Starting phenix.real_space_refine on Sat Jul 4 15:49:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9w_64890/07_2026/9v9w_64890.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9w_64890/07_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_64890/07_2026/9v9w_64890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9w_64890/07_2026/9v9w_64890.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9w_64890/07_2026/9v9w_64890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9w_64890/07_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-dev-6108/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: 2.96, 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: 1.01 Conformation dependent library (CDL) restraints added in 429.3 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: 1.64 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: 2.14 Time building geometry restraints manager: 1.39 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: 18524 1.30 - 2.60: 1122 2.60 - 3.89: 87 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.600 Find NCS groups from input model: 0.100 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.150 ------------------------------------------------------------------------------- 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 : 0.626 6.490 19756 Z= 0.570 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 0.62540 / 0.57 (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 : 0.455 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: 0.8640 time to fit residues: 141.2850 Evaluate side-chains 124 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.171012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123237 restraints weight = 18321.685| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.27 r_work: 0.3199 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 13807 Z= 0.175 Angle : 0.590 6.744 19756 Z= 0.355 Chirality : 0.043 0.234 2259 Planarity : 0.004 0.034 1591 Dihedral : 28.984 172.890 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 : 1.94 % Allowed : 10.07 % 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: 2.37 (0.28), residues: 944 helix: 2.82 (0.21), residues: 561 sheet: 1.55 (0.89), residues: 41 loop : -0.63 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 35 TYR 0.012 0.002 TYR A 54 PHE 0.017 0.002 PHE H 62 TRP 0.012 0.002 TRP N 25 HIS 0.003 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (13799) covalent geometry : angle 0.58975 / 0.36 (19744) hydrogen bonds : bond 0.06176 / 4.03 ( 757) hydrogen bonds : angle 2.97930 / 2.09 ( 1910) metal coordination : bond 0.00464 / 0.22 ( 8) metal coordination : angle 1.33337 / 0.78 ( 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 155 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.455 Fit side-chains REVERT: A 105 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7376 (mt-10) REVERT: C 92 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7906 (mm-30) REVERT: D 31 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6186 (ttmt) REVERT: G 35 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7882 (mtm110) REVERT: G 56 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8519 (tt0) outliers start: 16 outliers final: 2 residues processed: 143 average time/residue: 0.8775 time to fit residues: 132.8939 Evaluate side-chains 135 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 G residue 35 ARG 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: 20.0000 chunk 78 optimal weight: 40.0000 chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 73 ASN D 46 HIS E 68 GLN F 93 GLN H 106 HIS ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.162431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114878 restraints weight = 17774.516| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.30 r_work: 0.3053 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 13807 Z= 0.335 Angle : 0.775 7.599 19756 Z= 0.434 Chirality : 0.053 0.290 2259 Planarity : 0.007 0.064 1591 Dihedral : 29.510 174.345 3911 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.16 % Allowed : 12.26 % Favored : 84.59 % 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: 1.15 (0.26), residues: 944 helix: 1.95 (0.21), residues: 556 sheet: 0.59 (0.88), residues: 44 loop : -1.26 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 39 TYR 0.025 0.003 TYR A 54 PHE 0.019 0.003 PHE G 25 TRP 0.012 0.003 TRP L 25 HIS 0.008 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.33 (13799) covalent geometry : angle 0.77409 / 0.43 (19744) hydrogen bonds : bond 0.09294 / 6.00 ( 757) hydrogen bonds : angle 3.30741 / 2.31 ( 1910) metal coordination : bond 0.00875 / 0.44 ( 8) metal coordination : angle 1.87648 / 1.17 ( 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 167 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.389 Fit side-chains REVERT: C 61 GLU cc_start: 0.8916 (tp30) cc_final: 0.8616 (mm-30) REVERT: C 110 ASN cc_start: 0.8296 (t0) cc_final: 0.8095 (t0) REVERT: D 31 LYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6263 (ttmt) REVERT: D 82 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8262 (mttp) REVERT: E 42 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6582 (mmp80) REVERT: G 56 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: G 74 LYS cc_start: 0.7882 (mmtt) cc_final: 0.7566 (mmmt) outliers start: 26 outliers final: 8 residues processed: 150 average time/residue: 0.8785 time to fit residues: 139.3007 Evaluate side-chains 144 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 chunk 88 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.164546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116910 restraints weight = 17843.612| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.18 r_work: 0.3104 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13807 Z= 0.186 Angle : 0.623 6.345 19756 Z= 0.360 Chirality : 0.045 0.215 2259 Planarity : 0.005 0.046 1591 Dihedral : 29.624 174.166 3911 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 2.55 % Allowed : 15.66 % Favored : 81.80 % 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: 1.56 (0.27), residues: 944 helix: 2.37 (0.21), residues: 555 sheet: 1.19 (0.88), residues: 41 loop : -1.31 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.013 0.002 TYR D 37 PHE 0.013 0.002 PHE B 61 TRP 0.012 0.003 TRP L 25 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (13799) covalent geometry : angle 0.62287 / 0.36 (19744) hydrogen bonds : bond 0.06884 / 4.46 ( 757) hydrogen bonds : angle 3.06843 / 2.15 ( 1910) metal coordination : bond 0.00487 / 0.24 ( 8) metal coordination : angle 1.23124 / 0.70 ( 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 156 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.362 Fit side-chains REVERT: A 59 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.6711 (pm20) REVERT: C 35 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.7931 (mtm110) REVERT: C 61 GLU cc_start: 0.8774 (tp30) cc_final: 0.8463 (mm-30) REVERT: C 92 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7886 (mm-30) REVERT: D 31 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6230 (ttmt) REVERT: D 82 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8284 (mttp) REVERT: G 56 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: G 74 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7546 (mmmt) outliers start: 21 outliers final: 6 residues processed: 142 average time/residue: 0.8291 time to fit residues: 124.7949 Evaluate side-chains 141 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 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 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 114 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 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 = 0.4038 r_free = 0.4038 target = 0.166134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119141 restraints weight = 18013.278| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.21 r_work: 0.3138 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13807 Z= 0.142 Angle : 0.567 5.292 19756 Z= 0.334 Chirality : 0.042 0.202 2259 Planarity : 0.004 0.054 1591 Dihedral : 29.611 175.033 3911 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.92 % Favored : 95.97 % Rotamer: Outliers : 2.18 % Allowed : 16.63 % Favored : 81.19 % 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: 1.97 (0.27), residues: 944 helix: 2.72 (0.22), residues: 555 sheet: 1.23 (0.88), residues: 41 loop : -1.15 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 20 TYR 0.010 0.001 TYR F 51 PHE 0.011 0.001 PHE L 32 TRP 0.009 0.002 TRP N 25 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (13799) covalent geometry : angle 0.56609 / 0.33 (19744) hydrogen bonds : bond 0.05842 / 3.78 ( 757) hydrogen bonds : angle 2.89235 / 2.03 ( 1910) metal coordination : bond 0.00412 / 0.21 ( 8) metal coordination : angle 1.04724 / 0.55 ( 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 153 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.333 Fit side-chains REVERT: L 33 ARG cc_start: 0.5881 (mmm-85) cc_final: 0.5339 (mmm-85) REVERT: A 59 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6752 (pm20) REVERT: C 35 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7931 (mtm110) REVERT: C 61 GLU cc_start: 0.8732 (tp30) cc_final: 0.8442 (mm-30) REVERT: D 31 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.6178 (ttmt) REVERT: E 42 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6575 (mmp80) REVERT: G 56 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8470 (tt0) REVERT: G 64 GLU cc_start: 0.8804 (tt0) cc_final: 0.8600 (tt0) REVERT: G 74 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7655 (mmmt) outliers start: 18 outliers final: 7 residues processed: 139 average time/residue: 0.8073 time to fit residues: 118.7724 Evaluate side-chains 143 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU 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 E residue 42 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 110 GLU 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: 4.9990 chunk 52 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 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: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN E 68 GLN F 27 GLN F 93 GLN G 89 ASN K 31 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.161562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114004 restraints weight = 17727.824| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.21 r_work: 0.3052 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 13807 Z= 0.269 Angle : 0.710 7.883 19756 Z= 0.401 Chirality : 0.051 0.265 2259 Planarity : 0.006 0.058 1591 Dihedral : 29.794 177.982 3911 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.77 % Favored : 95.13 % Rotamer: Outliers : 2.79 % Allowed : 16.02 % Favored : 81.19 % 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: 1.17 (0.26), residues: 944 helix: 2.12 (0.21), residues: 551 sheet: 0.71 (1.09), residues: 28 loop : -1.42 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 36 TYR 0.019 0.003 TYR K 59 PHE 0.016 0.003 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 0.00614 / 0.27 (13799) covalent geometry : angle 0.70866 / 0.40 (19744) hydrogen bonds : bond 0.08547 / 5.51 ( 757) hydrogen bonds : angle 3.21139 / 2.26 ( 1910) metal coordination : bond 0.00619 / 0.31 ( 8) metal coordination : angle 1.83411 / 1.08 ( 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 159 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.417 Fit side-chains REVERT: L 33 ARG cc_start: 0.5778 (mmm-85) cc_final: 0.5368 (mmm160) REVERT: A 59 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: A 94 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: A 133 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: C 61 GLU cc_start: 0.8825 (tp30) cc_final: 0.8558 (mm-30) REVERT: D 31 LYS cc_start: 0.6681 (OUTLIER) cc_final: 0.6201 (ttmt) REVERT: D 44 GLN cc_start: 0.8624 (tt0) cc_final: 0.8349 (mt0) REVERT: D 82 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8324 (mttp) REVERT: E 42 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6665 (mmp80) REVERT: G 35 ARG cc_start: 0.8297 (mtt90) cc_final: 0.7860 (mtm110) REVERT: G 56 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: G 74 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7712 (mmmt) outliers start: 23 outliers final: 8 residues processed: 144 average time/residue: 0.8609 time to fit residues: 131.2818 Evaluate side-chains 148 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 114 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 74 optimal weight: 0.9990 chunk 101 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.163567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116308 restraints weight = 17846.391| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.25 r_work: 0.3085 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3350 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= 0.159 Angle : 0.611 5.930 19756 Z= 0.353 Chirality : 0.044 0.222 2259 Planarity : 0.004 0.053 1591 Dihedral : 29.774 176.258 3911 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 2.79 % Allowed : 17.48 % Favored : 79.73 % 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: 1.63 (0.27), residues: 944 helix: 2.53 (0.22), residues: 552 sheet: 0.93 (0.93), residues: 38 loop : -1.39 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 20 TYR 0.011 0.002 TYR D 37 PHE 0.024 0.002 PHE L 32 TRP 0.007 0.002 TRP N 25 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (13799) covalent geometry : angle 0.61006 / 0.35 (19744) hydrogen bonds : bond 0.06558 / 4.23 ( 757) hydrogen bonds : angle 3.01074 / 2.11 ( 1910) metal coordination : bond 0.00458 / 0.22 ( 8) metal coordination : angle 1.36296 / 0.78 ( 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 157 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.316 Fit side-chains REVERT: L 33 ARG cc_start: 0.5894 (mmm-85) cc_final: 0.5306 (mmm-85) REVERT: A 94 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7895 (mp0) REVERT: A 133 