Starting phenix.real_space_refine on Sun Sep 13 06:32:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rof_54117/09_2026/9rof_54117_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rof_54117/09_2026/9rof_54117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rof_54117/09_2026/9rof_54117_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rof_54117/09_2026/9rof_54117_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rof_54117/09_2026/9rof_54117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rof_54117/09_2026/9rof_54117.map" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.018 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 3 5.49 5 S 61 5.16 5 Na 2 4.78 5 C 6595 2.51 5 N 1701 2.21 5 O 1937 1.98 5 H 10146 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20445 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 15227 Classifications: {'peptide': 984} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 942} Chain: "B" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4516 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 258} Chain: "C" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 543 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Unusual residues: {' NA': 2, 'ATP': 1, 'CLR': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.29, per 1000 atoms: 0.16 Number of scatterers: 20445 At special positions: 0 Unit cell: (90.6806, 81.9852, 172.666, 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) S 61 16.00 P 3 15.00 Na 2 11.00 O 1937 8.00 N 1701 7.00 C 6595 6.00 H 10146 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " 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=1, symmetry=0 Links applied NAG-ASN " NAG B 401 " - " ASN B 265 " " NAG B 402 " - " ASN B 158 " " NAG B 403 " - " ASN B 193 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 516.7 milliseconds 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 50.8% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 78 through 88 removed outlier: 3.910A pdb=" N GLY A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 108 removed outlier: 4.114A pdb=" N GLY A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 154 removed outlier: 3.704A pdb=" N LEU A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 4.332A pdb=" N THR A 209 " --> pdb=" O ASN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 272 through 303 Processing helix chain 'A' and resid 306 through 321 Processing helix chain 'A' and resid 324 through 344 removed outlier: 4.523A pdb=" N ALA A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 removed outlier: 4.268A pdb=" N THR A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 440 through 453 removed outlier: 3.634A pdb=" N SER A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.642A pdb=" N LEU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.616A pdb=" N ALA A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 646 through 650 Processing helix chain 'A' and resid 657 through 663 Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 684 through 698 Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 744 through 772 removed outlier: 3.775A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 793 through 806 Processing helix chain 'A' and resid 806 through 812 removed outlier: 3.737A pdb=" N LEU A 812 " --> pdb=" O PRO A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 820 through 824 removed outlier: 3.938A pdb=" N ARG A 824 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 846 Processing helix chain 'A' and resid 846 through 866 removed outlier: 4.006A pdb=" N ILE A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 876 through 882 Processing helix chain 'A' and resid 897 through 927 removed outlier: 3.870A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 941 through 961 removed outlier: 3.537A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 968 Processing helix chain 'A' and resid 974 through 980 removed outlier: 3.632A pdb=" N CYS A 980 " --> pdb=" O TRP A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'B' and resid 28 through 59 Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.684A pdb=" N VAL B 72 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 73' Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 110 removed outlier: 3.543A pdb=" N VAL B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 5.961A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 217 through 224 Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.792A pdb=" N SER B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 56 removed outlier: 3.817A pdb=" N LEU C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 171 removed outlier: 4.667A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A 193 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.270A pdb=" N GLY A 721 " --> pdb=" O MET A 738 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU