Starting phenix.real_space_refine on Fri Aug 7 13:17:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9w_64890/08_2026/9v9w_64890.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9w_64890/08_2026/9v9w_64890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9w_64890/08_2026/9v9w_64890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9w_64890/08_2026/9v9w_64890.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9w_64890/08_2026/9v9w_64890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9w_64890/08_2026/9v9w_64890.cif" } resolution = 3.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11069 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 262 5.49 5 S 26 5.16 5 C 7373 2.51 5 N 2433 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13048 Number of models: 1 Model: "" Number of chains: 16 Chain: "L" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 252 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "N" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 279 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "A" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2671 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2700 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "K" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39 SG CYS L 27 83.738 33.655 54.099 1.00 86.02 S ATOM 58 SG CYS L 30 84.046 30.927 51.488 1.00 85.21 S ATOM 146 SG CYS L 41 86.840 33.442 51.857 1.00 86.97 S ATOM 166 SG CYS L 44 83.519 34.594 50.444 1.00 89.81 S ATOM 291 SG CYS N 27 42.378 89.050 44.098 1.00 76.06 S ATOM 310 SG CYS N 30 41.966 89.606 40.353 1.00 78.36 S ATOM 398 SG CYS N 41 39.290 87.735 42.266 1.00 72.40 S ATOM 418 SG CYS N 44 42.666 86.118 41.670 1.00 79.34 S Time building chain proxies: 3.04, per 1000 atoms: 0.23 Number of scatterers: 13048 At special positions: 0 Unit cell: (126.5, 116.6, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 26 16.00 P 262 15.00 O 2952 8.00 N 2433 7.00 C 7373 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: 1.10 Conformation dependent library (CDL) restraints added in 476.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 30 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 27 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 44 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 30 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 41 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 44 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 27 " Number of angles added : 12 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 59.8% alpha, 5.3% beta 127 base pairs and 210 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.643A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.595A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.567A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.945A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.541A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.482A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.944A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.507A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.722A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.705A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.975A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.507A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.388A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.674A pdb=" N MET H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.802A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 34 removed outlier: 3.836A pdb=" N VAL K 26 " --> pdb=" O THR K 22 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS K 27 " --> pdb=" O ILE K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 59 Processing helix chain 'O' and resid 22 through 34 Processing helix chain 'O' and resid 55 through 59 removed outlier: 3.595A pdb=" N ASP O 58 " --> pdb=" O THR O 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'N' and resid 25 through 26 removed outlier: 3.847A pdb=" N TRP N 25 " --> pdb=" O ASN N 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.873A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.157A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.872A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.204A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'K' and resid 12 through 14 removed outlier: 8.932A pdb=" N LEU K 69 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS K 6 " --> pdb=" O LEU K 69 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE K 45 " --> pdb=" O LYS K 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.876A pdb=" N VAL O 70 " --> pdb=" O ARG O 42 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG O 42 " --> pdb=" O VAL O 70 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 328 hydrogen bonds 656 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 210 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2860 1.34 - 1.45: 3945 1.45 - 1.57: 6434 