Starting phenix.real_space_refine on Fri Sep 11 06:27:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v0v_21003/09_2026/6v0v_21003.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v0v_21003/09_2026/6v0v_21003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6v0v_21003/09_2026/6v0v_21003.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v0v_21003/09_2026/6v0v_21003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v0v_21003/09_2026/6v0v_21003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v0v_21003/09_2026/6v0v_21003.map" model { file = "/net/cci-nas-00/data/ceres_data/6v0v_21003/09_2026/6v0v_21003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v0v_21003/09_2026/6v0v_21003.cif" } resolution = 3.61 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= 0.001 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 Ca 2 9.91 5 Zn 1 6.06 5 P 60 5.49 5 S 51 5.16 5 C 5002 2.51 5 N 1428 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s 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: 8192 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4286 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2673 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 617 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "I" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2016 SG CYS A 727 70.241 55.803 61.715 1.00 82.81 S ATOM 2037 SG CYS A 730 72.316 58.531 60.217 1.00 86.87 S Time building chain proxies: 2.13, per 1000 atoms: 0.26 Number of scatterers: 8192 At special positions: 0 Unit cell: (107.06, 95.4, 118.72, 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) Zn 1 29.99 Ca 2 19.99 S 51 16.00 P 60 15.00 O 1648 8.00 N 1428 7.00 C 5002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 337.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1103 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 727 " Number of angles added : 2 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1662 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 33.8% alpha, 25.0% beta 28 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.849A pdb=" N CYS A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 493 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.670A pdb=" N ALA A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 removed outlier: 3.603A pdb=" N SER A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 682 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.579A pdb=" N GLU A 716 " --> pdb=" O VAL A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 Processing helix chain 'A' and resid 750 through 763 Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 793 through 814 removed outlier: 3.964A pdb=" N GLY A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 841 Processing helix chain 'A' and resid 850 through 858 removed outlier: 4.005A pdb=" N MET A 858 " --> pdb=" O ALA A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 870 removed outlier: 3.548A pdb=" N VAL A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 890 removed outlier: 3.769A pdb=" N GLU A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.843A pdb=" N CYS A 902 " --> pdb=" O PRO A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 924 removed outlier: 5.330A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N PHE A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.904A pdb=" N HIS A 937 " --> pdb=" O THR A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 950 removed outlier: 3.787A pdb=" N GLU A 948 " --> pdb=" O PRO A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 Processing helix chain 'A' and resid 964 through 975 removed outlier: 3.567A pdb=" N PHE A 968 " --> pdb=" O GLY A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.815A pdb=" N VAL A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 988 " --> pdb=" O MET A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 Processing helix chain 'A' and resid 1002 through 1005 Processing helix chain 'B' and resid 11 through 15 removed outlier: 4.008A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 520 removed outlier: 10.087A pdb=" N PHE A 591 " --> pdb=" O PHE A 700 " (cutoff:3.500A) removed outlier: 10.936A pdb=" N PHE A 702 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N VAL A 593 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N GLY A 704 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL A 595 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLY A 706 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU A 597 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520 removed outlier: 10.087A pdb=" N PHE A 591 " --> pdb=" O PHE A 700 " (cutoff:3.500A) removed outlier: 10.936A pdb=" N PHE A 702 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N