Starting phenix.real_space_refine on Fri Oct 11 21:46:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/10_2024/8wos_37697_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/10_2024/8wos_37697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/10_2024/8wos_37697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/10_2024/8wos_37697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/10_2024/8wos_37697_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/10_2024/8wos_37697_neut.cif" } resolution = 3.37 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= 0.013 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 Zn 2 6.06 5 S 58 5.16 5 C 7106 2.51 5 N 1644 2.21 5 O 1862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 10672 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5139 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 611} Chain breaks: 3 Chain: "B" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5139 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 611} Chain breaks: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.66, per 1000 atoms: 0.72 Number of scatterers: 10672 At special positions: 0 Unit cell: (97.865, 86.802, 137.011, 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) Zn 2 29.99 S 58 16.00 O 1862 8.00 N 1644 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 901 " - " ASN A 67 " " NAG A 902 " - " ASN A 136 " " NAG B 901 " - " ASN B 67 " " NAG B 902 " - " ASN B 136 " " NAG C 1 " - " ASN A 83 " " NAG D 1 " - " ASN A 57 " " NAG E 1 " - " ASN B 83 " " NAG F 1 " - " ASN B 57 " Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 907 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 907 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 800 " 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 50.8% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 302 through 336 removed outlier: 3.884A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 474 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.941A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 501 through 529 removed outlier: 3.863A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 removed outlier: 3.602A pdb=" N GLU A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 565 removed outlier: 3.609A pdb=" N TYR A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N CYS A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 4.228A pdb=" N PHE A 571 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 594 removed outlier: 3.748A pdb=" N TYR A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 622 removed outlier: 3.922A pdb=" N TYR A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 649 Processing helix chain 'A' and resid 689 through 709 Processing helix chain 'A' and resid 713 through 740 Processing helix chain 'A' and resid 745 through 768 removed outlier: 3.667A pdb=" N GLN A 768 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 794 through 817 Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'B' and resid 38 through 43 Processing helix chain 'B' and resid 302 through 336 removed outlier: 3.866A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 474 removed outlier: 3.564A pdb=" N VAL B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 482 through 486 removed outlier: 4.030A pdb=" N ALA B 486 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 501 through 529 removed outlier: 3.833A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 508 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 removed outlier: 3.637A pdb=" N GLU B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 565 removed outlier: 3.522A pdb=" N TYR B 546 " --> pdb=" O PHE B 542 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N CYS B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.872A pdb=" N PHE B 571 " --> pdb=" O TYR B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 594 removed outlier: 3.926A pdb=" N MET B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 621 removed outlier: 3.660A pdb=" N TYR B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 649 Processing helix chain 'B' and resid 689 through 709 Processing helix chain 'B' and resid 713 through 740 Processing helix chain 'B' and resid 745 through 768 removed outlier: 3.524A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 768 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 782 Processing helix chain 'B' and resid 794 through 817 Processing helix chain 'B' and resid 818 through 822 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 removed outlier: 4.739A pdb=" N LYS A 192 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 178 through 181 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 70 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA9, first strand: chain 'B' and resid 170 through 171 removed outlier: 4.919A pdb=" N LYS B 192 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 181 615 hydrogen bonds defined for protein. 