1.57 - 1.69: 522 1.69 - 1.81: 38 Bond restraints: 13799 Sorted by residual: bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DG I 44 " pdb=" C2' DG I 44 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DA I 106 " pdb=" C2' DA I 106 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT I 104 " pdb=" C2' DT I 104 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DG I 13 " pdb=" C2' DG I 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 13794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 18506 1.30 - 2.60: 1139 2.60 - 3.89: 88 3.89 - 5.19: 10 5.19 - 6.49: 1 Bond angle restraints: 19744 Sorted by residual: angle pdb=" N3 DT I 57 " pdb=" C4 DT I 57 " pdb=" O4 DT I 57 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT J 89 " pdb=" C4 DT J 89 " pdb=" O4 DT J 89 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT J 140 " pdb=" C4 DT J 140 " pdb=" O4 DT J 140 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 ... (remaining 19739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 6504 35.12 - 70.24: 1124 70.24 - 105.36: 24 105.36 - 140.47: 0 140.47 - 175.59: 2 Dihedral angle restraints: 7654 sinusoidal: 4848 harmonic: 2806 Sorted by residual: dihedral pdb=" C4' DT J 57 " pdb=" C3' DT J 57 " pdb=" O3' DT J 57 " pdb=" P DT J 58 " ideal model delta sinusoidal sigma weight residual -140.00 35.59 -175.59 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 79.52 140.48 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" CB GLU A 73 " pdb=" CG GLU A 73 " pdb=" CD GLU A 73 " pdb=" OE1 GLU A 73 " ideal model delta sinusoidal sigma weight residual 0.00 88.65 -88.65 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 7651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1144 0.026 - 0.052: 698 0.052 - 0.078: 232 0.078 - 0.104: 144 0.104 - 0.130: 41 Chirality restraints: 2259 Sorted by residual: chirality pdb=" CA ILE O 36 " pdb=" N ILE O 36 " pdb=" C ILE O 36 " pdb=" CB ILE O 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE H 51 " pdb=" N ILE H 51 " pdb=" C ILE H 51 " pdb=" CB ILE H 51 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 2256 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR N 31 " -0.006 2.00e-02 2.50e+03 1.22e-02 1.48e+00 pdb=" C THR N 31 " 0.021 2.00e-02 2.50e+03 pdb=" O THR N 31 " -0.008 2.00e-02 2.50e+03 pdb=" N PHE N 32 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 91 " -0.016 2.00e-02 2.50e+03 7.19e-03 1.42e+00 pdb=" N9 DA I 91 " 0.015 2.00e-02 2.50e+03 pdb=" C8 DA I 91 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 91 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 91 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 91 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 91 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 91 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 91 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 91 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 91 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO G 80 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.016 5.00e-02 4.00e+02 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1935 2.77 - 3.30: 11292 3.30 - 3.84: 24079 3.84 - 4.37: 27255 4.37 - 4.90: 41311 Nonbonded interactions: 105872 Sorted by model distance: nonbonded pdb=" NH2 ARG G 77 " pdb=" OP1 DC J 20 " model vdw 2.239 3.120 nonbonded pdb=" NE2 GLN K 31 " pdb=" O ILE K 36 " model vdw 2.247 3.120 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.258 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O LEU G 23 " model vdw 2.303 3.040 nonbonded pdb=" O ASP O 21 " pdb=" OG1 THR O 55 " model vdw 2.327 3.040 ... (remaining 105867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 133) selection = (chain 'E' and resid 40 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 14 through 119) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 30 through 120) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'L' selection = (chain 'N' and (resid 24 through 55 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.700 Find NCS groups from input model: 0.170 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.005 0.036 13807 Z= 0.463 Angle : 0.631 6.490 19756 Z= 0.575 Chirality : 0.041 0.130 2259 Planarity : 0.003 0.029 1591 Dihedral : 25.475 175.593 5836 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.82 (0.28), residues: 944 helix: 3.20 (0.22), residues: 552 sheet: 1.03 (0.91), residues: 40 loop : -0.26 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 35 TYR 0.010 0.001 TYR H 39 PHE 0.006 0.001 PHE D 67 TRP 0.001 0.000 TRP L 25 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.46 (13799) covalent geometry : angle 0.63087 / 0.58 (19744) hydrogen bonds : bond 0.11148 / 7.09 ( 757) hydrogen bonds : angle 3.83500 / 2.78 ( 1910) metal coordination : bond 0.00144 / 0.07 ( 8) metal coordination : angle 0.93554 / 0.