VAL A 593 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N GLY A 704 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL A 595 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLY A 706 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU A 597 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N HIS A 633 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 6 removed outlier: 4.650A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.147A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.102A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N CYS B 124 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.722A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 212 removed outlier: 4.540A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 267 removed outlier: 3.809A pdb=" N ILE B 262 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 266 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2196 1.33 - 1.45: 2147 1.45 - 1.58: 3960 1.58 - 1.70: 117 1.70 - 1.82: 78 Bond restraints: 8498 Sorted by residual: bond pdb=" C3' DG I 6 " pdb=" O3' DG I 6 " ideal model delta sigma weight residual 1.435 1.491 -0.056 1.30e-02 5.92e+03 1.88e+01 bond pdb=" C3' DA I 20 " pdb=" O3' DA I 20 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.53e+01 bond pdb=" O3' DT F 29 " pdb=" P DG F 30 " ideal model delta sigma weight residual 1.607 1.562 0.045 1.20e-02 6.94e+03 1.43e+01 bond pdb=" C3' DT I 3 " pdb=" O3' DT I 3 " ideal model delta sigma weight residual 1.435 1.479 -0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" C3' DA F 33 " pdb=" O3' DA F 33 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.10e+01 ... (remaining 8493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 11445 2.70 - 5.41: 284 5.41 - 8.11: 23 8.11 - 10.82: 5 10.82 - 13.52: 1 Bond angle restraints: 11758 Sorted by residual: angle pdb=" O4' DT I 14 " pdb=" C4' DT I 14 " pdb=" C3' DT I 14 " ideal model delta sigma weight residual 106.00 102.09 3.91 6.00e-01 2.78e+00 4.26e+01 angle pdb=" C4' DT F 29 " pdb=" C3' DT F 29 " pdb=" O3' DT F 29 " ideal model delta sigma weight residual 109.70 96.18 13.52 2.50e+00 1.60e-01 2.93e+01 angle pdb=" O4' DG I 11 " pdb=" C1' DG I 11 " pdb=" N9 DG I 11 " ideal model delta sigma weight residual 108.00 111.74 -3.74 7.00e-01 2.04e+00 2.85e+01 angle pdb=" C3' DG I 6 " pdb=" O3' DG I 6 " pdb=" P DG I 7 " ideal model delta sigma weight residual 119.70 125.96 -6.26 1.20e+00 6.94e-01 2.72e+01 angle pdb=" O4' DG F 30 " pdb=" C1' DG F 30 " pdb=" N9 DG F 30 " ideal model delta sigma weight residual 108.00 111.63 -3.63 7.00e-01 2.04e+00 2.69e+01 ... (remaining 11753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 4578 35.36 - 70.72: 347 70.72 - 106.09: 9 106.09 - 141.45: 1 141.45 - 176.81: 2 Dihedral angle restraints: 4937 sinusoidal: 2358 harmonic: 2579 Sorted by residual: dihedral pdb=" CA ARG B 212 " pdb=" C ARG B 212 " pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA CYS B 41 " pdb=" C CYS B 41 " pdb=" N PRO B 42 " pdb=" CA PRO B 42 " ideal model delta harmonic sigma weight residual -180.00 -157.91 -22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA PRO A 871 " pdb=" C PRO A 871 " pdb=" N SER A 872 " pdb=" CA SER A 872 " ideal model delta harmonic sigma weight residual -180.00 -158.23 -21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 4934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 936 0.058 - 0.117: 288 0.117 - 0.175: 63 0.175 - 0.233: 7 0.233 - 0.291: 4 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CB VAL A 943 " pdb=" CA VAL A 943 " pdb=" CG1 VAL A 943 " pdb=" CG2 VAL A 943 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C1' DC F 26 " pdb=" O4' DC F 26 " pdb=" C2' DC F 26 " pdb=" N1 DC F 26 " both_signs ideal model delta sigma weight residual False 2.43 2.15 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C3' DG I 6 " pdb=" C4' DG I 6 " pdb=" O3' DG I 6 " pdb=" C2' DG I 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1295 not shown) Planarity restraints: 1303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC F 26 " 0.095 2.00e-02 2.50e+03 4.30e-02 4.17e+01 pdb=" N1 DC F 26 " -0.043 2.00e-02 2.50e+03 pdb=" C2 DC F 26 " -0.021 2.00e-02 2.50e+03 pdb=" O2 DC F 26 " -0.030 2.00e-02 2.50e+03 pdb=" N3 DC F 26 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DC F 26 " 0.009 2.00e-02 2.50e+03 pdb=" N4 DC F 26 " 0.044 2.00e-02 2.50e+03 pdb=" C5 DC F 26 " -0.018 2.00e-02 2.50e+03 pdb=" C6 DC F 26 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 212 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" C ARG B 212 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG B 212 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN B 213 