Starting phenix.real_space_refine on Sat Jul 4 14:12:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9s_64886/07_2026/9v9s_64886.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9s_64886/07_2026/9v9s_64886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v9s_64886/07_2026/9v9s_64886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9s_64886/07_2026/9v9s_64886.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v9s_64886/07_2026/9v9s_64886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9s_64886/07_2026/9v9s_64886.map" } resolution = 3.8 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 10725 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 245 5.49 5 S 28 5.16 5 C 7234 2.51 5 N 2378 2.21 5 O 2861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 12748 Number of models: 1 Model: "" Number of chains: 16 Chain: "L" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 362 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "N" 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: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 774 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} 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: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 711 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} 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: "I" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2485 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "J" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2538 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} 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 72.784 34.886 54.356 1.00 91.05 S ATOM 58 SG CYS L 30 72.537 32.573 51.376 1.00 95.53 S ATOM 146 SG CYS L 41 75.224 35.217 51.356 1.00 88.03 S ATOM 166 SG CYS L 44 71.638 36.332 51.086 1.00 87.51 S ATOM 401 SG CYS N 27 37.831 95.429 43.471 1.00104.89 S ATOM 420 SG CYS N 30 37.453 94.914 39.720 1.00106.82 S ATOM 508 SG CYS N 41 34.736 93.657 41.944 1.00102.49 S ATOM 528 SG CYS N 44 38.005 91.880 42.018 1.00 96.30 S Time building chain proxies: 2.50, per 1000 atoms: 0.20 Number of scatterers: 12748 At special positions: 0 Unit cell: (118.8, 123.2, 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 28 16.00 P 245 15.00 O 2861 8.00 N 2378 7.00 C 7234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 377.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 44 " 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 30 " pdb=" ZN N 401 " 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 30 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 27 " Number of angles added : 12 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 60.1% alpha, 4.8% beta 120 base pairs and 188 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'L' and resid 59 through 68 removed outlier: 4.351A pdb=" N ALA L 63 " --> pdb=" O SER L 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.886A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.808A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.848A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.589A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.652A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.513A 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 35 through 44 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: 3.905A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.733A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.577A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.930A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.500A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.458A 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 35 through 46 Processing helix chain 'H' and resid 53 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.559A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 removed outlier: 4.072A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 34 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 55 through 59 removed outlier: 3.603A pdb=" N ASP K 58 " --> pdb=" O THR K 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 34 removed outlier: 3.543A pdb=" N LYS O 27 " --> pdb=" O ILE O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 41 removed outlier: 4.170A pdb=" N GLN O 40 " --> pdb=" O PRO O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 59 removed outlier: 3.787A pdb=" N ASP O 58 " --> pdb=" O THR O 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.886A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.526A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.338A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.016A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.534A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.502A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 12 through 14 removed outlier: 3.695A pdb=" N LEU K 69 " --> pdb=" O LYS K 6 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS K 68 " --> pdb=" O ILE K 44 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 13 through 14 removed outlier: 4.029A pdb=" N ILE O 13 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL O 5 " --> pdb=" O ILE O 13 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 