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.377 Fit side-chains REVERT: A 105 GLU cc_start: 0.6377 (mt-10) cc_final: 0.6151 (mt-10) REVERT: G 64 GLU cc_start: 0.7722 (tt0) cc_final: 0.7519 (tt0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.8831 time to fit residues: 144.3159 Evaluate side-chains 123 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 73 ASN D 60 ASN D 81 ASN E 68 GLN F 27 GLN F 93 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.171186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123143 restraints weight = 18364.146| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.26 r_work: 0.3220 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13807 Z= 0.177 Angle : 0.597 6.432 19756 Z= 0.358 Chirality : 0.043 0.244 2259 Planarity : 0.004 0.033 1591 Dihedral : 28.899 173.303 3911 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.58 % Allowed : 10.44 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.39 (0.28), residues: 944 helix: 2.85 (0.21), residues: 561 sheet: 0.87 (0.89), residues: 40 loop : -0.56 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 35 TYR 0.012 0.002 TYR A 54 PHE 0.016 0.002 PHE H 62 TRP 0.011 0.002 TRP L 25 HIS 0.003 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 (13799) covalent geometry : angle 0.59632 / 0.36 (19744) hydrogen bonds : bond 0.06065 / 3.97 ( 757) hydrogen bonds : angle 2.96715 / 2.09 ( 1910) metal coordination : bond 0.00513 / 0.25 ( 8) metal coordination : angle 1.29726 / 0.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.359 Fit side-chains REVERT: A 105 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7293 (mt-10) REVERT: C 92 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: D 31 LYS cc_start: 0.6700 (OUTLIER) cc_final: 0.6184 (ttmt) REVERT: F 26 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8102 (tp) REVERT: G 56 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8506 (tt0) outliers start: 13 outliers final: 2 residues processed: 141 average time/residue: 0.8980 time to fit residues: 134.2631 Evaluate side-chains 134 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 78 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 73 ASN D 46 HIS E 68 GLN F 75 HIS F 93 GLN G 89 ASN H 106 HIS K 31 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115037 restraints weight = 17799.989| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.32 r_work: 0.3027 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 13807 Z= 0.299 Angle : 0.803 7.631 19756 Z= 0.444 Chirality : 0.056 0.302 2259 Planarity : 0.007 0.078 1591 Dihedral : 29.685 175.716 3911 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.79 % Allowed : 13.35 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.99 (0.26), residues: 944 helix: 1.87 (0.21), residues: 555 sheet: 0.49 (0.87), residues: 44 loop : -1.40 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 36 TYR 0.027 0.003 TYR A 54 PHE 0.019 0.003 PHE G 25 TRP 0.012 0.003 TRP L 25 HIS 0.012 0.003 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.30 (13799) covalent geometry : angle 0.80148 / 0.44 (19744) hydrogen bonds : bond 0.09904 / 6.38 ( 757) hydrogen bonds : angle 3.40470 / 2.38 ( 1910) metal coordination : bond 0.00735 / 0.38 ( 8) metal coordination : angle 2.06428 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.386 Fit side-chains REVERT: A 57 SER cc_start: 0.8954 (t) cc_final: 0.8731 (t) REVERT: C 35 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.7749 (mtm110) REVERT: C 61 GLU cc_start: 0.8656 (tp30) cc_final: 0.8363 (mm-30) REVERT: C 73 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.8082 (t0) REVERT: D 31 LYS cc_start: 0.6761 (OUTLIER) cc_final: 0.6251 (ttmt) REVERT: D 54 LYS cc_start: 0.8714 (mmtm) cc_final: 0.8370 (mmtm) REVERT: D 82 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8247 (mttp) REVERT: E 45 THR cc_start: 0.8649 (m) cc_final: 0.8448 (p) REVERT: G 56 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: G 74 LYS cc_start: 0.7776 (mmtt) cc_final: 0.7500 (mmmt) REVERT: K 1 MET cc_start: 0.2360 (OUTLIER) cc_final: 0.2053 (tmm) outliers start: 23 outliers final: 4 residues processed: 155 average time/residue: 0.9089 time to fit residues: 149.2652 Evaluate side-chains 144 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 chunk 88 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 overall best weight: 6.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN D 64 ASN E 68 GLN F 27 GLN F 93 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.160357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113491 restraints weight = 17746.818| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.27 r_work: 0.3020 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 13807 Z= 0.331 Angle : 0.784 7.861 19756 Z= 0.436 Chirality : 0.056 0.282 2259 Planarity : 0.006 0.051 1591 Dihedral : 29.781 178.241 3911 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.13 % Favored : 95.76 % Rotamer: Outliers : 3.16 % Allowed : 15.41 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.26), residues: 944 helix: 1.72 (0.21), residues: 550 sheet: 0.34 (1.05), residues: 28 loop : -1.71 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 20 TYR 0.022 0.003 TYR K 59 PHE 0.016 0.003 PHE B 61 TRP 0.016 0.003 TRP L 25 HIS 0.010 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00764 / 0.33 (13799) covalent geometry : angle 0.78293 / 0.44 (19744) hydrogen bonds : bond 0.09065 / 5.83 ( 757) hydrogen bonds : angle 3.34815 / 2.35 ( 1910) metal coordination : bond 0.00738 / 0.36 ( 8) metal coordination : angle 2.08728 / 1.