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO B 99 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.042 5.00e-02 4.00e+02 ... (remaining 1300 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 83 2.53 - 3.12: 5775 3.12 - 3.71: 13865 3.71 - 4.31: 18150 4.31 - 4.90: 28488 Nonbonded interactions: 66361 Sorted by model distance: nonbonded pdb=" OP1 DC I 17 " pdb="CA CA A1102 " model vdw 1.932 2.510 nonbonded pdb=" OE1 GLU A 962 " pdb="CA CA A1102 " model vdw 2.026 2.510 nonbonded pdb=" OD1 ASP A 600 " pdb="CA CA A1101 " model vdw 2.193 2.510 nonbonded pdb=" OE2 GLU A 803 " pdb=" OH TYR A 928 " model vdw 2.231 3.040 nonbonded pdb=" O SER A 958 " pdb=" OG SER A 958 " model vdw 2.266 3.040 ... (remaining 66356 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.040 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 0.156 8502 Z= 0.511 Angle : 1.139 46.250 11760 Z= 0.709 Chirality : 0.059 0.291 1298 Planarity : 0.007 0.075 1303 Dihedral : 21.033 176.809 3275 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.28 % Favored : 92.61 % Rotamer: Outliers : 0.40 % Allowed : 6.88 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -3.85 (0.23), residues: 879 helix: -2.89 (0.22), residues: 271 sheet: -1.77 (0.40), residues: 158 loop : -2.63 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 696 TYR 0.016 0.002 TYR A 805 PHE 0.035 0.003 PHE A 804 TRP 0.022 0.003 TRP A 893 HIS 0.008 0.002 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00799 / 0.51 ( 8498) covalent geometry : angle 1.04720 / 0.70 (11758) hydrogen bonds : bond 0.14331 / 9.53 ( 359) hydrogen bonds : angle 7.42489 / 5.27 ( 977) metal coordination : bond 0.10255 / 6.37 ( 4) metal coordination : angle 34.40681 / 12.37 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 576 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8011 (tm-30) REVERT: A 753 ASN cc_start: 0.8184 (t0) cc_final: 0.6963 (t0) REVERT: A 857 LEU cc_start: 0.9194 (mt) cc_final: 0.8898 (tt) REVERT: B 24 PHE cc_start: 0.6579 (m-10) cc_final: 0.6235 (m-80) REVERT: B 80 TYR cc_start: 0.7482 (t80) cc_final: 0.6994 (t80) REVERT: B 90 GLN cc_start: 0.8212 (pt0) cc_final: 0.7826 (pt0) REVERT: B 281 ASN cc_start: 0.7903 (p0) cc_final: 0.7242 (p0) REVERT: B 313 HIS cc_start: 0.8340 (t70) cc_final: 0.7987 (t-90) outliers start: 3 outliers final: 0 residues processed: 138 average time/residue: 0.0890 time to fit residues: 17.0828 Evaluate side-chains 81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A 820 ASN A 908 GLN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.085809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.063973 restraints weight = 25080.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.065686 restraints weight = 14430.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.066773 restraints weight = 10274.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067495 restraints weight = 8345.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.067835 restraints weight = 7341.003| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8502 Z= 0.175 Angle : 0.757 9.954 11760 Z= 0.408 Chirality : 0.050 0.348 1298 Planarity : 0.006 0.062 1303 Dihedral : 23.937 174.362 1618 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.98 % Allowed : 14.15 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -2.51 (0.25), residues: 879 helix: -1.33 (0.28), residues: 270 sheet: -1.01 (0.40), residues: 168 loop : -2.14 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 838 TYR 0.029 0.002 TYR B 346 PHE 0.030 0.002 PHE A 804 TRP 0.025 0.002 TRP B 317 HIS 0.010 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 ( 8498) covalent geometry : angle 0.75011 / 0.41 (11758) hydrogen bonds : bond 0.05028 / 3.38 ( 359) hydrogen bonds : angle 5.47589 / 3.85 ( 977) metal coordination : bond 0.01292 / 0.70 ( 4) metal coordination : angle 7.62549 / 2.80 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.297 Fit side-chains REVERT: A 576 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8120 (tm-30) REVERT: A 883 MET cc_start: 0.8064 (tpp) cc_final: 0.7733 (tpt) REVERT: B 80 TYR cc_start: 0.7580 (t80) cc_final: 0.7276 (t80) REVERT: B 289 LEU cc_start: 0.7663 (tp) cc_final: 0.7367 (tt) REVERT: B 313 HIS cc_start: 0.8380 (t70) cc_final: 0.8067 (t-90) outliers start: 15 outliers final: 6 residues processed: 104 average time/residue: 0.0840 time to fit residues: 12.4636 Evaluate side-chains 78 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 919 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 16 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 22 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN B 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.085429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.063473 restraints weight = 24808.