1758 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: 3.17 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3170 1.34 - 1.46: 2808 1.46 - 1.58: 4908 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 10976 Sorted by residual: bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 ... (remaining 10971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 14591 1.55 - 3.10: 339 3.10 - 4.65: 45 4.65 - 6.20: 1 6.20 - 7.75: 4 Bond angle restraints: 14980 Sorted by residual: angle pdb=" C SER B 600 " pdb=" CA SER B 600 " pdb=" CB SER B 600 " ideal model delta sigma weight residual 116.54 110.30 6.24 1.15e+00 7.56e-01 2.94e+01 angle pdb=" C LEU A 789 " pdb=" CA LEU A 789 " pdb=" CB LEU A 789 " ideal model delta sigma weight residual 116.63 111.62 5.01 1.16e+00 7.43e-01 1.87e+01 angle pdb=" CA SER B 600 " pdb=" C SER B 600 " pdb=" N ALA B 601 " ideal model delta sigma weight residual 119.52 116.43 3.09 7.90e-01 1.60e+00 1.53e+01 angle pdb=" C LEU A 704 " pdb=" N PHE A 705 " pdb=" CA PHE A 705 " ideal model delta sigma weight residual 122.06 114.81 7.25 1.86e+00 2.89e-01 1.52e+01 angle pdb=" C LEU B 789 " pdb=" CA LEU B 789 " pdb=" CB LEU B 789 " ideal model delta sigma weight residual 117.23 112.78 4.45 1.36e+00 5.41e-01 1.07e+01 ... (remaining 14975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.77: 6322 25.77 - 51.54: 518 51.54 - 77.30: 55 77.30 - 103.07: 23 103.07 - 128.84: 10 Dihedral angle restraints: 6928 sinusoidal: 3148 harmonic: 3780 Sorted by residual: dihedral pdb=" CB CYS A 212 " pdb=" SG CYS A 212 " pdb=" SG CYS A 271 " pdb=" CB CYS A 271 " ideal model delta sinusoidal sigma weight residual 93.00 128.21 -35.21 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" C2 NAG B 901 " pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " pdb=" C5 NAG B 901 " ideal model delta sinusoidal sigma weight residual -62.96 65.88 -128.84 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " pdb=" C5 NAG A 901 " ideal model delta sinusoidal sigma weight residual -62.96 65.20 -128.16 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 6925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1612 0.074 - 0.149: 135 0.149 - 0.223: 3 0.223 - 0.298: 0 0.298 - 0.372: 2 Chirality restraints: 1752 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 1749 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 83 " 0.001 2.00e-02 2.50e+03 2.76e-02 9.53e+00 pdb=" CG ASN B 83 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B 83 " -0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN B 83 " 0.038 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 702 " -0.024 2.00e-02 2.50e+03 2.16e-02 8.15e+00 pdb=" CG PHE A 702 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 702 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 702 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 702 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 702 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 702 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 717 " -0.023 2.00e-02 2.50e+03 1.43e-02 4.10e+00 pdb=" CG TYR A 717 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 717 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 717 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 717 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 717 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 717 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 717 " -0.007 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 98 2.53 - 3.13: 8838 3.13 - 3.72: 16130 3.72 - 4.31: 21203 4.31 - 4.90: 36523 Nonbonded interactions: 82792 Sorted by model distance: nonbonded pdb=" OH TYR A 64 " pdb=" OH TYR A 159 " model vdw 1.943 3.040 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 1.961 3.040 nonbonded pdb=" OG SER B 701 " pdb=" OH