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.389 Fit side-chains REVERT: A 59 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: A 94 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: C 61 GLU cc_start: 0.8881 (tp30) cc_final: 0.8590 (mm-30) REVERT: C 92 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7928 (mm-30) REVERT: D 82 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8254 (mttp) REVERT: E 133 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7727 (mt-10) REVERT: G 56 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8450 (tt0) REVERT: G 74 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7767 (mmmt) outliers start: 26 outliers final: 9 residues processed: 146 average time/residue: 0.9045 time to fit residues: 140.0046 Evaluate side-chains 147 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 68 GLN F 27 GLN F 93 GLN K 49 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.163719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.117373 restraints weight = 17829.962| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.31 r_work: 0.3074 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13807 Z= 0.145 Angle : 0.635 6.116 19756 Z= 0.365 Chirality : 0.046 0.233 2259 Planarity : 0.004 0.048 1591 Dihedral : 29.672 176.053 3911 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.39 % Favored : 96.50 % Rotamer: Outliers : 2.43 % Allowed : 17.96 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.48 (0.27), residues: 944 helix: 2.49 (0.22), residues: 551 sheet: 0.48 (1.06), residues: 28 loop : -1.49 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 20 TYR 0.010 0.001 TYR H 118 PHE 0.011 0.001 PHE N 24 TRP 0.008 0.002 TRP L 25 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (13799) covalent geometry : angle 0.63480 / 0.37 (19744) hydrogen bonds : bond 0.06511 / 4.19 ( 757) hydrogen bonds : angle 3.07562 / 2.15 ( 1910) metal coordination : bond 0.00433 / 0.21 ( 8) metal coordination : angle 1.26468 / 0.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.373 Fit side-chains REVERT: C 61 GLU cc_start: 0.8531 (tp30) cc_final: 0.8237 (mm-30) REVERT: C 92 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: D 82 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8169 (mttp) REVERT: G 56 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: G 74 LYS cc_start: 0.7893 (mmtt) cc_final: 0.7683 (mmmt) REVERT: G 77 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8050 (mtm-85) REVERT: K 1 MET cc_start: 0.2433 (tmt) cc_final: 0.1850 (tmm) outliers start: 20 outliers final: 5 residues processed: 139 average time/residue: 0.9110 time to fit residues: 134.1885 Evaluate side-chains 140 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 102 optimal weight: 40.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 27 GLN F 93 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.161322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114184 restraints weight = 17713.885| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.23 r_work: 0.3043 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13807 Z= 0.225 Angle : 0.681 7.134 19756 Z= 0.386 Chirality : 0.049 0.263 2259 Planarity : 0.005 0.048 1591 Dihedral : 29.770 178.454 3911 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 3.16 % Allowed : 17.48 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.27), residues: 944 helix: 2.23 (0.21), residues: 550 sheet: 0.44 (1.07), residues: 28 loop : -1.58 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 20 TYR 0.016 0.002 TYR H 39 PHE 0.021 0.002 PHE L 32 TRP 0.008 0.002 TRP L 25 HIS 0.008 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (13799) covalent geometry : angle 0.68020 / 0.39 (19744) hydrogen bonds : bond 0.07826 / 5.04 ( 757) hydrogen bonds : angle 3.16811 / 2.22 ( 1910) metal coordination : bond 0.00578 / 0.28 ( 8) metal coordination : angle 1.51143 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.375 Fit side-chains REVERT: L 33 ARG cc_start: 0.5114 (mmm-85) cc_final: 0.4444 (mmm-85) REVERT: A 94 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: C 61 GLU cc_start: 0.8832 (tp30) cc_final: 0.8566 (mm-30) REVERT: D 82 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8354 (mttp) REVERT: G 56 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: G 74 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7906 (mmmt) REVERT: H 82 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7727 (mttp) REVERT: K 1 MET cc_start: 0.2471 (OUTLIER) cc_final: 0.1733 (tmm) outliers start: 26 outliers final: 8 residues processed: 142 average time/residue: 0.8983 time to fit residues: 135.1820 Evaluate side-chains 144 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 74 optimal weight: 0.9980 chunk 101 optimal weight: 40.0000 chunk 24 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 111 optimal weight: 0.0570 chunk 71 optimal weight: 0.6980 overall best weight: 2.