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.065161 restraints weight = 14359.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.066272 restraints weight = 10275.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.066899 restraints weight = 8337.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.067397 restraints weight = 7380.817| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8502 Z= 0.166 Angle : 0.713 9.774 11760 Z= 0.381 Chirality : 0.048 0.377 1298 Planarity : 0.005 0.051 1303 Dihedral : 23.834 175.714 1618 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.59 % Allowed : 15.87 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.85 (0.27), residues: 879 helix: -0.63 (0.30), residues: 271 sheet: -0.51 (0.41), residues: 166 loop : -1.90 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 875 TYR 0.014 0.001 TYR A 926 PHE 0.041 0.002 PHE A 804 TRP 0.018 0.002 TRP B 317 HIS 0.004 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 ( 8498) covalent geometry : angle 0.70738 / 0.38 (11758) hydrogen bonds : bond 0.04611 / 3.12 ( 359) hydrogen bonds : angle 5.09364 / 3.59 ( 977) metal coordination : bond 0.00598 / 0.33 ( 4) metal coordination : angle 6.99572 / 2.44 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.256 Fit side-chains REVERT: A 576 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8091 (tm-30) REVERT: A 602 MET cc_start: 0.7938 (ptt) cc_final: 0.7678 (ptm) REVERT: A 627 MET cc_start: 0.7774 (ttm) cc_final: 0.7568 (ttm) REVERT: A 919 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8151 (tt) REVERT: B 80 TYR cc_start: 0.7573 (t80) cc_final: 0.7314 (t80) REVERT: B 313 HIS cc_start: 0.8397 (t70) cc_final: 0.8075 (t-90) outliers start: 12 outliers final: 6 residues processed: 87 average time/residue: 0.0703 time to fit residues: 9.1068 Evaluate side-chains 76 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 93 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN ** A 912 ASN ** 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 = 0.3660 r_free = 0.3660 target = 0.085308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.063492 restraints weight = 24944.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065216 restraints weight = 14208.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.066353 restraints weight = 9996.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067052 restraints weight = 8032.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067329 restraints weight = 7046.026| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8502 Z= 0.146 Angle : 0.669 9.110 11760 Z= 0.359 Chirality : 0.047 0.373 1298 Planarity : 0.004 0.053 1303 Dihedral : 23.696 174.612 1618 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.65 % Allowed : 16.53 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.37 (0.28), residues: 879 helix: -0.21 (0.31), residues: 269 sheet: -0.17 (0.42), residues: 166 loop : -1.65 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 875 TYR 0.016 0.001 TYR A 926 PHE 0.042 0.002 PHE A 804 TRP 0.014 0.001 TRP B 317 HIS 0.003 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 ( 8498) covalent geometry : angle 0.66604 / 0.36 (11758) hydrogen bonds : bond 0.04125 / 2.79 ( 359) hydrogen bonds : angle 4.78784 / 3.37 ( 977) metal coordination : bond 0.00425 / 0.24 ( 4) metal coordination : angle 4.81490 / 1.68 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.287 Fit side-chains REVERT: A 531 ASP cc_start: 0.7796 (t0) cc_final: 0.7588 (t0) REVERT: A 576 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8101 (tm-30) REVERT: A 627 MET cc_start: 0.7753 (ttm) cc_final: 0.7505 (ttm) REVERT: A 849 MET cc_start: 0.7627 (mtp) cc_final: 0.7177 (ttp) REVERT: A 853 PHE cc_start: 0.8845 (t80) cc_final: 0.8478 (t80) REVERT: A 919 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8195 (tt) REVERT: B 80 TYR cc_start: 0.7649 (t80) cc_final: 0.7094 (t80) REVERT: B 313 HIS cc_start: 0.8403 (t70) cc_final: 0.8123 (t-90) REVERT: B 322 MET cc_start: 0.8601 (mtm) cc_final: 0.8155 (mpp) outliers start: 20 outliers final: 9 residues processed: 97 average time/residue: 0.0662 time to fit residues: 9.9202 Evaluate side-chains 81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 75 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 86 optimal weight: 0.5980 chunk 29 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 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 = 0.3699 r_free = 0.3699 target = 0.087293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065187 restraints weight = 24937.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.067039 restraints weight = 13778.