality : 0.039 0.171 1832 Planarity : 0.004 0.039 1976 Dihedral : 13.514 86.486 4200 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 1.04 (0.23), residues: 1440 helix: 1.58 (0.18), residues: 886 sheet: -4.21 (0.63), residues: 20 loop : -0.59 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 278 HIS 0.002 0.001 HIS A 834 PHE 0.023 0.001 PHE B 101 TYR 0.007 0.001 TYR A 781 ARG 0.004 0.000 ARG B 501 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 ARG cc_start: 0.7411 (mtp180) cc_final: 0.7083 (mtp85) REVERT: B 374 ARG cc_start: 0.7404 (mtp180) cc_final: 0.7077 (mtp85) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2880 time to fit residues: 97.5416 Evaluate side-chains 121 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.4980 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 132 optimal weight: 0.0980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 452 GLN A 764 GLN B 444 ASN B 764 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11646 Z= 0.179 Angle : 0.511 6.959 15804 Z= 0.261 Chirality : 0.039 0.148 1832 Planarity : 0.004 0.035 1976 Dihedral : 8.626 89.063 1632 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.08 % Favored : 97.78 % Rotamer: Outliers : 0.97 % Allowed : 6.94 % Favored : 92.10 % 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: 1.20 (0.23), residues: 1440 helix: 1.73 (0.18), residues: 886 sheet: -4.28 (0.61), residues: 20 loop : -0.57 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 278 HIS 0.002 0.001 HIS B 327 PHE 0.010 0.001 PHE A 351 TYR 0.008 0.001 TYR A 781 ARG 0.003 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 670 GLU cc_start: 0.7335 (tm-30) cc_final: 0.7082 (tm-30) REVERT: B 354 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7827 (mp) REVERT: B 670 GLU cc_start: 0.7279 (tm-30) cc_final: 0.7065 (tm-30) outliers start: 12 outliers final: 6 residues processed: 136 average time/residue: 0.2468 time to fit residues: 48.2336 Evaluate side-chains 117 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 594 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 367 HIS ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN B 355 ASN B 367 HIS ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 11646 Z= 0.409 Angle : 0.639 7.315 15804 Z= 0.328 Chirality : 0.045 0.167 1832 Planarity : 0.005 0.040 1976 Dihedral : 8.967 89.138 1632 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.19 % Favored : 96.67 % Rotamer: Outliers : 1.85 % Allowed : 10.65 % Favored : 87.50 % 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: 0.80 (0.23), residues: 1440 helix: 1.38 (0.18), residues: 886 sheet: -4.28 (0.61), residues: 20 loop : -0.66 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 303 HIS 0.005 0.001 HIS A 819 PHE 0.020 0.002 PHE A 289 TYR 0.010 0.001 TYR B 806 ARG 0.003 0.001 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.310 Fit side-chains REVERT: A 670 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7216 (tm-30) REVERT: B 381 VAL cc_start: 0.8264 (t) cc_final: 0.8024 (t) REVERT: B 670 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7240 (tm-30) outliers start: 23 outliers final: 17 residues processed: 138 average time/residue: 0.2327 time to fit residues: 47.0424 Evaluate side-chains 119 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 444 ASN A 742 HIS B 355 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11646 Z= 0.157 Angle : 0.501 8.402 15804 Z= 0.254 Chirality : 0.038 0.143 1832 Planarity : 0.004 0.033 1976 Dihedral : 8.388 89.175 1632 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.74 % Favored : 98.12 % Rotamer: Outliers : 0.97 % Allowed : 13.39 % Favored : 85.65 % 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: 1.29 (0.23), residues: 1440 helix: 1.80 (0.18), residues: 886 sheet: -4.28 (0.70), residues: 20 loop : -0.54 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 278 HIS 0.002 0.000 HIS B 579 PHE 0.013 0.001 PHE A 300 TYR 0.008 0.001 TYR B 76 ARG 0.003 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 381 VAL cc_start: 0.8147 (t) cc_final: 0.7938 (t) outliers start: 12 outliers final: 11 residues processed: 121 average time/residue: 0.2428 time to fit residues: 42.5811 Evaluate side-chains 112 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 355 ASN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN B 355 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 11646 Z= 0.514 Angle : 0.697 7.092 15804 Z= 0.357 Chirality : 0.047 0.189 1832 Planarity : 0.005 0.043 1976 Dihedral : 8.815 77.799 1632 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.19 % Favored : 96.67 % Rotamer: Outliers : 2.50 % Allowed : 14.27 % Favored : 83.23 % 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: 0.62 (0.23), residues: 1440 helix: 1.20 (0.18), residues: 886 sheet: None (None), residues: 0 loop : -0.85 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 303 HIS 0.006 0.002 HIS B 819 PHE 0.024 0.002 PHE A 289 TYR 0.010 0.001 TYR B 806 ARG 0.004 0.001 ARG B 783 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 VAL cc_start: 0.8345 (t) cc_final: 0.8070 (t) REVERT: B 381 VAL cc_start: 0.8300 (t) cc_final: 0.8061 (t) outliers start: 31 outliers final: 20 residues processed: 137 average time/residue: 0.2226 time to fit residues: 44.6786 Evaluate side-chains 121 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 141 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11646 Z= 0.161 Angle : 0.492 6.023 15804 Z= 0.253 Chirality : 0.038 0.145 1832 Planarity : 0.004 0.035 1976 Dihedral : 7.988 71.099 1632 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.01 % Favored : 97.85 % Rotamer: Outliers : 1.69 % Allowed : 15.24 % Favored : 83.06 % 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: 1.29 (0.23), residues: 1440 helix: 1.83 (0.18), residues: 886 sheet: -4.29 (0.71), residues: 20 loop : -0.57 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 278 HIS 0.002 0.000 HIS B 819 PHE 0.011 0.001 PHE B 300 TYR 0.009 0.001 TYR A 76 ARG 0.003 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 VAL cc_start: 0.8190 (t) cc_final: 0.7974 (t) outliers start: 21 outliers final: 17 residues processed: 123 average time/residue: 0.2296 time to fit residues: 41.2752 Evaluate side-chains 120 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 103 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11646 Z= 0.259 Angle : 0.537 8.675 15804 Z= 0.275 Chirality : 0.040 0.143 1832 Planarity : 0.004 0.034 1976 Dihedral : 7.784 68.322 1632 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.71 % Favored : 97.15 % Rotamer: Outliers : 1.77 % Allowed : 15.32 % Favored : 82.90 % 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: 1.25 (0.23), residues: 1440 helix: 1.81 (0.18), residues: 884 sheet: -4.32 (0.69), residues: 20 loop : -0.62 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 278 HIS 0.003 0.001 HIS B 819 PHE 0.017 0.001 PHE A 289 TYR 0.008 0.001 TYR A 76 ARG 0.003 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 VAL cc_start: 0.8210 (t) cc_final: 0.7972 (t) outliers start: 22 outliers final: 21 residues processed: 126 average time/residue: 0.2292 time to fit residues: 42.2070 Evaluate side-chains 122 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11646 Z= 0.214 Angle : 0.514 5.857 15804 Z= 0.267 Chirality : 0.039 0.144 1832 Planarity : 0.004 0.035 1976 Dihedral : 7.448 65.405 1632 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.50 % Favored : 97.36 % Rotamer: Outliers : 1.69 % Allowed : 15.97 % Favored : 82.34 % 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: 1.31 (0.23), residues: 1440 helix: 1.88 (0.18), residues: 880 sheet: -4.42 (0.69), residues: 20 loop : -0.59 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 278 HIS 0.003 0.001 HIS B 819 PHE 0.015 0.001 PHE A 289 TYR 0.009 0.001 TYR A 76 ARG 0.004 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 VAL cc_start: 0.8186 (t) cc_final: 0.7965 (t) outliers start: 21 outliers final: 19 residues processed: 128 average time/residue: 0.2238 time to fit residues: 41.9818 Evaluate side-chains 123 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11646 Z= 0.220 Angle : 0.509 5.826 15804 Z= 0.264 Chirality : 0.040 0.143 1832 Planarity : 0.004 0.035 1976 Dihedral : 7.061 64.422 1632 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.85 % Favored : 97.01 % Rotamer: Outliers : 1.77 % Allowed : 16.05 % Favored : 82.18 % 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: 1.27 (0.23), residues: 1440 helix: 1.86 (0.18), residues: 880 sheet: -4.40 (0.68), residues: 20 loop : -0.64 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.003 0.001 HIS A 819 PHE 0.015 0.001 PHE A 289 TYR 0.008 0.001 TYR A 76 ARG 0.004 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 VAL cc_start: 0.8184 (t) cc_final: 0.7952 (t) REVERT: B 381 VAL cc_start: 0.8182 (t) cc_final: 0.7932 (t) outliers start: 22 outliers final: 22 residues processed: 132 average time/residue: 0.2719 time to fit residues: 52.9000 Evaluate side-chains 130 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11646 Z= 0.142 Angle : 0.484 8.746 15804 Z= 0.249 Chirality : 0.038 0.144 1832 Planarity : 0.004 0.036 1976 Dihedral : 6.358 60.256 1632 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.08 % Favored : 97.78 % Rotamer: Outliers : 1.53 % Allowed : 16.21 % Favored : 82.26 % 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: 1.50 (0.23), residues: 1440 helix: 2.05 (0.18), residues: 884 sheet: -4.41 (0.73), residues: 20 loop : -0.59 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 278 HIS 0.002 0.000 HIS B 819 PHE 0.015 0.001 PHE B 300 TYR 0.008 0.001 TYR A 76 ARG 0.004 0.000 ARG A 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.261 Fit side-chains REVERT: A 381 VAL cc_start: 0.8104 (t) cc_final: 0.7902 (t) REVERT: B 381 VAL cc_start: 0.8111 (t) cc_final: 0.7882 (t) outliers start: 19 outliers final: 17 residues processed: 132 average time/residue: 0.2362 time to fit residues: 45.4039 Evaluate side-chains 127 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 106 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 HIS ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111356 restraints weight = 16385.154| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.21 r_work: 0.3188 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11646 Z= 0.209 Angle : 0.524 9.866 15804 Z= 0.266 Chirality : 0.040 0.144 1832 Planarity : 0.004 0.035 1976 Dihedral : 6.232 60.867 1632 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.78 % Favored : 97.08 % Rotamer: Outliers : 1.45 % Allowed : 16.29 % Favored : 82.26 % 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: 1.38 (0.23), residues: 1440 helix: 1.97 (0.18), residues: 890 sheet: -4.41 (0.73), residues: 20 loop : -0.70 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 278 HIS 0.003 0.001 HIS A 819 PHE 0.016 0.001 PHE A 289 TYR 0.008 0.001 TYR A 76 ARG 0.004 0.000 ARG A 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.59 seconds wall clock time: 42 minutes 18.37 seconds (2538.37 seconds total)