Starting phenix.real_space_refine on Fri Jul 3 09:57:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dbp_30161/07_2026/7dbp_30161.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dbp_30161/07_2026/7dbp_30161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dbp_30161/07_2026/7dbp_30161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dbp_30161/07_2026/7dbp_30161.map" model { file = "/net/cci-nas-00/data/ceres_data/7dbp_30161/07_2026/7dbp_30161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dbp_30161/07_2026/7dbp_30161.cif" } resolution = 4.5 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 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: 5 Type Number sf(0) Gaussians P 350 5.49 5 S 15 5.16 5 C 7571 2.51 5 N 2590 2.21 5 O 3275 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: 13801 Number of models: 1 Model: "" Number of chains: 11 Chain: "K" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 590 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} 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: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 3569 Classifications: {'DNA': 175} Link IDs: {'rna3p': 174} Chain: "J" Number of atoms: 3606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 3606 Classifications: {'DNA': 175} Link IDs: {'rna3p': 174} Time building chain proxies: 3.04, per 1000 atoms: 0.22 Number of scatterers: 13801 At special positions: 0 Unit cell: (123.2, 88, 160.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 350 15.00 O 3275 8.00 N 2590 7.00 C 7571 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: 1.05 Conformation dependent library (CDL) restraints added in 314.8 milliseconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1558 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 8 sheets defined 68.8% alpha, 2.4% beta 36 base pairs and 212 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'K' and resid 7 through 19 Processing helix chain 'K' and resid 27 through 38 Processing helix chain 'K' and resid 41 through 46 Processing helix chain 'K' and resid 46 through 59 removed outlier: 4.586A pdb=" N LEU K 50 " --> pdb=" O SER K 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.824A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.682A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.517A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.528A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.841A 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: 4.566A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.897A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.519A 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 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.557A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.517A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.570A pdb=" N MET D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.835A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.824A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.680A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.517A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.528A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.841A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.567A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.898A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.557A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.518A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.570A pdb=" N MET H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.835A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 25 through 26 removed outlier: 3.501A pdb=" N SER K 25 " --> pdb=" O PHE K 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.432A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.535A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.081A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.727A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.519A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 404 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 212 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2627 1.33 - 1.45: 4905 1.45 - 1.57: 6504 1.57 - 1.69: 698 1.69 - 1.81: 26 Bond restraints: 14760 Sorted by residual: bond pdb=" C3' DT I 54 " pdb=" C2' DT I 54 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DT I -38 " pdb=" C2' DT I -38 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DT I -58 " pdb=" C2' DT I -58 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DC J 23 " pdb=" C2' DC J 23 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DC J 81 " pdb=" C2' DC J 81 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 ... (remaining 14755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 19660 1.15 - 2.29: 1481 2.29 - 3.44: 274 3.44 - 4.59: 6 4.59 - 5.73: 8 Bond angle restraints: 