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068241 restraints weight = 9566.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.069016 restraints weight = 7631.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069471 restraints weight = 6656.487| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8502 Z= 0.122 Angle : 0.660 13.492 11760 Z= 0.351 Chirality : 0.047 0.370 1298 Planarity : 0.004 0.057 1303 Dihedral : 23.501 174.141 1618 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.25 % Allowed : 17.59 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.11 (0.28), residues: 879 helix: 0.10 (0.32), residues: 271 sheet: -0.09 (0.42), residues: 169 loop : -1.55 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 875 TYR 0.010 0.001 TYR A 757 PHE 0.052 0.001 PHE A 804 TRP 0.013 0.001 TRP B 317 HIS 0.002 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 ( 8498) covalent geometry : angle 0.65864 / 0.35 (11758) hydrogen bonds : bond 0.03901 / 2.64 ( 359) hydrogen bonds : angle 4.64254 / 3.28 ( 977) metal coordination : bond 0.00564 / 0.33 ( 4) metal coordination : angle 3.34580 / 1.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.315 Fit side-chains REVERT: A 531 ASP cc_start: 0.7800 (t0) cc_final: 0.7543 (t0) REVERT: A 568 MET cc_start: 0.8045 (ttm) cc_final: 0.7403 (ttm) REVERT: A 576 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8056 (tm-30) REVERT: A 627 MET cc_start: 0.7668 (ttm) cc_final: 0.7434 (ttm) REVERT: A 919 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8180 (tt) REVERT: B 80 TYR cc_start: 0.7622 (t80) cc_final: 0.7076 (t80) REVERT: B 170 GLU cc_start: 0.8163 (mp0) cc_final: 0.7950 (mp0) REVERT: B 313 HIS cc_start: 0.8390 (t70) cc_final: 0.8173 (t-90) REVERT: B 322 MET cc_start: 0.8514 (mtm) cc_final: 0.8128 (mpp) outliers start: 17 outliers final: 9 residues processed: 90 average time/residue: 0.0676 time to fit residues: 9.3413 Evaluate side-chains 78 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 26 optimal weight: 0.0570 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 0.1980 chunk 80 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 HIS ** A 912 ASN ** 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 = 0.3680 r_free = 0.3680 target = 0.086298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.064209 restraints weight = 24745.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.065967 restraints weight = 13883.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.067150 restraints weight = 9773.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067908 restraints weight = 7841.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.068306 restraints weight = 6847.608| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8502 Z= 0.146 Angle : 0.672 10.727 11760 Z= 0.355 Chirality : 0.046 0.361 1298 Planarity : 0.004 0.055 1303 Dihedral : 23.395 173.946 1618 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.12 % Allowed : 19.31 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.94 (0.28), residues: 879 helix: 0.36 (0.32), residues: 268 sheet: 0.09 (0.43), residues: 164 loop : -1.54 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 875 TYR 0.009 0.001 TYR A 926 PHE 0.048 0.002 PHE A 804 TRP 0.013 0.001 TRP B 317 HIS 0.003 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 ( 8498) covalent geometry : angle 0.67063 / 0.36 (11758) hydrogen bonds : bond 0.04026 / 2.73 ( 359) hydrogen bonds : angle 4.58666 / 3.23 ( 977) metal coordination : bond 0.00345 / 0.19 ( 4) metal coordination : angle 3.29045 / 1.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.302 Fit side-chains REVERT: A 576 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 627 MET cc_start: 0.7748 (ttm) cc_final: 0.7480 (ttm) REVERT: A 883 MET cc_start: 0.8132 (tpp) cc_final: 0.7887 (tpt) REVERT: A 919 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8173 (tt) REVERT: B 80 TYR cc_start: 0.7696 (t80) cc_final: 0.7194 (t80) REVERT: B 170 GLU cc_start: 0.8166 (mp0) cc_final: 0.7956 (mp0) REVERT: B 313 HIS cc_start: 0.8449 (t70) cc_final: 0.8240 (t-90) REVERT: B 322 MET cc_start: 0.8590 (mtm) cc_final: 0.8123 (mpp) outliers start: 16 outliers final: 9 residues processed: 85 average time/residue: 0.0656 time to fit residues: 8.5552 Evaluate side-chains 78 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 93 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 ASN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN B 33 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.083733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.061714 restraints weight = 24841.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.063406 restraints weight = 14179.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.064501 restraints weight = 10046.