A 740 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA A 723 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET A 724 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR A 362 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR A 705 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N CYS A 364 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 603 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N PHE A 680 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N CYS A 653 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA A 681 " --> pdb=" O CYS A 653 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 655 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 389 removed outlier: 7.088A pdb=" N SER A 580 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N MET A 381 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 578 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N PHE A 383 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N VAL A 576 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N PHE A 575 " --> pdb=" O HIS A 547 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N HIS A 547 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY A 577 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389 removed outlier: 7.088A pdb=" N SER A 580 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N MET A 381 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 578 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N PHE A 383 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N VAL A 576 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLY A 577 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 422 through 423 removed outlier: 3.812A pdb=" N VAL A 422 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 89 520 hydrogen bonds defined for protein. 1458 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: 4.64 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10122 1.03 - 1.23: 68 1.23 - 1.43: 4229 1.43 - 1.62: 6153 1.62 - 1.82: 90 Bond restraints: 20662 Sorted by residual: bond pdb=" C1 NAG B 402 " pdb=" O5 NAG B 402 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" C1 NAG B 403 " pdb=" O5 NAG B 403 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" C5 NAG B 402 " pdb=" O5 NAG B 402 " ideal model delta sigma weight residual 1.413 1.438 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C5 NAG B 403 " pdb=" O5 NAG B 403 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" CG1 ILE A 582 " pdb=" CD1 ILE A 582 " ideal model delta sigma weight residual 1.513 1.554 -0.041 3.90e-02 6.57e+02 1.13e+00 ... (remaining 20657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 36826 1.61 - 3.21: 491 3.21 - 4.82: 63 4.82 - 6.43: 10 6.43 - 8.04: 4 Bond angle restraints: 37394 Sorted by residual: angle pdb=" N VAL A 50 " pdb=" CA VAL A 50 " pdb=" C VAL A 50 " ideal model delta sigma weight residual 113.71 110.65 3.06 9.50e-01 1.11e+00 1.04e+01 angle pdb=" CA TYR A 478 " pdb=" CB TYR A 478 " pdb=" CG TYR A 478 " ideal model delta sigma weight residual 113.90 119.44 -5.54 1.80e+00 3.09e-01 9.46e+00 angle pdb=" N SER A 858 " pdb=" CA SER A 858 " pdb=" C SER A 858 " ideal model delta sigma weight residual 110.97 107.89 3.08 1.09e+00 8.42e-01 7.99e+00 angle pdb=" CB MET A 148 " pdb=" CG MET A 148 " pdb=" SD MET A 148 " ideal model delta sigma weight residual 112.70 120.74 -8.04 3.00e+00 1.11e-01 7.18e+00 angle pdb=" CB MET A 581 " pdb=" CG MET A 581 " pdb=" SD MET A 581 " ideal model delta sigma weight residual 112.70 120.16 -7.46 3.00e+00 1.11e-01 6.19e+00 ... (remaining 37389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.40: 9094 23.40 - 46.80: 607 46.80 - 70.21: 178 70.21 - 93.61: 23 93.61 - 117.01: 25 Dihedral angle restraints: 9927 sinusoidal: 5584 harmonic: 4343 Sorted by residual: dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual -86.00 -139.28 53.28 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CA ASN A 473 " pdb=" C ASN A 473 " pdb=" N SER A 474 " pdb=" CA SER A 474 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ASN B 193 " pdb=" C ASN B 193 " pdb=" N GLU B 194 " pdb=" CA GLU B 194 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 9924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1473 0.065 - 0.131: 150 0.131 - 0.196: 4 0.196 - 0.262: 0 0.262 - 0.327: 4 Chirality restraints: 1631 Sorted by residual: chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C2' ATP A1104 " pdb=" C1' ATP A1104 " pdb=" C3' ATP A1104 " pdb=" O2' ATP A1104 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C3' ATP A1104 " pdb=" C2' ATP A1104 " pdb=" C4' ATP A1104 " pdb=" O3' ATP A1104 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1628 not shown) Planarity restraints: 3052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 205 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 206 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 