43 through 45 removed outlier: 4.331A pdb=" N LEU O 43 " --> pdb=" O LEU O 50 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 309 hydrogen bonds 614 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 188 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 1.01 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: 3184 1.34 - 1.46: 3614 1.46 - 1.58: 6130 1.58 - 1.70: 488 1.70 - 1.82: 40 Bond restraints: 13456 Sorted by residual: bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DG J 76 " pdb=" C2' DG J 76 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DG J 97 " pdb=" C2' DG J 97 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC I 118 " pdb=" C2' DC I 118 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DC I 45 " pdb=" C2' DC I 45 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 13451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 18363 1.62 - 3.24: 809 3.24 - 4.86: 32 4.86 - 6.48: 4 6.48 - 8.10: 2 Bond angle restraints: 19210 Sorted by residual: angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 57 " pdb=" C4 DT I 57 " pdb=" O4 DT I 57 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT J 35 " pdb=" C4 DT J 35 " pdb=" O4 DT J 35 " 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 I 46 " pdb=" C4 DT I 46 " pdb=" O4 DT I 46 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 ... (remaining 19205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 6404 35.43 - 70.85: 1060 70.85 - 106.28: 29 106.28 - 141.71: 1 141.71 - 177.14: 3 Dihedral angle restraints: 7497 sinusoidal: 4670 harmonic: 2827 Sorted by residual: dihedral pdb=" C4' DC I 3 " pdb=" C3' DC I 3 " pdb=" O3' DC I 3 " pdb=" P DG I 4 " ideal model delta sinusoidal sigma weight residual -140.00 37.14 -177.14 1 3.50e+01 8.16e-04 1.57e+01 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 34.41 -174.41 1 3.50e+01 8.16e-04 1.56e+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 76.54 143.46 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 7494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1440 0.035 - 0.070: 551 0.070 - 0.106: 174 0.106 - 0.141: 35 0.141 - 0.176: 1 Chirality restraints: 2201 Sorted by residual: chirality pdb=" C3' DG I 4 " pdb=" C4' DG I 4 " pdb=" O3' DG I 4 " pdb=" C2' DG I 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA ILE K 36 " pdb=" N ILE K 36 " pdb=" C ILE K 36 " pdb=" CB ILE K 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" P DA I 5 " pdb=" OP1 DA I 5 " pdb=" OP2 DA I 5 " pdb=" O5' DA I 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.47 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 2198 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU K 18 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.23e+00 pdb=" N PRO K 19 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO K 19 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO K 19 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 118 " 0.019 2.00e-02 2.50e+03 1.10e-02 3.04e+00 pdb=" N1 DT J 118 " -0.022 2.00e-02 2.50e+03 pdb=" C2 DT J 118 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DT J 118 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DT J 118 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DT J 118 " 0.009 2.00e-02 2.50e+03 pdb=" O4 DT J 118 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT J 118 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT J 118 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT J 118 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " 0.018 2.00e-02 2.50e+03 7.47e-03 1.67e+00 pdb=" N9 DG I 121 " -0.016 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " -0.001 2.00e-02 2.50e+03 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 367 2.69 - 3.24: 11053 3.24 - 3.79: 22292 3.79 - 4.35: 27658 4.35 - 4.90: 41200 Nonbonded interactions: 102570 Sorted by model distance: nonbonded pdb=" O2 DC I 95 " pdb=" N2 DG J 53 " model vdw 2.132 2.496 nonbonded pdb=" N MET O 1 " pdb=" O VAL O 17 " model vdw 2.157 3.120 nonbonded pdb=" O THR K 14 " pdb=" NZ LYS K 29 " model vdw 2.236 3.120 nonbonded pdb=" NE2 GLN K 40 " pdb=" O ARG K 72 " model vdw 2.270 3.120 nonbonded pdb=" NZ LYS B 91 " pdb=" OH TYR D 80 " model vdw 2.272 3.120 ... (remaining 102565 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' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 119) } ncs_group { reference = (chain 'D' and resid 30 through 120) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.600 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 0.038 13464 Z= 0.452 Angle : 0.656 8.104 19222 Z= 0.581 Chirality : 0.041 0.176 2201 Planarity : 0.003 0.057 1586 Dihedral : 25.724 177.136 5665 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 2.01 (0.28), residues: 951 helix: 2.58 (0.22), residues: 566 sheet: 1.59 (0.97), residues: 22 loop : -0.79 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 42 TYR 0.014 0.001 TYR G 50 PHE 0.017 0.001 PHE K 4 TRP 0.001 0.000 TRP N 25 HIS 0.001 0.000 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.45 (13456) covalent geometry : angle 0.65389 / 0.58 (19210) hydrogen bonds : bond 0.11563 / 7.79 ( 735) hydrogen bonds : angle 3.99125 / 2.92 ( 1871) metal coordination : bond 0.00210 / 0.14 ( 8) metal coordination : angle 2.35633 / 1.