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 27 GLN F 93 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.162851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116580 restraints weight = 17777.948| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.23 r_work: 0.3086 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13807 Z= 0.158 Angle : 0.619 5.979 19756 Z= 0.357 Chirality : 0.045 0.234 2259 Planarity : 0.004 0.054 1591 Dihedral : 29.744 177.535 3911 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.03 % Favored : 95.87 % Rotamer: Outliers : 2.91 % Allowed : 18.33 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.48 (0.27), residues: 944 helix: 2.50 (0.22), residues: 552 sheet: 0.54 (1.07), residues: 28 loop : -1.51 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.011 0.002 TYR D 37 PHE 0.021 0.002 PHE L 32 TRP 0.006 0.002 TRP N 25 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (13799) covalent geometry : angle 0.61812 / 0.36 (19744) hydrogen bonds : bond 0.06526 / 4.20 ( 757) hydrogen bonds : angle 3.02554 / 2.12 ( 1910) metal coordination : bond 0.00495 / 0.24 ( 8) metal coordination : angle 1.34789 / 0.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.345 Fit side-chains REVERT: L 33 ARG cc_start: 0.5209 (mmm-85) cc_final: 0.4445 (mmm-85) REVERT: A 94 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: C 61 GLU cc_start: 0.8796 (tp30) cc_final: 0.8534 (mm-30) REVERT: C 73 ASN cc_start: 0.8235 (t0) cc_final: 0.7935 (t0) REVERT: D 82 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8293 (mttp) REVERT: G 56 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: G 77 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8190 (mtm-85) REVERT: H 82 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7608 (mttp) REVERT: K 1 MET cc_start: 0.2563 (OUTLIER) cc_final: 0.2015 (tmm) outliers start: 24 outliers final: 12 residues processed: 140 average time/residue: 0.8642 time to fit residues: 128.3259 Evaluate side-chains 147 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 43 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 88 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 77 optimal weight: 50.0000 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 86 optimal weight: 30.0000 chunk 102 optimal weight: 50.0000 chunk 89 optimal weight: 50.0000 chunk 10 optimal weight: 6.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 27 GLN F 93 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.159298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111750 restraints weight = 17485.786| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.21 r_work: 0.3018 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 13807 Z= 0.340 Angle : 0.798 7.940 19756 Z= 0.440 Chirality : 0.056 0.308 2259 Planarity : 0.007 0.062 1591 Dihedral : 29.954 179.284 3911 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.40 % Favored : 94.49 % Rotamer: Outliers : 2.79 % Allowed : 18.45 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.59 (0.26), residues: 944 helix: 1.75 (0.21), residues: 550 sheet: 0.12 (1.07), residues: 28 loop : -1.80 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 35 TYR 0.017 0.003 TYR D 39 PHE 0.027 0.003 PHE L 32 TRP 0.008 0.002 TRP L 25 HIS 0.011 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.34 (13799) covalent geometry : angle 0.79587 / 0.44 (19744) hydrogen bonds : bond 0.09408 / 6.06 ( 757) hydrogen bonds : angle 3.32955 / 2.33 ( 1910) metal coordination : bond 0.00754 / 0.37 ( 8) metal coordination : angle 2.26520 / 1.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: L 33 ARG cc_start: 0.5442 (mmm-85) cc_final: 0.4829 (mmm-85) REVERT: A 94 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: C 61 GLU cc_start: 0.8861 (tp30) cc_final: 0.8640 (mm-30) REVERT: D 31 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6270 (ttmt) REVERT: D 82 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8288 (mttp) REVERT: G 56 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: G 77 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8315 (mtm-85) REVERT: K 1 MET cc_start: 0.2823 (OUTLIER) cc_final: 0.2281 (tmm) outliers start: 23 outliers final: 12 residues processed: 142 average time/residue: 0.9054 time to fit residues: 136.2706 Evaluate side-chains 148 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 88 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 113 optimal weight: 0.0870 chunk 90 optimal weight: 50.0000 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 