206 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 206 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 189 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.60e+00 pdb=" N PRO A 190 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 190 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 190 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 76 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 77 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " 0.025 5.00e-02 4.00e+02 ... (remaining 3049 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 859 2.14 - 2.76: 39608 2.76 - 3.37: 61231 3.37 - 3.99: 76651 3.99 - 4.60: 119259 Nonbonded interactions: 297608 Sorted by model distance: nonbonded pdb=" H THR A 368 " pdb=" O1B ATP A1104 " model vdw 1.526 2.450 nonbonded pdb=" OG1 THR A 929 " pdb=" HZ3 LYS A 996 " model vdw 1.547 2.450 nonbonded pdb=" H GLY A 186 " pdb=" O CYS A 239 " model vdw 1.563 2.450 nonbonded pdb=" H LYS A 184 " pdb=" OD2 ASP A 187 " model vdw 1.574 2.450 nonbonded pdb="HE22 GLN A 696 " pdb=" O LYS A 717 " model vdw 1.584 2.450 ... (remaining 297603 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.010 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 0.008 0.764 10524 Z= 0.754 Angle : 0.575 8.037 14296 Z= 0.286 Chirality : 0.042 0.327 1631 Planarity : 0.003 0.050 1817 Dihedral : 18.158 117.012 4127 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.45 % Allowed : 19.24 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1291 helix: 0.98 (0.22), residues: 580 sheet: -0.19 (0.49), residues: 115 loop : -1.17 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 27 TYR 0.013 0.001 TYR B 43 PHE 0.016 0.001 PHE B 38 TRP 0.011 0.001 TRP B 32 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10516) covalent geometry : angle 0.57213 / 0.29 (14279) SS BOND : bond 0.00218 / 0.07 ( 4) SS BOND : angle 0.83972 / 0.54 ( 8) hydrogen bonds : bond 0.15899 / 10.63 ( 513) hydrogen bonds : angle 6.98165 / 5.13 ( 1458) Misc. bond : bond 0.76418 / 40.22 ( 1) link_NAG-ASN : bond 0.00423 / 0.21 ( 3) link_NAG-ASN : angle 2.10455 / 1.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 108 average time/residue: 0.2059 time to fit residues: 32.4205 Evaluate side-chains 104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 193 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.0970 chunk 35 optimal weight: 20.0000 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.122454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.081984 restraints weight = 81380.131| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.64 r_work: 0.3225 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10524 Z= 0.121 Angle : 0.587 8.429 14296 Z= 0.296 Chirality : 0.043 0.316 1631 Planarity : 0.004 0.049 1817 Dihedral : 12.182 107.767 1695 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.35 % Allowed : 17.99 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1291 helix: 0.94 (0.22), residues: 586 sheet: -0.58 (0.46), residues: 126 loop : -1.18 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 194 TYR 0.015 0.001 TYR A 478 PHE 0.012 0.001 PHE B 108 TRP 0.005 0.001 TRP B 32 HIS 0.003 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10516) covalent geometry : angle 0.58574 / 0.30 (14279) SS BOND : bond 0.00257 / 0.10 ( 4) SS BOND : angle 0.55524 / 0.33 ( 8) hydrogen bonds : bond 0.04167 / 2.81 ( 513) hydrogen bonds : angle 5.24022 / 3.78 ( 1458) Misc. bond : bond 0.00158 / 0.08 ( 1) link_NAG-ASN : bond 0.00466 / 0.24 ( 3) link_NAG-ASN : angle 1.78182 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8210 (pmm) cc_final: 0.7843 (pmm) REVERT: B 249 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8846 (tt) outliers start: 15 outliers final: 7 residues processed: 118 average time/residue: 0.2282 time to fit residues: 39.5056 Evaluate side-chains 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 34 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 886 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.120455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.079357 restraints weight = 81906.086| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.62 r_work: 0.3170 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10524 Z= 0.226 Angle : 0.597 9.724 14296 Z= 0.307 Chirality : 0.042 0.406 1631 Planarity : 0.004 0.047 1817 Dihedral : 9.941 110.315 1691 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.89 % Allowed : 17.81 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.24), residues: 1291 helix: 0.96 (0.22), residues: 584 sheet: -0.91 (0.45), residues: 126 loop : -1.28 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 507 TYR 0.014 0.001 TYR A 984 PHE 0.009 0.001 PHE B 186 TRP 0.004 0.001 TRP A 921 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 (10516) covalent geometry : angle 0.59517 / 0.31 (14279) SS BOND : bond 