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.353 Fit side-chains REVERT: C 84 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7922 (tp40) REVERT: E 59 GLU cc_start: 0.6945 (pp20) cc_final: 0.6550 (pp20) REVERT: F 63 GLU cc_start: 0.8106 (tt0) cc_final: 0.7171 (tp30) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1070 time to fit residues: 22.2295 Evaluate side-chains 118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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: 30.0000 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 chunk 113 optimal weight: 30.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN D 46 HIS K 68 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.130906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.098189 restraints weight = 28703.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097870 restraints weight = 32845.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.098170 restraints weight = 33569.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098497 restraints weight = 29064.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098579 restraints weight = 26586.971| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13464 Z= 0.209 Angle : 0.655 7.406 19222 Z= 0.374 Chirality : 0.047 0.337 2201 Planarity : 0.005 0.052 1586 Dihedral : 29.345 177.387 3736 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.05 % Allowed : 10.12 % Favored : 87.83 % 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 (0.28), residues: 951 helix: 2.13 (0.22), residues: 575 sheet: 0.97 (0.85), residues: 28 loop : -1.05 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 72 TYR 0.040 0.002 TYR H 39 PHE 0.042 0.003 PHE L 32 TRP 0.005 0.001 TRP L 25 HIS 0.006 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (13456) covalent geometry : angle 0.65116 / 0.37 (19210) hydrogen bonds : bond 0.06705 / 4.37 ( 735) hydrogen bonds : angle 3.43356 / 2.48 ( 1871) metal coordination : bond 0.00971 / 0.48 ( 8) metal coordination : angle 3.07889 / 1.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.358 Fit side-chains REVERT: B 88 TYR cc_start: 0.8416 (m-80) cc_final: 0.8205 (m-80) REVERT: E 123 ASP cc_start: 0.8913 (m-30) cc_final: 0.8710 (m-30) REVERT: F 63 GLU cc_start: 0.7976 (tt0) cc_final: 0.7674 (tp30) REVERT: O 49 GLN cc_start: 0.6457 (tm-30) cc_final: 0.5735 (pp30) REVERT: O 55 THR cc_start: 0.2540 (OUTLIER) cc_final: 0.1950 (p) outliers start: 17 outliers final: 9 residues processed: 140 average time/residue: 0.1009 time to fit residues: 20.0865 Evaluate side-chains 129 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain O residue 55 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 93 optimal weight: 50.0000 chunk 24 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.130473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.096761 restraints weight = 28732.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097028 restraints weight = 30661.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097500 restraints weight = 28452.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097544 restraints weight = 27607.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.097665 restraints weight = 24001.201| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13464 Z= 0.157 Angle : 0.569 7.913 19222 Z= 0.335 Chirality : 0.042 0.352 2201 Planarity : 0.005 0.091 1586 Dihedral : 29.544 176.399 3736 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.33 % Allowed : 13.37 % Favored : 85.30 % 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 (0.28), residues: 951 helix: 2.32 (0.22), residues: 577 sheet: 1.00 (0.82), residues: 28 loop : -1.03 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.020 0.001 TYR H 39 PHE 0.049 0.002 PHE L 32 TRP 0.005 0.001 TRP N 25 HIS 0.005 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (13456) covalent geometry : angle 0.56406 / 0.33 (19210) hydrogen bonds : bond 0.05688 / 3.80 ( 735) hydrogen bonds : angle 3.19898 / 2.31 ( 1871) metal coordination : bond 0.00724 / 0.35 ( 8) metal coordination : angle 2.90915 / 1.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.339 Fit side-chains REVERT: B 52 GLU cc_start: 0.6752 (pm20) cc_final: 0.6418 (mp0) REVERT: B 84 MET cc_start: 0.8149 (tpp) cc_final: 0.7888 (tpp) REVERT: E 123 ASP cc_start: 0.8821 (m-30) cc_final: 0.8593 (m-30) REVERT: O 8 LEU cc_start: 0.6440 (pp) cc_final: 0.6121 (pt) REVERT: O 49 GLN cc_start: 0.6481 (tm-30) cc_final: 0.5813 (pp30) REVERT: O 55 THR cc_start: 0.2258 (OUTLIER) cc_final: 0.1767 (p) outliers start: 11 outliers final: 8 residues processed: 134 average time/residue: 0.1068 time to fit residues: 20.7443 Evaluate side-chains 128 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain O residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 114 optimal weight: 30.0000 chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 106 optimal weight: 50.0000 chunk 98 optimal weight: 30.0000 chunk 42 optimal weight: 9.9990 chunk 101 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 64 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.127746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094043 restraints weight = 28431.