21429 Sorted by residual: angle pdb=" O4' DG J -9 " pdb=" C4' DG J -9 " pdb=" C3' DG J -9 " ideal model delta sigma weight residual 106.00 102.96 3.04 6.00e-01 2.78e+00 2.56e+01 angle pdb=" O4' DC I -73 " pdb=" C4' DC I -73 " pdb=" C3' DC I -73 " ideal model delta sigma weight residual 106.00 103.15 2.85 6.00e-01 2.78e+00 2.25e+01 angle pdb=" O4' DC I -28 " pdb=" C4' DC I -28 " pdb=" C3' DC I -28 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" O4' DG J 77 " pdb=" C4' DG J 77 " pdb=" C3' DG J 77 " ideal model delta sigma weight residual 106.00 103.28 2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N3 DT J -77 " pdb=" C4 DT J -77 " pdb=" O4 DT J -77 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 21424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 6501 35.47 - 70.94: 1431 70.94 - 106.42: 32 106.42 - 141.89: 6 141.89 - 177.36: 3 Dihedral angle restraints: 7973 sinusoidal: 5554 harmonic: 2419 Sorted by residual: dihedral pdb=" C4' DT J -81 " pdb=" C3' DT J -81 " pdb=" O3' DT J -81 " pdb=" P DA J -80 " ideal model delta sinusoidal sigma weight residual -140.00 37.36 -177.36 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT I 54 " pdb=" C3' DT I 54 " pdb=" O3' DT I 54 " pdb=" P DG I 55 " ideal model delta sinusoidal sigma weight residual -140.00 36.20 -176.20 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 51.88 168.12 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 7970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1162 0.027 - 0.054: 827 0.054 - 0.081: 315 0.081 - 0.108: 110 0.108 - 0.135: 20 Chirality restraints: 2434 Sorted by residual: chirality pdb=" C3' DT I -38 " pdb=" C4' DT I -38 " pdb=" O3' DT I -38 " pdb=" C2' DT I -38 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" C3' DT J -81 " pdb=" C4' DT J -81 " pdb=" O3' DT J -81 " pdb=" C2' DT J -81 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" C3' DC I 20 " pdb=" C4' DC I 20 " pdb=" O3' DC I 20 " pdb=" C2' DC I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 2431 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I -74 " 0.018 2.00e-02 2.50e+03 9.01e-03 1.83e+00 pdb=" N1 DC I -74 " -0.016 2.00e-02 2.50e+03 pdb=" C2 DC I -74 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC I -74 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DC I -74 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC I -74 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC I -74 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I -74 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC I -74 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 81 " -0.018 2.00e-02 2.50e+03 7.95e-03 1.74e+00 pdb=" N9 DA I 81 " 0.017 2.00e-02 2.50e+03 pdb=" C8 DA I 81 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 81 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 81 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 81 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 81 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 81 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 81 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 81 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 81 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 60 " -0.017 2.00e-02 2.50e+03 7.71e-03 1.63e+00 pdb=" N9 DA I 60 " 0.017 2.00e-02 2.50e+03 pdb=" C8 DA I 60 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 60 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 60 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 60 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 60 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA I 60 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 60 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 60 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 60 " 0.003 2.00e-02 2.50e+03 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1767 2.76 - 3.30: 12189 3.30 - 3.83: 24588 3.83 - 4.37: 27978 4.37 - 4.90: 41372 Nonbonded interactions: 107894 Sorted by model distance: nonbonded pdb=" OG1 THR E 45 " pdb=" OP1 DC J 70 " model vdw 2.226 3.040 nonbonded pdb=" N2 DG I 26 " pdb=" O2 DT J -25 " model vdw 2.294 3.120 nonbonded pdb=" N2 DG J 76 " pdb=" O6 DG J 77 " model vdw 2.306 3.120 nonbonded pdb=" O LEU D 77 " pdb=" ND2 ASN D 81 " model vdw 2.320 3.120 nonbonded pdb=" O LEU H 77 " pdb=" ND2 ASN H 81 " model vdw 2.320 3.120 ... (remaining 107889 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 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 118) selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 27 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.090 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 0.032 14760 Z= 0.489 Angle : 0.655 5.734 21429 Z= 0.617 Chirality : 0.041 0.135 2434 Planarity : 0.003 0.026 1497 Dihedral : 27.262 177.360 6415 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.40 % Favored : 94.87 % Rotamer: Outliers : 0.57 % Allowed : 2.15 % Favored : 97.28 % 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: -0.94 (0.27), residues: 819 helix: 0.21 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -2.58 (0.30), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 54 TYR 0.010 0.001 TYR C 50 PHE 0.007 0.001 PHE D 62 HIS 0.001 0.000 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.49 (14760) covalent geometry : angle 0.65484 / 0.62 (21429) hydrogen bonds : bond 0.14740 / 10.12 ( 484) hydrogen bonds : angle 6.82359 / 4.83 ( 1362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 65 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.5878 (pttt) REVERT: B 98 TYR cc_start: 0.7815 (m-10) cc_final: 0.7502 (m-10) REVERT: C 38 ASN cc_start: 0.9559 (m110) cc_final: 0.9130 (t0) REVERT: C 56 GLU cc_start: 0.9307 (tt0) cc_final: 0.9105 (pp20) REVERT: D 34 TYR cc_start: 0.8684 (m-80) cc_final: 0.8456 (m-80) REVERT: D 54 LYS cc_start: 0.9186 (mttt) cc_final: 0.8979 (mppt) REVERT: D 68 GLU cc_start: 0.9595 (mt-10) cc_final: 0.9386 (tm-30) REVERT: E 94 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9124 (tp30) REVERT: E 107 THR cc_start: 0.9627 (m) cc_final: 0.9258 (p) REVERT: F 97 LEU cc_start: 0.8431 (tp) cc_final: 0.8206 (tp) REVERT: G 38 ASN cc_start: 0.9646 (m110) cc_final: 0.9305 (t0) REVERT: H 68 GLU cc_start: 0.9382 (mt-10) cc_final: 0.8992 (pp20) outliers start: 4 outliers final: 2 residues processed: 210 average time/residue: 0.1631 time to fit residues: 44.8967 Evaluate side-chains 75 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 40.0000 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 50.0000 chunk 106 optimal weight: 40.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 5 HIS K 17 GLN K 31 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN B 64 ASN C 38 ASN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS F 93 GLN G 38 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.040265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.031183 restraints weight = 211964.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.032060 restraints weight = 116431.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.032639 restraints weight = 78688.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.033021 restraints weight = 60410.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.033270 restraints weight = 50682.298| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 14760 Z= 0.244 Angle : 0.764 11.193 21429 Z= 0.427 Chirality : 0.047 0.280 2434 Planarity : 0.006 0.037 1497 Dihedral : 31.544 173.401 4757 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.83 % Favored : 97.92 % Rotamer: Outliers : 0.57 % Allowed : 2.15 % Favored : 97.28 % 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: 0.15 (0.28), residues: 819 helix: 1.06 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -2.35 (0.32), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 81 TYR 0.030 0.003 TYR B 88 PHE 0.014 0.002 PHE C 25 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.24 (14760) covalent geometry : angle 0.76450 / 0.43 (21429) hydrogen bonds : bond 0.09915 / 6.69 ( 484) hydrogen bonds : angle 4.09248 / 2.92 ( 1362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.7060 (m-10) cc_final: 0.6782 (m-10) REVERT: E 94 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8686 (tp30) REVERT: G 38 ASN cc_start: 0.9151 (m-40) cc_final: 0.8865 (t0) REVERT: H 73 GLU cc_start: 0.8566 (tp30) cc_final: 0.8278 (tp30) outliers start: 4 outliers final: 1 residues processed: 105 average time/residue: 0.1376 time to fit residues: 20.1977 Evaluate side-chains 49 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 50.0000 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 97 optimal weight: 40.0000 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 93 optimal weight: 40.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 37 HIS ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** G 82 HIS ** 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 = 0.3214 r_free = 0.3214 target = 0.039470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.030237 restraints weight = 213572.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.031080 restraints weight = 115884.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.031652 restraints weight = 78068.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.032039 restraints weight = 59926.