0.00377 / 0.15 ( 4) SS BOND : angle 0.55755 / 0.31 ( 8) hydrogen bonds : bond 0.04079 / 2.70 ( 513) hydrogen bonds : angle 5.13374 / 3.70 ( 1458) Misc. bond : bond 0.00320 / 0.17 ( 1) link_NAG-ASN : bond 0.00287 / 0.13 ( 3) link_NAG-ASN : angle 2.04232 / 1.01 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8176 (pmm) cc_final: 0.7786 (pmm) REVERT: A 497 MET cc_start: 0.7130 (ttt) cc_final: 0.6925 (ttt) REVERT: B 175 CYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8429 (t) REVERT: B 266 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8503 (tt) outliers start: 21 outliers final: 18 residues processed: 114 average time/residue: 0.2232 time to fit residues: 37.6309 Evaluate side-chains 119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 127 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.121647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.080485 restraints weight = 81981.690| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.62 r_work: 0.3202 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10524 Z= 0.128 Angle : 0.553 9.396 14296 Z= 0.281 Chirality : 0.040 0.292 1631 Planarity : 0.004 0.048 1817 Dihedral : 8.840 94.257 1691 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.34 % Allowed : 17.72 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.24), residues: 1291 helix: 1.05 (0.22), residues: 584 sheet: -0.83 (0.45), residues: 126 loop : -1.21 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 930 TYR 0.014 0.001 TYR A 478 PHE 0.009 0.001 PHE A 783 TRP 0.003 0.001 TRP A 880 HIS 0.003 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10516) covalent geometry : angle 0.54959 / 0.28 (14279) SS BOND : bond 0.00281 / 0.10 ( 4) SS BOND : angle 0.49635 / 0.28 ( 8) hydrogen bonds : bond 0.03631 / 2.40 ( 513) hydrogen bonds : angle 4.82287 / 3.48 ( 1458) Misc. bond : bond 0.00021 / 0.01 ( 1) link_NAG-ASN : bond 0.00431 / 0.22 ( 3) link_NAG-ASN : angle 2.40166 / 1.15 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8153 (pmm) cc_final: 0.7737 (pmm) REVERT: A 366 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: A 690 ILE cc_start: 0.9305 (mm) cc_final: 0.9071 (tp) REVERT: B 249 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8874 (tt) REVERT: B 266 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8383 (tt) outliers start: 26 outliers final: 20 residues processed: 121 average time/residue: 0.2351 time to fit residues: 41.7186 Evaluate side-chains 122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 0.3980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.120196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.078871 restraints weight = 82117.425| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.65 r_work: 0.3148 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10524 Z= 0.270 Angle : 0.605 9.142 14296 Z= 0.315 Chirality : 0.042 0.344 1631 Planarity : 0.004 0.047 1817 Dihedral : 8.949 93.460 1691 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.79 % Allowed : 17.63 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.24), residues: 1291 helix: 0.91 (0.22), residues: 587 sheet: -1.01 (0.44), residues: 128 loop : -1.39 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 507 TYR 0.015 0.001 TYR A 984 PHE 0.011 0.001 PHE B 186 TRP 0.005 0.001 TRP A 977 HIS 0.005 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.27 (10516) covalent geometry : angle 0.60270 / 0.31 (14279) SS BOND : bond 0.00437 / 0.17 ( 4) SS BOND : angle 0.65962 / 0.36 ( 8) hydrogen bonds : bond 0.03744 / 2.48 ( 513) hydrogen bonds : angle 4.94322 / 3.56 ( 1458) Misc. bond : bond 0.00073 / 0.04 ( 1) link_NAG-ASN : bond 0.00337 / 0.11 ( 3) link_NAG-ASN : angle 2.38125 / 1.13 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8180 (pmm) cc_final: 0.7775 (pmm) REVERT: A 366 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8190 (m-30) REVERT: A 497 MET cc_start: 0.7103 (ttt) cc_final: 0.6794 (ttt) REVERT: B 249 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8946 (tt) REVERT: B 266 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8568 (tt) outliers start: 31 outliers final: 25 residues processed: 118 average time/residue: 0.2215 time to fit residues: 38.9154 Evaluate side-chains 122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 36 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 30.0000 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 49 optimal weight: 0.0020 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.121072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.079864 restraints weight = 81407.854| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.61 r_work: 0.3174 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10524 Z= 0.157 Angle : 0.570 10.029 14296 Z= 0.289 Chirality : 0.041 0.303 1631 Planarity : 0.004 0.048 1817 Dihedral : 8.759 87.920 1691 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.70 % Allowed : 18.08 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.24), residues: 1291 helix: 1.00 (0.22), residues: 585 sheet: -1.04 (0.44), residues: 127 loop : -1.28 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 217 TYR 0.013 0.001 TYR A 478 PHE 0.010 0.001 PHE B 139 TRP 0.004 0.001 TRP B 32 HIS 0.002 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (10516) covalent geometry : angle 0.56661 / 0.29 (14279) SS BOND : bond 0.00313 / 0.12 ( 4) SS BOND : angle 0.57226 / 0.32 ( 8) hydrogen bonds : bond 0.03585 / 2.37 ( 513) hydrogen bonds : angle 4.76019 / 3.44 ( 1458) Misc. bond : bond 0.00025 / 0.01 ( 1) link_NAG-ASN : bond 0.00286 / 0.11 ( 3) link_NAG-ASN : angle 2.43671 / 1.12 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8169 (pmm) cc_final: 0.7761 (pmm) REVERT: A 366 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8164 (m-30) REVERT: A 497 MET cc_start: 0.6918 (ttt) cc_final: 0.6631 (ttt) REVERT: B 249 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8881 (tt) REVERT: B 266 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8477 (tt) outliers start: 30 outliers final: 24 residues processed: 117 average time/residue: 0.2199 time to fit residues: 38.2729 Evaluate side-chains 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 67 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.120953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.079730 restraints weight = 81616.683| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.59 r_work: 0.3187 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10524 Z= 0.133 Angle : 0.555 9.751 14296 Z= 0.278 Chirality : 0.040 0.285 1631 Planarity : 0.004 0.048 1817 Dihedral : 8.403 83.246 1691 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.52 % Allowed : 17.81 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.24), residues: 1291 helix: 1.08 (0.22), residues: 586 sheet: -0.96 (0.44), residues: 127 loop : -1.16 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 901 TYR 0.013 0.001 TYR A 478 PHE 0.008 0.001 PHE B 108 TRP 0.004 0.001 TRP A 880 HIS 0.002 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10516) covalent geometry : angle 0.55176 / 0.28 (14279) SS BOND : bond 0.00236 / 0.09 ( 4) SS BOND : angle 0.47135 / 0.27 ( 8) hydrogen bonds : bond 0.03401 / 2.27 ( 513) hydrogen bonds : angle 4.61724 / 3.34 ( 1458) Misc. bond : bond 0.00012 / 0.01 ( 1) link_NAG-ASN : bond 0.00261 / 0.11 ( 3) link_NAG-ASN : angle 2.34817 / 1.11 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8162 (pmm) cc_final: 0.7748 (pmm) REVERT: A 366 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8140 (m-30) REVERT: A 497 MET cc_start: 0.6975 (ttt) cc_final: 0.6662 (ttt) REVERT: B 249 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8863 (tt) REVERT: B 266 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8438 (tt) outliers start: 28 outliers final: 24 residues processed: 123 average time/residue: 0.2277 time to fit residues: 41.7011 Evaluate side-chains 126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 113 optimal weight: 0.0870 chunk 66 optimal weight: 2.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.121939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.080150 restraints weight = 82804.276| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.73 r_work: 0.3196 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10524 Z= 0.110 Angle : 0.552 10.318 14296 Z= 0.274 Chirality : 0.040 0.245 1631 Planarity : 0.004 0.048 1817 Dihedral : 8.156 76.109 1691 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.07 % Allowed : 18.71 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.24), residues: 1291 helix: 1.18 (0.22), residues: 588 sheet: -0.98 (0.44), residues: 129 loop : -1.06 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 901 TYR 0.013 0.001 TYR A 478 PHE 0.009 0.001 PHE B 108 TRP 0.004 0.001 TRP A 880 HIS 0.002 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10516) covalent geometry : angle 0.54825 / 0.27 (14279) SS BOND : bond 0.00239 / 0.09 ( 4) SS BOND : angle 0.50180 / 0.29 ( 8) hydrogen bonds : bond 0.03315 / 2.21 ( 513) hydrogen bonds : angle 4.51440 / 3.27 ( 1458) Misc. bond : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : bond 0.00193 / 0.07 ( 3) link_NAG-ASN : angle 2.51627 / 1.