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.094256 restraints weight = 32438.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.094329 restraints weight = 31751.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.094669 restraints weight = 28830.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.094698 restraints weight = 27168.945| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13464 Z= 0.209 Angle : 0.639 7.917 19222 Z= 0.362 Chirality : 0.044 0.352 2201 Planarity : 0.005 0.072 1586 Dihedral : 29.750 176.347 3736 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.05 % Allowed : 14.94 % Favored : 83.01 % 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: 1.20 (0.28), residues: 951 helix: 2.01 (0.22), residues: 573 sheet: 0.75 (0.83), residues: 28 loop : -1.33 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 33 TYR 0.022 0.002 TYR H 39 PHE 0.057 0.003 PHE L 32 TRP 0.006 0.001 TRP N 25 HIS 0.006 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 (13456) covalent geometry : angle 0.63309 / 0.36 (19210) hydrogen bonds : bond 0.06829 / 4.49 ( 735) hydrogen bonds : angle 3.42849 / 2.46 ( 1871) metal coordination : bond 0.00981 / 0.48 ( 8) metal coordination : angle 3.55772 / 1.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.372 Fit side-chains REVERT: B 52 GLU cc_start: 0.7035 (pm20) cc_final: 0.6722 (mp0) REVERT: B 84 MET cc_start: 0.8262 (tpp) cc_final: 0.8059 (tpp) REVERT: B 88 TYR cc_start: 0.8158 (m-80) cc_final: 0.7527 (m-80) REVERT: O 49 GLN cc_start: 0.6360 (tm-30) cc_final: 0.5765 (pp30) outliers start: 17 outliers final: 13 residues processed: 132 average time/residue: 0.1150 time to fit residues: 22.1052 Evaluate side-chains 128 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 14 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 50.0000 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 chunk 13 optimal weight: 0.6980 chunk 107 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 116 optimal weight: 50.0000 chunk 23 optimal weight: 2.9990 overall best weight: 0.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.130332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.097014 restraints weight = 28671.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097547 restraints weight = 27892.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097819 restraints weight = 25925.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.098054 restraints weight = 23030.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.098035 restraints weight = 21666.805| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13464 Z= 0.129 Angle : 0.552 7.925 19222 Z= 0.324 Chirality : 0.042 0.356 2201 Planarity : 0.004 0.071 1586 Dihedral : 29.722 176.990 3736 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.81 % Allowed : 15.54 % Favored : 82.65 % 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: 1.71 (0.28), residues: 951 helix: 2.44 (0.22), residues: 573 sheet: 0.47 (0.77), residues: 29 loop : -1.14 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 33 TYR 0.017 0.001 TYR H 39 PHE 0.050 0.002 PHE L 32 TRP 0.002 0.000 TRP N 25 HIS 0.002 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.13 (13456) covalent geometry : angle 0.54877 / 0.32 (19210) hydrogen bonds : bond 0.05230 / 3.52 ( 735) hydrogen bonds : angle 3.04672 / 2.19 ( 1871) metal coordination : bond 0.00547 / 0.27 ( 8) metal coordination : angle 2.60921 / 1.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.386 Fit side-chains REVERT: H 73 GLU cc_start: 0.8184 (tp30) cc_final: 0.7933 (tp30) REVERT: O 8 LEU cc_start: 0.6190 (pp) cc_final: 0.5856 (pt) REVERT: O 49 GLN cc_start: 0.6474 (tm-30) cc_final: 0.5836 (pp30) outliers start: 15 outliers final: 13 residues processed: 131 average time/residue: 0.1086 time to fit residues: 20.7215 Evaluate side-chains 128 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 16 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 30.0000 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 109 optimal weight: 30.0000 chunk 106 optimal weight: 50.0000 chunk 26 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.126905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094009 restraints weight = 28186.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.094179 restraints weight = 29135.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.094349 restraints weight = 29367.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.094654 restraints weight = 26578.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.094623 restraints weight = 25287.487| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13464 Z= 0.223 Angle : 0.662 7.990 19222 Z= 0.370 Chirality : 0.045 0.355 2201 Planarity : 0.005 0.068 1586 Dihedral : 29.911 176.049 3736 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.53 % Allowed : 15.66 % Favored : 81.81 % 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: 1.07 (0.28), residues: 951 helix: 1.94 (0.22), residues: 576 sheet: -0.02 (0.76), residues: 32 loop : -1.43 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 33 TYR 0.014 0.002 TYR H 39 PHE 0.050 0.003 PHE L 32 TRP 0.006 0.001 TRP N 25 HIS 0.005 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (13456) covalent geometry : angle 0.65575 / 0.37 (19210) hydrogen bonds : bond 0.06918 / 4.56 ( 735) hydrogen bonds : angle 3.38567 / 2.42 ( 1871) metal coordination : bond 0.01091 / 0.53 ( 8) metal coordination : angle 3.55666 / 2.