TYR B 717 " model vdw 1.981 3.040 nonbonded pdb=" OG SER A 740 " pdb=" OE2 GLU A 742 " model vdw 2.036 3.040 nonbonded pdb=" OH TYR A 321 " pdb=" O LEU A 506 " model vdw 2.086 3.040 ... (remaining 82787 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' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.920 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.730 Find NCS groups from input model: 0.370 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 0.053 10976 Z= 0.201 Angle : 0.552 7.753 14980 Z= 0.301 Chirality : 0.041 0.372 1752 Planarity : 0.003 0.049 1802 Dihedral : 18.351 128.840 4470 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 39.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.35 % Allowed : 33.39 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.07 (0.25), residues: 1256 helix: 2.71 (0.21), residues: 568 sheet: 0.51 (0.33), residues: 272 loop : -2.17 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 446 HIS 0.005 0.001 HIS B 636 PHE 0.050 0.001 PHE A 702 TYR 0.032 0.001 TYR A 717 ARG 0.001 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 767 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.6557 (m-80) outliers start: 4 outliers final: 3 residues processed: 148 average time/residue: 0.1789 time to fit residues: 41.9983 Evaluate side-chains 143 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 767 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 10.0000 chunk 95 optimal weight: 0.0060 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 286 ASN B 594 HIS ** B 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10976 Z= 0.248 Angle : 0.683 9.610 14980 Z= 0.334 Chirality : 0.048 0.505 1752 Planarity : 0.004 0.054 1802 Dihedral : 12.854 113.451 2162 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.53 % Favored : 93.31 % Rotamer: Outliers : 3.62 % Allowed : 27.21 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.50 (0.25), residues: 1256 helix: 1.91 (0.21), residues: 578 sheet: 0.55 (0.32), residues: 280 loop : -2.32 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 446 HIS 0.010 0.001 HIS B 636 PHE 0.020 0.002 PHE B 705 TYR 0.047 0.002 TYR A 717 ARG 0.004 0.001 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5502 (mt) REVERT: A 605 TYR cc_start: 0.8526 (m-80) cc_final: 0.8324 (m-80) REVERT: A 713 ASP cc_start: 0.8001 (t0) cc_final: 0.7722 (t0) REVERT: B 36 ARG cc_start: 0.4885 (OUTLIER) cc_final: 0.3177 (mtt180) REVERT: B 160 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7737 (mttp) REVERT: B 208 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.5585 (ppp) REVERT: B 613 MET cc_start: 0.8494 (mmm) cc_final: 0.8237 (mmm) REVERT: B 722 PHE cc_start: 0.8630 (m-10) cc_final: 0.8398 (m-10) REVERT: B 736 MET cc_start: 0.8053 (mmt) cc_final: 0.7821 (mmt) REVERT: B 767 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7579 (m-80) outliers start: 41 outliers final: 17 residues processed: 177 average time/residue: 0.1834 time to fit residues: 49.4260 Evaluate side-chains 157 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 113 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 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 286 ASN A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10976 Z= 0.245 Angle : 0.652 9.578 14980 Z= 0.319 Chirality : 0.048 0.501 1752 Planarity : 0.004 0.046 1802 Dihedral : 12.335 113.292 2158 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.29 % Favored : 93.55 % Rotamer: Outliers : 4.51 % Allowed : 27.30 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.41 (0.24), residues: 1256 helix: 1.75 (0.21), residues: 578 sheet: 0.59 (0.32), residues: 280 loop : -2.30 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 446 HIS 0.008 0.001 HIS B 636 PHE 0.024 0.001 PHE A 445 TYR 0.036 0.002 TYR A 717 ARG 0.003 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 149 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.5193 (mt) REVERT: A 605 TYR cc_start: 0.8516 (m-80) cc_final: 0.8305 (m-80) REVERT: A 702 PHE cc_start: 0.7986 (m-80) cc_final: 0.7257 (m-80) REVERT: B 208 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.5608 (ppp) REVERT: B 613 MET cc_start: 0.8463 (mmm) cc_final: 0.8204 (mmm) REVERT: B 722 PHE cc_start: 0.8627 (m-10) cc_final: 0.8358 (m-10) REVERT: B 736 MET cc_start: 0.8041 (mmt) cc_final: 0.7770 (mmt) REVERT: B 767 