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8168 (pmm) cc_final: 0.7796 (pmm) REVERT: A 497 MET cc_start: 0.7026 (ttt) cc_final: 0.6755 (ttt) REVERT: B 266 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8373 (tt) outliers start: 23 outliers final: 20 residues processed: 120 average time/residue: 0.2193 time to fit residues: 39.1411 Evaluate side-chains 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 106 optimal weight: 0.0370 chunk 36 optimal weight: 0.0020 chunk 9 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 overall best weight: 0.7868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.122317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.080779 restraints weight = 82027.562| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.67 r_work: 0.3210 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10524 Z= 0.104 Angle : 0.544 9.802 14296 Z= 0.270 Chirality : 0.040 0.228 1631 Planarity : 0.003 0.047 1817 Dihedral : 8.017 71.442 1691 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.16 % Allowed : 18.62 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.24), residues: 1291 helix: 1.23 (0.22), residues: 588 sheet: -0.92 (0.45), residues: 129 loop : -1.02 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 901 TYR 0.012 0.001 TYR A 478 PHE 0.009 0.001 PHE B 108 TRP 0.004 0.001 TRP A 382 HIS 0.006 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (10516) covalent geometry : angle 0.54063 / 0.27 (14279) SS BOND : bond 0.00178 / 0.07 ( 4) SS BOND : angle 0.42987 / 0.25 ( 8) hydrogen bonds : bond 0.03258 / 2.18 ( 513) hydrogen bonds : angle 4.44634 / 3.22 ( 1458) Misc. bond : bond 0.00000 / 0.00 ( 1) link_NAG-ASN : bond 0.00172 / 0.07 ( 3) link_NAG-ASN : angle 2.50128 / 1.22 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.9252 (mmm) cc_final: 0.8966 (mmm) REVERT: A 168 MET cc_start: 0.8152 (pmm) cc_final: 0.7788 (pmm) REVERT: A 366 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: A 381 MET cc_start: 0.8164 (mpp) cc_final: 0.7811 (mpp) REVERT: A 497 MET cc_start: 0.6890 (ttt) cc_final: 0.6627 (ttt) REVERT: B 266 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8387 (tt) outliers start: 24 outliers final: 22 residues processed: 122 average time/residue: 0.2053 time to fit residues: 37.5554 Evaluate side-chains 124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 109 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.120795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.078586 restraints weight = 82871.701| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.74 r_work: 0.3173 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10524 Z= 0.192 Angle : 0.575 8.828 14296 Z= 0.293 Chirality : 0.040 0.221 1631 Planarity : 0.004 0.048 1817 Dihedral : 8.071 70.959 1691 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.34 % Allowed : 18.44 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.24), residues: 1291 helix: 1.18 (0.22), residues: 587 sheet: -1.05 (0.44), residues: 129 loop : -1.10 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 217 TYR 0.013 0.001 TYR A 859 PHE 0.009 0.001 PHE A 860 TRP 0.005 0.001 TRP A 977 HIS 0.006 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (10516) covalent geometry : angle 0.57130 / 0.29 (14279) SS BOND : bond 0.00369 / 0.14 ( 4) SS BOND : angle 0.64884 / 0.36 ( 8) hydrogen bonds : bond 0.03366 / 2.23 ( 513) hydrogen bonds : angle 4.56236 / 3.30 ( 1458) Misc. bond : bond 0.00047 / 0.02 ( 1) link_NAG-ASN : bond 0.00240 / 0.09 ( 3) link_NAG-ASN : angle 2.71776 / 1.34 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 368 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.9230 (mmm) cc_final: 0.8932 (mmm) REVERT: A 168 MET cc_start: 0.8138 (pmm) cc_final: 0.7736 (pmm) REVERT: A 366 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: A 497 MET cc_start: 0.7022 (ttt) cc_final: 0.6718 (ttt) REVERT: B 266 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8489 (tt) outliers start: 26 outliers final: 24 residues processed: 116 average time/residue: 0.2214 time to fit residues: 38.0741 Evaluate side-chains 122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 104 optimal weight: 0.0870 chunk 119 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.122316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.080786 restraints weight = 82099.502| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.69 r_work: 0.3205 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 0.002 0.057 10524 Z= 0.104 Angle : 0.549 9.545 14296 Z= 0.273 Chirality : 0.040 0.158 1631 Planarity : 0.003 0.047 1817 Dihedral : 7.873 71.968 1691 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.25 % Allowed : 18.79 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.24), residues: 1291 helix: 1.24 (0.22), residues: 590 sheet: -0.93 (0.45), residues: 129 loop : -1.01 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 586 TYR 0.012 0.001 TYR A 478 PHE 0.008 0.001 PHE A 783 TRP 0.005 0.001 TRP A 880 HIS 0.005 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 (10516) covalent geometry : angle 0.54412 / 0.27 (14279) SS BOND : bond 0.00182 / 0.07 ( 4) SS BOND : angle 0.43796 / 0.26 ( 8) hydrogen bonds : bond 0.03273 / 2.17 ( 513) hydrogen bonds : angle 4.42450 / 3.21 ( 1458) Misc. bond : bond 0.00002 / 0.00 ( 1) link_NAG-ASN : bond 0.00145 / 0.06 ( 3) link_NAG-ASN : angle 2.92058 / 1.47 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5340.05 seconds wall clock time: 91 minutes 35.79 seconds (5495.79 seconds total)