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.384 Fit side-chains REVERT: B 88 TYR cc_start: 0.8237 (m-80) cc_final: 0.7602 (m-80) REVERT: E 123 ASP cc_start: 0.8936 (m-30) cc_final: 0.8716 (m-30) REVERT: K 56 LEU cc_start: 0.6299 (pt) cc_final: 0.6094 (pp) REVERT: O 49 GLN cc_start: 0.6421 (tm-30) cc_final: 0.5830 (pp30) outliers start: 21 outliers final: 17 residues processed: 129 average time/residue: 0.1163 time to fit residues: 21.7316 Evaluate side-chains 132 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain O residue 14 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 50.0000 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 87 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.126862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.093641 restraints weight = 28019.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.093708 restraints weight = 32200.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.093907 restraints weight = 30597.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094219 restraints weight = 27977.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094218 restraints weight = 26293.775| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13464 Z= 0.190 Angle : 0.632 8.232 19222 Z= 0.357 Chirality : 0.045 0.361 2201 Planarity : 0.005 0.072 1586 Dihedral : 30.030 176.744 3736 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.29 % Allowed : 16.51 % Favored : 81.20 % 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: 1.05 (0.28), residues: 951 helix: 1.96 (0.22), residues: 571 sheet: 0.05 (0.77), residues: 31 loop : -1.47 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 33 TYR 0.014 0.002 TYR H 39 PHE 0.053 0.002 PHE L 32 TRP 0.006 0.001 TRP N 25 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (13456) covalent geometry : angle 0.62613 / 0.36 (19210) hydrogen bonds : bond 0.06526 / 4.33 ( 735) hydrogen bonds : angle 3.33143 / 2.38 ( 1871) metal coordination : bond 0.00956 / 0.47 ( 8) metal coordination : angle 3.39870 / 2.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.389 Fit side-chains REVERT: B 88 TYR cc_start: 0.8260 (m-80) cc_final: 0.7546 (m-80) REVERT: E 123 ASP cc_start: 0.8842 (m-30) cc_final: 0.8611 (m-30) REVERT: K 40 GLN cc_start: 0.5902 (tp40) cc_final: 0.5612 (tp40) REVERT: O 49 GLN cc_start: 0.6371 (tm-30) cc_final: 0.5790 (pp30) outliers start: 19 outliers final: 15 residues processed: 129 average time/residue: 0.1175 time to fit residues: 21.9900 Evaluate side-chains 132 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain O residue 12 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 44 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.128132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094400 restraints weight = 27783.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.094735 restraints weight = 29381.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.095154 restraints weight = 26050.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.095108 restraints weight = 27157.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.095450 restraints weight = 22738.641| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13464 Z= 0.141 Angle : 0.584 8.295 19222 Z= 0.337 Chirality : 0.042 0.355 2201 Planarity : 0.004 0.069 1586 Dihedral : 29.954 177.192 3736 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.81 % Allowed : 17.23 % Favored : 80.96 % 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: 1.36 (0.28), residues: 951 helix: 2.24 (0.22), residues: 574 sheet: -0.14 (0.77), residues: 31 loop : -1.40 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 33 TYR 0.013 0.001 TYR H 80 PHE 0.031 0.002 PHE L 32 TRP 0.003 0.001 TRP N 25 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (13456) covalent geometry : angle 0.58080 / 0.34 (19210) hydrogen bonds : bond 0.05657 / 3.77 ( 735) hydrogen bonds : angle 3.13139 / 2.25 ( 1871) metal coordination : bond 0.00638 / 0.32 ( 8) metal coordination : angle 2.67162 / 1.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.352 Fit side-chains REVERT: B 88 TYR cc_start: 0.8162 (m-80) cc_final: 0.7468 (m-80) REVERT: E 123 ASP cc_start: 0.8723 (m-30) cc_final: 0.8494 (m-30) REVERT: H 73 GLU cc_start: 0.8085 (tp30) cc_final: 0.7711 (tp30) REVERT: K 40 GLN cc_start: 0.6068 (tp40) cc_final: 0.5716 (tp40) REVERT: O 49 GLN cc_start: 0.6507 (tm-30) cc_final: 0.5924 (pp30) outliers start: 15 outliers final: 14 residues processed: 132 average time/residue: 0.1152 time to fit residues: 22.1683 Evaluate side-chains 133 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 48 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 109 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.128096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.094231 restraints weight = 28048.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.094791 restraints weight = 29042.