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: C 61 GLU cc_start: 0.8753 (tp30) cc_final: 0.8487 (mm-30) REVERT: D 31 LYS cc_start: 0.6644 (OUTLIER) cc_final: 0.6142 (ttmt) REVERT: D 82 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8347 (mttp) REVERT: E 42 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6692 (mmp80) REVERT: G 56 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8480 (tt0) REVERT: G 74 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7788 (mmmt) REVERT: G 77 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8164 (mtm-85) outliers start: 23 outliers final: 7 residues processed: 143 average time/residue: 0.8265 time to fit residues: 125.3217 Evaluate side-chains 145 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 133 GLU 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 42 ARG 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 120 SER 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: 0.8980 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 102 optimal weight: 40.0000 chunk 89 optimal weight: 50.0000 chunk 10 optimal weight: 5.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 27 GLN F 75 HIS F 93 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3963 r_free = 0.3963 target = 0.159821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112475 restraints weight = 17531.885| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.22 r_work: 0.3025 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 13807 Z= 0.312 Angle : 0.766 8.064 19756 Z= 0.428 Chirality : 0.054 0.284 2259 Planarity : 0.007 0.063 1591 Dihedral : 29.982 179.806 3911 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.40 % Favored : 94.49 % Rotamer: Outliers : 2.31 % Allowed : 18.20 % Favored : 79.49 % 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: 0.75 (0.26), residues: 944 helix: 1.85 (0.21), residues: 550 sheet: 0.35 (1.08), residues: 28 loop : -1.69 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 35 TYR 0.018 0.003 TYR D 39 PHE 0.030 0.003 PHE L 32 TRP 0.008 0.002 TRP L 25 HIS 0.009 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.31 (13799) covalent geometry : angle 0.76425 / 0.43 (19744) hydrogen bonds : bond 0.09183 / 5.91 ( 757) hydrogen bonds : angle 3.30824 / 2.32 ( 1910) metal coordination : bond 0.00715 / 0.35 ( 8) metal coordination : angle 2.30262 / 1.40 ( 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 160 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.382 Fit side-chains REVERT: L 33 ARG cc_start: 0.5781 (mmm-85) cc_final: 0.5328 (mmm-85) REVERT: A 94 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: A 133 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: C 61 GLU cc_start: 0.8802 (tp30) cc_final: 0.8572 (mm-30) REVERT: D 31 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6193 (ttmt) REVERT: D 82 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8315 (mttp) REVERT: E 42 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6728 (mmp80) REVERT: G 35 ARG cc_start: 0.8326 (mtt90) cc_final: 0.7988 (mtm110) REVERT: G 56 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: G 74 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7745 (mmmt) REVERT: G 77 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8259 (mtm-85) REVERT: K 1 MET cc_start: 0.2636 (tmt) cc_final: 0.1667 (tmm) outliers start: 19 outliers final: 7 residues processed: 149 average time/residue: 0.8381 time to fit residues: 132.4508 Evaluate side-chains 152 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 133 GLU 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 42 ARG 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 88 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 90 optimal weight: 50.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.163254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116389 restraints weight = 17794.727| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.22 r_work: 0.3085 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13807 Z= 0.146 Angle : 0.628 8.076 19756 Z= 0.361 Chirality : 0.045 0.242 2259 Planarity : 0.004 0.054 1591 Dihedral : 29.897 177.058 3911 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.50 % Favored : 96.40 % Rotamer: Outliers : 2.31 % Allowed : 19.17 % Favored : 78.52 % 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: 1.49 (0.27), residues: 944 helix: 2.51 (0.22), residues: 552 sheet: 0.43 (1.07), residues: 28 loop : -1.50 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 35 TYR 0.010 0.002 TYR E 41 PHE 0.025 0.002 PHE L 32 TRP 0.006 0.002 TRP N 25 HIS 0.007 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (13799) covalent geometry : angle 0.62630 / 0.36 (19744) hydrogen