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7490 (m-80) outliers start: 51 outliers final: 26 residues processed: 188 average time/residue: 0.1649 time to fit residues: 48.9725 Evaluate side-chains 166 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10976 Z= 0.233 Angle : 0.655 10.654 14980 Z= 0.316 Chirality : 0.047 0.505 1752 Planarity : 0.004 0.046 1802 Dihedral : 11.864 113.344 2158 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.13 % Favored : 93.71 % Rotamer: Outliers : 5.12 % Allowed : 27.65 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1256 helix: 1.69 (0.21), residues: 576 sheet: 0.82 (0.33), residues: 268 loop : -2.40 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 446 HIS 0.006 0.001 HIS B 636 PHE 0.022 0.001 PHE B 705 TYR 0.025 0.001 TYR A 717 ARG 0.003 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 152 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: A 326 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5181 (mt) REVERT: A 455 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: A 702 PHE cc_start: 0.7860 (m-80) cc_final: 0.7228 (m-80) REVERT: A 713 ASP cc_start: 0.8059 (t0) cc_final: 0.7768 (t0) REVERT: B 36 ARG cc_start: 0.4917 (OUTLIER) cc_final: 0.3256 (mtt180) REVERT: B 61 GLU cc_start: 0.7696 (mp0) cc_final: 0.7162 (mp0) REVERT: B 160 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7785 (mttp) REVERT: B 208 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.5627 (ppp) REVERT: B 454 PHE cc_start: 0.8430 (m-80) cc_final: 0.7712 (m-80) REVERT: B 613 MET cc_start: 0.8455 (mmm) cc_final: 0.8175 (mmm) REVERT: B 722 PHE cc_start: 0.8681 (m-10) cc_final: 0.8385 (m-10) REVERT: B 767 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7469 (m-80) outliers start: 58 outliers final: 32 residues processed: 194 average time/residue: 0.1784 time to fit residues: 53.0884 Evaluate side-chains 182 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 143 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10976 Z= 0.311 Angle : 0.685 10.984 14980 Z= 0.333 Chirality : 0.048 0.515 1752 Planarity : 0.004 0.046 1802 Dihedral : 11.643 114.027 2158 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.61 % Favored : 93.23 % Rotamer: Outliers : 5.39 % Allowed : 27.56 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.25 (0.24), residues: 1256 helix: 1.62 (0.21), residues: 576 sheet: 0.72 (0.33), residues: 268 loop : -2.44 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 446 HIS 0.005 0.001 HIS B 636 PHE 0.023 0.002 PHE A 445 TYR 0.024 0.002 TYR A 717 ARG 0.007 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 145 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: A 326 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5189 (mt) REVERT: A 455 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7565 (m-80) REVERT: A 702 PHE cc_start: 0.7841 (m-80) cc_final: 0.7366 (m-80) REVERT: A 713 ASP cc_start: 0.8041 (t0) cc_final: 0.7840 (t0) REVERT: B 36 ARG cc_start: 0.4948 (OUTLIER) cc_final: 0.3354 (mtt-85) REVERT: B 160 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7796 (mttp) REVERT: B 208 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.5736 (ppp) REVERT: B 454 PHE cc_start: 0.8394 (m-80) cc_final: 0.7829 (m-80) REVERT: B 613 MET cc_start: 0.8465 (mmm) cc_final: 0.8165 (mmm) REVERT: B 722 PHE cc_start: 0.8708 (m-10) cc_final: 0.8408 (m-10) REVERT: B 736 MET cc_start: 0.8004 (mmt) cc_final: 0.7760 (mmt) REVERT: B 767 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7589 (m-80) outliers start: 61 outliers final: 42 residues processed: 188 average time/residue: 0.1771 time to fit residues: 51.7232 Evaluate side-chains 187 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 138 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 56 optimal weight: 0.0970 chunk 10 optimal weight: 0.0040 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 796 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10976 Z= 0.169 Angle : 0.634 11.351 14980 Z= 0.303 Chirality : 0.047 0.506 1752 Planarity : 0.004 0.042 1802 Dihedral : 11.146 112.678 2158 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.67 % Rotamer: Outliers : 2.56 % Allowed : 30.12 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.41 (0.24), residues: 1256 helix: 1.82 (0.22), residues: 564 sheet: 0.95 (0.33), residues: 268 loop : -2.48 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 