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065126 restraints weight = 8129.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.065603 restraints weight = 7182.948| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8502 Z= 0.191 Angle : 0.706 12.123 11760 Z= 0.371 Chirality : 0.047 0.358 1298 Planarity : 0.005 0.076 1303 Dihedral : 23.372 174.358 1618 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.25 % Allowed : 19.84 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.88 (0.28), residues: 879 helix: 0.39 (0.32), residues: 268 sheet: 0.06 (0.42), residues: 166 loop : -1.46 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 970 TYR 0.011 0.001 TYR A 805 PHE 0.042 0.002 PHE A 804 TRP 0.015 0.002 TRP B 317 HIS 0.003 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 8498) covalent geometry : angle 0.70434 / 0.37 (11758) hydrogen bonds : bond 0.04219 / 2.87 ( 359) hydrogen bonds : angle 4.61602 / 3.25 ( 977) metal coordination : bond 0.00709 / 0.40 ( 4) metal coordination : angle 4.03553 / 1.42 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.306 Fit side-chains REVERT: A 576 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8111 (tm-30) REVERT: A 627 MET cc_start: 0.7775 (ttm) cc_final: 0.7433 (ttm) REVERT: A 919 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8198 (tt) REVERT: B 322 MET cc_start: 0.8667 (mtm) cc_final: 0.8140 (mpp) outliers start: 17 outliers final: 11 residues processed: 84 average time/residue: 0.0691 time to fit residues: 8.8166 Evaluate side-chains 82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 74 optimal weight: 8.9990 chunk 82 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 59 optimal weight: 0.0050 chunk 63 optimal weight: 0.1980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 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 = 0.3673 r_free = 0.3673 target = 0.086018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.063934 restraints weight = 24761.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.065731 restraints weight = 13755.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066892 restraints weight = 9596.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067637 restraints weight = 7681.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.068066 restraints weight = 6713.671| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8502 Z= 0.131 Angle : 0.670 8.487 11760 Z= 0.358 Chirality : 0.046 0.357 1298 Planarity : 0.004 0.057 1303 Dihedral : 23.309 173.555 1618 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.72 % Allowed : 21.16 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.73 (0.28), residues: 879 helix: 0.51 (0.33), residues: 269 sheet: 0.24 (0.42), residues: 164 loop : -1.40 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 838 TYR 0.009 0.001 TYR A 757 PHE 0.045 0.002 PHE A 804 TRP 0.014 0.001 TRP B 317 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 8498) covalent geometry : angle 0.66958 / 0.36 (11758) hydrogen bonds : bond 0.03874 / 2.63 ( 359) hydrogen bonds : angle 4.49090 / 3.16 ( 977) metal coordination : bond 0.00268 / 0.17 ( 4) metal coordination : angle 2.70781 / 0.94 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.316 Fit side-chains REVERT: A 576 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8073 (tm-30) REVERT: A 627 MET cc_start: 0.7693 (ttm) cc_final: 0.7360 (ttm) REVERT: A 919 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8214 (tt) REVERT: B 322 MET cc_start: 0.8585 (mtm) cc_final: 0.8155 (mpp) outliers start: 13 outliers final: 9 residues processed: 80 average time/residue: 0.0769 time to fit residues: 9.2543 Evaluate side-chains 75 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 HIS ** A 912 ASN ** 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 = 0.3643 r_free = 0.3643 target = 0.084634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.062499 restraints weight = 24721.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.064258 restraints weight = 13773.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.065321 restraints weight = 9608.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.066084 restraints weight = 7757.