bonds : bond 0.06387 / 4.10 ( 757) hydrogen bonds : angle 3.03551 / 2.13 ( 1910) metal coordination : bond 0.00425 / 0.21 ( 8) metal coordination : angle 1.71428 / 0.98 ( 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 154 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.373 Fit side-chains REVERT: L 33 ARG cc_start: 0.5764 (mmm-85) cc_final: 0.5433 (mmm-85) REVERT: A 94 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: A 133 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7211 (mt-10) REVERT: C 61 GLU cc_start: 0.8752 (tp30) cc_final: 0.8493 (mm-30) REVERT: D 31 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.6214 (ttmt) REVERT: E 42 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6777 (mmp80) REVERT: G 35 ARG cc_start: 0.8293 (mtt90) cc_final: 0.7948 (mtm110) REVERT: G 56 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: G 74 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7831 (mmmt) REVERT: K 1 MET cc_start: 0.2829 (tmt) cc_final: 0.1872 (tmm) outliers start: 19 outliers final: 6 residues processed: 141 average time/residue: 0.9195 time to fit residues: 137.2671 Evaluate side-chains 144 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 73 ASN 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: 4.9990 chunk 82 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.163123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116335 restraints weight = 17829.367| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.23 r_work: 0.3088 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13807 Z= 0.160 Angle : 0.609 6.782 19756 Z= 0.354 Chirality : 0.044 0.223 2259 Planarity : 0.004 0.051 1591 Dihedral : 29.866 178.003 3911 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.03 % Favored : 95.87 % Rotamer: Outliers : 1.82 % Allowed : 19.42 % 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: 1.60 (0.27), residues: 944 helix: 2.58 (0.22), residues: 555 sheet: 0.54 (1.09), residues: 28 loop : -1.46 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 35 TYR 0.012 0.002 TYR D 37 PHE 0.029 0.002 PHE N 24 TRP 0.005 0.001 TRP N 25 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (13799) covalent geometry : angle 0.60808 / 0.35 (19744) hydrogen bonds : bond 0.06405 / 4.13 ( 757) hydrogen bonds : angle 2.97978 / 2.09 ( 1910) metal coordination : bond 0.00467 / 0.23 ( 8) metal coordination : angle 1.65825 / 0.92 ( 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 145 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: A 133 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7227 (mt-10) REVERT: C 35 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.7847 (mtm110) REVERT: C 61 GLU cc_start: 0.8734 (tp30) cc_final: 0.8476 (mm-30) REVERT: D 31 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6271 (ttmt) REVERT: E 42 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6734 (mmp80) REVERT: G 35 ARG cc_start: 0.8314 (mtt90) cc_final: 0.7954 (mtm110) REVERT: G 56 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: G 74 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7887 (mmmt) REVERT: K 1 MET cc_start: 0.3038 (tmt) cc_final: 0.1995 (tmm) outliers start: 15 outliers final: 5 residues processed: 136 average time/residue: 0.9189 time to fit residues: 132.2411 Evaluate side-chains 138 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain E residue 42 ARG 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 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 84 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.163247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115775 restraints weight = 17785.836| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.23 r_work: 0.3087 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13807 Z= 0.164 Angle : 0.616 6.691 19756 Z= 0.356 Chirality : 0.044 0.224 2259 Planarity : 0.005 0.076 1591 Dihedral : 29.881 178.160 3911 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 1.58 % Allowed : 20.15 % 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: 1.64 (0.27), residues: 944 helix: 2.59 (0.22), residues: 555 sheet: 0.75 (0.93), residues: 38 loop : -1.47 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 33 TYR 0.011 0.002 TYR D 37 PHE 0.026 0.002 PHE N 24 TRP 0.005 0.001 TRP N 25 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (13799) covalent geometry : angle 0.61444 / 0.36 (19744) hydrogen bonds : bond 0.06341 / 4.09 ( 757) hydrogen bonds : angle 2.96710 / 2.07 ( 1910) metal coordination : bond 0.00447 / 0.22 ( 8) metal coordination : angle 1.67283 / 0.93 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4778.23 seconds wall clock time: 81 minutes 46.55 seconds (4906.55 seconds total)