446 HIS 0.005 0.001 HIS B 636 PHE 0.025 0.001 PHE B 705 TYR 0.027 0.001 TYR A 717 ARG 0.004 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: A 702 PHE cc_start: 0.7813 (m-80) cc_final: 0.7391 (m-80) REVERT: A 713 ASP cc_start: 0.8066 (t0) cc_final: 0.7843 (t0) REVERT: B 36 ARG cc_start: 0.4926 (OUTLIER) cc_final: 0.3498 (mtt-85) REVERT: B 160 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7894 (mttp) REVERT: B 208 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.5499 (ppp) REVERT: B 454 PHE cc_start: 0.8235 (m-10) cc_final: 0.7826 (m-80) REVERT: B 613 MET cc_start: 0.8477 (mmm) cc_final: 0.8065 (mmm) REVERT: B 722 PHE cc_start: 0.8729 (m-10) cc_final: 0.8385 (m-10) REVERT: B 736 MET cc_start: 0.8036 (mmt) cc_final: 0.7745 (mmt) REVERT: B 767 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7445 (m-80) outliers start: 29 outliers final: 17 residues processed: 176 average time/residue: 0.1719 time to fit residues: 47.0786 Evaluate side-chains 162 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10976 Z= 0.189 Angle : 0.644 11.642 14980 Z= 0.308 Chirality : 0.047 0.510 1752 Planarity : 0.004 0.037 1802 Dihedral : 10.809 112.425 2156 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.35 % Rotamer: Outliers : 2.83 % Allowed : 29.86 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.43 (0.24), residues: 1256 helix: 1.81 (0.22), residues: 566 sheet: 1.04 (0.34), residues: 268 loop : -2.52 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 446 HIS 0.004 0.001 HIS B 636 PHE 0.027 0.001 PHE A 705 TYR 0.030 0.001 TYR A 481 ARG 0.007 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5379 (mt) REVERT: A 455 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7523 (m-80) REVERT: A 702 PHE cc_start: 0.7769 (m-80) cc_final: 0.7395 (m-80) REVERT: B 36 ARG cc_start: 0.4943 (OUTLIER) cc_final: 0.3492 (mtt-85) REVERT: B 160 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7928 (mttp) REVERT: B 208 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.5447 (ppp) REVERT: B 454 PHE cc_start: 0.8261 (m-10) cc_final: 0.7915 (m-80) REVERT: B 613 MET cc_start: 0.8491 (mmm) cc_final: 0.8178 (mmm) REVERT: B 722 PHE cc_start: 0.8699 (m-10) cc_final: 0.8383 (m-10) REVERT: B 736 MET cc_start: 0.8027 (mmt) cc_final: 0.7757 (mmt) REVERT: B 767 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7493 (m-80) outliers start: 32 outliers final: 24 residues processed: 166 average time/residue: 0.1767 time to fit residues: 45.7893 Evaluate side-chains 169 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10976 Z= 0.175 Angle : 0.636 12.037 14980 Z= 0.303 Chirality : 0.047 0.508 1752 Planarity : 0.004 0.037 1802 Dihedral : 10.502 111.719 2156 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.94 % Favored : 94.90 % Rotamer: Outliers : 3.98 % Allowed : 29.06 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.48 (0.24), residues: 1256 helix: 1.86 (0.22), residues: 566 sheet: 1.08 (0.34), residues: 268 loop : -2.52 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 446 HIS 0.004 0.001 HIS B 636 PHE 0.026 0.001 PHE B 705 TYR 0.024 0.001 TYR A 481 ARG 0.003 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: A 326 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5460 (mt) REVERT: A 455 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: A 702 PHE cc_start: 0.7792 (m-80) cc_final: 0.7421 (m-80) REVERT: B 36 ARG cc_start: 0.4904 (OUTLIER) cc_final: 0.3521 (mtt-85) REVERT: B 160 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7942 (mttp) REVERT: B 221 MET cc_start: 0.7812 (mmm) cc_final: 0.7493 (mmm) REVERT: B 454 PHE cc_start: 0.8300 (m-10) cc_final: 0.7955 (m-80) REVERT: B 613 MET cc_start: 0.8458 (mmm) cc_final: 0.8126 (mmm) REVERT: B 722 PHE cc_start: 0.8729 (m-10) cc_final: 0.8404 (m-10) REVERT: B 736 MET cc_start: 0.8080 (mmt) cc_final: 0.7764 (mmt) REVERT: B 767 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7415 (m-80) outliers start: 45 outliers final: 29 residues processed: 176 average time/residue: 0.1762 time to fit residues: 48.3363 Evaluate side-chains 177 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.2980 chunk 116 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10976 Z= 0.181 Angle : 0.657 12.441 14980 Z= 0.308 Chirality : 0.047 0.507 1752 Planarity : 0.004 0.037 1802 Dihedral : 10.299 111.518 2156 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.33 % Favored : 94.51 % Rotamer: Outliers : 3.89 % Allowed : 29.15 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.52 (0.24), residues: 1256 helix: 1.87 (0.22), residues: 566 sheet: 1.10 (0.34), residues: 268 loop : -2.47 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 446 HIS 0.003 0.001 HIS B 636 PHE 0.036 0.001 PHE A 705 TYR 0.021 0.001 TYR A 188 ARG 0.003 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: A 326 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5421 (mt) REVERT: A 455 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: A 555 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8280 (tp30) REVERT: A 689 MET cc_start: 0.9239 (mmp) cc_final: 0.9021 (mmt) REVERT: A 702 PHE cc_start: 0.7735 (m-80) cc_final: 0.7381 (m-80) REVERT: B 36 ARG cc_start: 0.4866 (OUTLIER) cc_final: 0.3558 (mtt-85) REVERT: B 160 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7949 (mttp) REVERT: B 208 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.5419 (ppp) REVERT: B 454 PHE cc_start: 0.8366 (m-10) cc_final: 0.8031 (m-80) REVERT: B 613 MET cc_start: 0.8484 (mmm) cc_final: 0.8150 (mmm) REVERT: B 722 PHE cc_start: 0.8726 (m-10) cc_final: 0.8420 (m-10) REVERT: B 736 MET cc_start: 0.8106 (mmt) cc_final: 0.7742 (mmt) REVERT: B 767 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7433 (m-80) outliers start: 44 outliers final: 27 residues processed: 182 average time/residue: 0.1714 time to fit residues: 48.8525 Evaluate side-chains 174 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 522 HIS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.0010 chunk 56 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 0.0000 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10976 Z= 0.204 Angle : 0.676 12.070 14980 Z= 0.316 Chirality : 0.047 0.511 1752 Planarity : 0.004 0.038 1802 Dihedral : 10.213 111.789 2156 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.51 % Rotamer: Outliers : 3.45 % Allowed : 29.77 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.46 (0.24), residues: 1256 helix: 1.81 (0.22), residues: 566 sheet: 1.06 (0.33), residues: 268 loop : -2.45 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 446 HIS 0.004 0.001 HIS B 636 PHE 0.035 0.001 PHE A 705 TYR 0.022 0.001 TYR A 188 ARG 0.003 0.000 ARG B 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: A 326 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5258 (mt) REVERT: A 455 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: A 702 PHE cc_start: 0.7759 (m-80) cc_final: 0.7399 (m-80) REVERT: B 36 ARG cc_start: 0.4862 (OUTLIER) cc_final: 0.3457 (mtt-85) REVERT: B 160 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7920 (mttp) REVERT: B 208 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.5505 (ppp) REVERT: B 221 MET cc_start: 0.7917 (mmm) cc_final: 0.7572 (mmm) REVERT: B 586 MET cc_start: 0.8339 (mmm) cc_final: 0.8133 (mmm) REVERT: B 613 MET cc_start: 0.8500 (mmm) cc_final: 0.8180 (mmm) REVERT: B 722 PHE cc_start: 0.8762 (m-10) cc_final: 0.8433 (m-10) REVERT: B 736 MET cc_start: 0.8173 (mmt) cc_final: 0.7759 (mmt) REVERT: B 767 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7493 (m-80) outliers start: 39 outliers final: 29 residues processed: 174 average time/residue: 0.1695 time to fit residues: 45.8981 Evaluate side-chains 176 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 140 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.140994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.102914 restraints weight = 19611.678| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.06 r_work: 0.3461 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10976 Z= 0.275 Angle : 0.701 12.012 14980 Z= 0.337 Chirality : 0.049 0.528 1752 Planarity : 0.004 0.040 1802 Dihedral : 10.272 112.723 2156 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.37 % Favored : 93.55 % Rotamer: Outliers : 3.45 % Allowed : 29.68 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.43 (0.24), residues: 1256 helix: 1.85 (0.22), residues: 554 sheet: 0.91 (0.33), residues: 268 loop : -2.35 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 446 HIS 0.004 0.001 HIS B 636 PHE 0.042 0.002 PHE A 705 TYR 0.025 0.001 TYR A 188 ARG 0.003 0.000 ARG B 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2183.06 seconds wall clock time: 40 minutes 49.29 seconds (2449.29 seconds total)