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066497 restraints weight = 6764.845| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8502 Z= 0.152 Angle : 0.699 14.010 11760 Z= 0.363 Chirality : 0.046 0.349 1298 Planarity : 0.004 0.056 1303 Dihedral : 23.303 173.554 1618 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.59 % Allowed : 22.22 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.62 (0.28), residues: 879 helix: 0.59 (0.33), residues: 268 sheet: 0.27 (0.42), residues: 163 loop : -1.31 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 679 TYR 0.008 0.001 TYR A 757 PHE 0.043 0.002 PHE A 804 TRP 0.016 0.002 TRP B 317 HIS 0.003 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 8498) covalent geometry : angle 0.69788 / 0.36 (11758) hydrogen bonds : bond 0.03929 / 2.67 ( 359) hydrogen bonds : angle 4.40224 / 3.11 ( 977) metal coordination : bond 0.00400 / 0.22 ( 4) metal coordination : angle 2.57844 / 0.90 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.290 Fit side-chains REVERT: A 576 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8116 (tm-30) REVERT: A 627 MET cc_start: 0.7725 (ttm) cc_final: 0.7366 (ttm) REVERT: A 844 LYS cc_start: 0.6493 (mmtt) cc_final: 0.5750 (tptt) REVERT: A 919 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8209 (tt) REVERT: B 322 MET cc_start: 0.8651 (mtm) cc_final: 0.8122 (mpp) outliers start: 12 outliers final: 8 residues processed: 80 average time/residue: 0.0748 time to fit residues: 8.9907 Evaluate side-chains 80 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 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 = 0.3667 r_free = 0.3667 target = 0.085999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.064273 restraints weight = 24669.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.066097 restraints weight = 13469.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.067238 restraints weight = 9250.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.068001 restraints weight = 7372.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068400 restraints weight = 6409.699| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8502 Z= 0.144 Angle : 0.709 16.114 11760 Z= 0.366 Chirality : 0.046 0.348 1298 Planarity : 0.004 0.055 1303 Dihedral : 23.285 173.380 1618 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.46 % Allowed : 22.75 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.60 (0.28), residues: 879 helix: 0.56 (0.33), residues: 269 sheet: 0.40 (0.43), residues: 161 loop : -1.31 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 679 TYR 0.008 0.001 TYR A 757 PHE 0.043 0.002 PHE A 804 TRP 0.016 0.001 TRP B 317 HIS 0.003 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 8498) covalent geometry : angle 0.70828 / 0.37 (11758) hydrogen bonds : bond 0.03816 / 2.59 ( 359) hydrogen bonds : angle 4.38371 / 3.12 ( 977) metal coordination : bond 0.00342 / 0.19 ( 4) metal coordination : angle 2.37540 / 0.82 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.304 Fit side-chains REVERT: A 576 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 627 MET cc_start: 0.7709 (ttm) cc_final: 0.7367 (ttm) REVERT: A 844 LYS cc_start: 0.6599 (mmtt) cc_final: 0.5811 (tptt) REVERT: A 883 MET cc_start: 0.8072 (tpp) cc_final: 0.7618 (tpt) REVERT: A 919 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8232 (tt) REVERT: B 55 LEU cc_start: 0.8344 (pp) cc_final: 0.8039 (mt) REVERT: B 322 MET cc_start: 0.8540 (mtm) cc_final: 0.8139 (mpp) outliers start: 11 outliers final: 9 residues processed: 82 average time/residue: 0.0796 time to fit residues: 9.6980 Evaluate side-chains 81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 90 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.0570 chunk 38 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.084618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062542 restraints weight = 24859.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.064272 restraints weight = 14055.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065377 restraints weight = 9881.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.066078 restraints weight = 7954.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.066473 restraints weight = 6971.173| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8502 Z= 0.155 Angle : 0.701 11.189 11760 Z= 0.364 Chirality : 0.046 0.344 1298 Planarity : 0.004 0.055 1303 Dihedral : 23.294 173.461 1618 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.32 % Allowed : 23.41 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.55 (0.28), residues: 879 helix: 0.60 (0.33), residues: 268 sheet: 0.32 (0.43), residues: 163 loop : -1.25 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 838 TYR 0.009 0.001 TYR A 926 PHE 0.042 0.002 PHE A 804 TRP 0.016 0.002 TRP B 317 HIS 0.003 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 8498) covalent geometry : angle 0.70016 / 0.36 (11758) hydrogen bonds : bond 0.03860 / 2.62 ( 359) hydrogen bonds : angle 4.35016 / 3.09 ( 977) metal coordination : bond 0.00428 / 0.24 ( 4) metal coordination : angle 2.34834 / 0.81 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1474.29 seconds wall clock time: 26 minutes 12.64 seconds (1572.64 seconds total)