27 GLN F 93 GLN K 31 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.164063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117186 restraints weight = 17851.375| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.23 r_work: 0.3105 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13807 Z= 0.141 Angle : 0.619 6.288 19756 Z= 0.356 Chirality : 0.044 0.250 2259 Planarity : 0.004 0.054 1591 Dihedral : 29.816 177.381 3911 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.50 % Favored : 96.40 % Rotamer: Outliers : 1.70 % Allowed : 20.02 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.27), residues: 944 helix: 2.54 (0.22), residues: 552 sheet: 0.37 (1.06), residues: 28 loop : -1.52 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 35 TYR 0.010 0.001 TYR D 80 PHE 0.019 0.001 PHE L 32 TRP 0.007 0.001 TRP N 25 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (13799) covalent geometry : angle 0.61831 / 0.36 (19744) hydrogen bonds : bond 0.05926 / 3.80 ( 757) hydrogen bonds : angle 2.99223 / 2.10 ( 1910) metal coordination : bond 0.00488 / 0.24 ( 8) metal coordination : angle 1.50552 / 0.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: C 35 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7658 (mtm110) REVERT: C 61 GLU cc_start: 0.8743 (tp30) cc_final: 0.8520 (mm-30) REVERT: C 73 ASN cc_start: 0.8148 (t0) cc_final: 0.7856 (t0) REVERT: H 82 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7603 (mttp) REVERT: K 1 MET cc_start: 0.3212 (tmt) cc_final: 0.2706 (tmm) outliers start: 14 outliers final: 5 residues processed: 129 average time/residue: 0.9043 time to fit residues: 123.6216 Evaluate side-chains 129 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain O residue 43 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 20.0000 chunk 53 optimal weight: 0.5980 chunk 82 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 64 optimal weight: 0.0670 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 0.0270 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS E 68 GLN F 27 GLN F 93 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.164945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118148 restraints weight = 17937.072| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.23 r_work: 0.3133 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13807 Z= 0.131 Angle : 0.583 7.681 19756 Z= 0.340 Chirality : 0.042 0.225 2259 Planarity : 0.004 0.052 1591 Dihedral : 29.747 178.224 3911 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 1.33 % Allowed : 20.63 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.92 (0.28), residues: 944 helix: 2.83 (0.22), residues: 552 sheet: 0.85 (0.94), residues: 38 loop : -1.36 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 35 TYR 0.008 0.001 TYR B 51 PHE 0.012 0.001 PHE L 32 TRP 0.004 0.001 TRP N 25 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.13 (13799) covalent geometry : angle 0.58187 / 0.34 (19744) hydrogen bonds : bond 0.05398 / 3.49 ( 757) hydrogen bonds : angle 2.86285 / 2.00 ( 1910) metal coordination : bond 0.00409 / 0.21 ( 8) metal coordination : angle 1.47124 / 0.82 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8115 (t0) cc_final: 0.7858 (t0) REVERT: G 64 GLU cc_start: 0.8732 (tt0) cc_final: 0.8510 (tt0) REVERT: H 82 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7568 (mttp) REVERT: K 1 MET cc_start: 0.3235 (tmt) cc_final: 0.2656 (tmm) outliers start: 11 outliers final: 4 residues processed: 131 average time/residue: 0.9154 time to fit residues: 126.9962 Evaluate side-chains 130 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain O residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 84 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS E 68 GLN F 27 GLN F 93 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.163220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116104 restraints weight = 17793.272| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.19 r_work: 0.3097 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13807 Z= 0.172 Angle : 0.617 7.139 19756 Z= 0.355 Chirality : 0.044 0.244 2259 Planarity : 0.005 0.056 1591 Dihedral : 29.797 178.759 3911 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 1.21 % Allowed : 20.75 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.68 (0.27), residues: 944 helix: 2.63 (0.22), residues: 552 sheet: 0.74 (0.94), residues: 38 loop : -1.43 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 35 TYR 0.011 0.002 TYR D 37 PHE 0.019 0.002 PHE L 32 TRP 0.006 0.001 TRP N 25 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (13799) covalent geometry : angle 0.61622 / 0.35 (19744) hydrogen bonds : bond 0.06391 / 4.12 ( 757) hydrogen bonds : angle 2.96394 / 2.08 ( 1910) metal coordination : bond 0.00416 / 0.20 ( 8) metal coordination : angle 1.56297 / 0.88 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4933.01 seconds wall clock time: 84 minutes 31.11 seconds (5071.11 seconds total)