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094813 restraints weight = 28809.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.095206 restraints weight = 24445.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.095151 restraints weight = 22556.862| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13464 Z= 0.147 Angle : 0.588 8.330 19222 Z= 0.336 Chirality : 0.042 0.355 2201 Planarity : 0.004 0.070 1586 Dihedral : 29.949 176.800 3736 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.81 % Allowed : 16.99 % Favored : 81.20 % 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: 1.36 (0.28), residues: 951 helix: 2.26 (0.22), residues: 574 sheet: -0.29 (0.76), residues: 31 loop : -1.42 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 33 TYR 0.014 0.001 TYR H 39 PHE 0.049 0.002 PHE L 32 TRP 0.003 0.001 TRP N 25 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (13456) covalent geometry : angle 0.58429 / 0.34 (19210) hydrogen bonds : bond 0.05700 / 3.78 ( 735) hydrogen bonds : angle 3.11271 / 2.23 ( 1871) metal coordination : bond 0.00682 / 0.34 ( 8) metal coordination : angle 2.66851 / 1.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.254 Fit side-chains REVERT: B 88 TYR cc_start: 0.8166 (m-80) cc_final: 0.7492 (m-80) REVERT: E 123 ASP cc_start: 0.8766 (m-30) cc_final: 0.8525 (m-30) REVERT: E 133 GLU cc_start: 0.6321 (pm20) cc_final: 0.5967 (pm20) REVERT: O 49 GLN cc_start: 0.6646 (tm-30) cc_final: 0.6019 (pp30) outliers start: 15 outliers final: 14 residues processed: 130 average time/residue: 0.1089 time to fit residues: 20.4892 Evaluate side-chains 132 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.8980 chunk 110 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.129372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.095804 restraints weight = 28196.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.096571 restraints weight = 27501.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.096753 restraints weight = 24962.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.097032 restraints weight = 21921.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.096994 restraints weight = 20433.087| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13464 Z= 0.127 Angle : 0.563 11.232 19222 Z= 0.326 Chirality : 0.041 0.353 2201 Planarity : 0.004 0.070 1586 Dihedral : 29.903 176.844 3736 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.69 % Allowed : 17.11 % Favored : 81.20 % 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 (0.28), residues: 951 helix: 2.47 (0.22), residues: 572 sheet: -0.33 (0.74), residues: 31 loop : -1.34 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 33 TYR 0.015 0.001 TYR H 80 PHE 0.041 0.002 PHE L 32 TRP 0.001 0.000 TRP N 25 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.13 (13456) covalent geometry : angle 0.56092 / 0.33 (19210) hydrogen bonds : bond 0.05096 / 3.40 ( 735) hydrogen bonds : angle 2.97561 / 2.14 ( 1871) metal coordination : bond 0.00445 / 0.24 ( 8) metal coordination : angle 2.21978 / 1.35 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.382 Fit side-chains REVERT: B 88 TYR cc_start: 0.8154 (m-80) cc_final: 0.7458 (m-80) REVERT: D 68 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7160 (mt-10) REVERT: E 123 ASP cc_start: 0.8682 (m-30) cc_final: 0.8446 (m-30) REVERT: H 73 GLU cc_start: 0.8101 (tp30) cc_final: 0.7722 (tp30) REVERT: O 49 GLN cc_start: 0.6674 (tm-30) cc_final: 0.6035 (pp30) outliers start: 14 outliers final: 14 residues processed: 133 average time/residue: 0.1128 time to fit residues: 22.0027 Evaluate side-chains 132 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 109 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN K 40 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.127241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.093428 restraints weight = 28020.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.093909 restraints weight = 29595.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094004 restraints weight = 28592.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094298 restraints weight = 25803.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094264 restraints weight = 23681.239| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13464 Z= 0.183 Angle : 0.619 7.862 19222 Z= 0.350 Chirality : 0.043 0.351 2201 Planarity : 0.005 0.072 1586 Dihedral : 30.003 175.993 3736 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.05 % Allowed : 17.23 % Favored : 80.72 % 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: 1.28 (0.28), residues: 951 helix: 2.17 (0.22), residues: 575 sheet: -0.25 (0.73), residues: 31 loop : -1.42 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 33 TYR 0.016 0.002 TYR H 80 PHE 0.047 0.002 PHE L 32 TRP 0.003 0.001 TRP N 25 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (13456) covalent geometry : angle 0.61510 / 0.35 (19210) hydrogen bonds : bond 0.06260 / 4.13 ( 735) hydrogen bonds : angle 3.20054 / 2.29 ( 1871) metal coordination : bond 0.00900 / 0.44 ( 8) metal coordination : angle 2.80310 / 1.62 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1569.65 seconds wall clock time: 27 minutes 48.77 seconds (1668.77 seconds total)