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.032263 restraints weight = 50042.957| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14760 Z= 0.159 Angle : 0.574 7.585 21429 Z= 0.345 Chirality : 0.039 0.241 2434 Planarity : 0.005 0.072 1497 Dihedral : 31.639 168.811 4757 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.69 % Favored : 97.07 % Rotamer: Outliers : 0.29 % Allowed : 3.44 % Favored : 96.28 % 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: 1.11 (0.29), residues: 819 helix: 1.79 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -2.00 (0.33), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 129 TYR 0.017 0.002 TYR F 88 PHE 0.006 0.001 PHE B 100 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.16 (14760) covalent geometry : angle 0.57413 / 0.34 (21429) hydrogen bonds : bond 0.05703 / 3.92 ( 484) hydrogen bonds : angle 3.55253 / 2.52 ( 1362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.7093 (m-10) cc_final: 0.6828 (m-10) REVERT: C 38 ASN cc_start: 0.9156 (m-40) cc_final: 0.8349 (t0) REVERT: D 68 GLU cc_start: 0.8805 (pt0) cc_final: 0.8596 (pt0) REVERT: E 94 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8763 (tp30) REVERT: F 97 LEU cc_start: 0.7582 (tt) cc_final: 0.6914 (tt) REVERT: G 38 ASN cc_start: 0.9178 (m-40) cc_final: 0.8450 (t0) REVERT: H 30 ARG cc_start: 0.8431 (mpp-170) cc_final: 0.7839 (ttp-170) REVERT: H 73 GLU cc_start: 0.8571 (tp30) cc_final: 0.8310 (tp30) outliers start: 2 outliers final: 0 residues processed: 94 average time/residue: 0.1303 time to fit residues: 17.1066 Evaluate side-chains 52 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 50.0000 chunk 61 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 82 optimal weight: 50.0000 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 99 optimal weight: 40.0000 chunk 110 optimal weight: 40.0000 chunk 19 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 28 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 38 ASN ** G 82 HIS ** 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 = 0.3090 r_free = 0.3090 target = 0.036228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.026938 restraints weight = 218207.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.027793 restraints weight = 108915.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.028352 restraints weight = 71160.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.028699 restraints weight = 54162.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.028893 restraints weight = 45336.207| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 14760 Z= 0.172 Angle : 0.580 6.251 21429 Z= 0.344 Chirality : 0.038 0.254 2434 Planarity : 0.005 0.075 1497 Dihedral : 31.723 167.358 4757 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.69 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: 1.27 (0.29), residues: 819 helix: 1.84 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.71 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 20 TYR 0.017 0.002 TYR B 72 PHE 0.015 0.002 PHE G 25 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.17 (14760) covalent geometry : angle 0.58011 / 0.34 (21429) hydrogen bonds : bond 0.06537 / 4.50 ( 484) hydrogen bonds : angle 3.54487 / 2.51 ( 1362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.6692 (m-10) cc_final: 0.6243 (m-10) REVERT: D 31 LYS cc_start: 0.8180 (mmpt) cc_final: 0.7736 (tmtt) REVERT: E 94 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8805 (tp30) REVERT: F 97 LEU cc_start: 0.7849 (tt) cc_final: 0.7464 (tt) REVERT: G 38 ASN cc_start: 0.9215 (m110) cc_final: 0.8896 (t0) REVERT: H 77 LEU cc_start: 0.8971 (mt) cc_final: 0.8682 (mt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1320 time to fit residues: 15.6504 Evaluate side-chains 43 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 25 optimal weight: 0.2980 chunk 26 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 81 optimal weight: 50.0000 chunk 65 optimal weight: 6.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 28 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** G 82 HIS ** 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 = 0.3142 r_free = 0.3142 target = 0.036481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.027724 restraints weight = 230293.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.028549 restraints weight = 120397.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.029100 restraints weight = 80217.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.029458 restraints weight = 61077.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.029675 restraints weight = 51022.384| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14760 Z= 0.162 Angle : 0.567 7.195 21429 Z= 0.338 Chirality : 0.038 0.242 2434 Planarity : 0.004 0.063 1497 Dihedral : 31.929 166.083 4757 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 1.43 (0.29), residues: 819 helix: 1.94 (0.21), residues: 579 sheet: None (None), residues: 0 loop : -1.62 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 76 TYR 0.016 0.002 TYR B 72 PHE 0.021 0.002 PHE D 62 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 (14760) covalent geometry : angle 0.56710 / 0.34 (21429) hydrogen bonds : bond 0.05605 / 3.90 ( 484) hydrogen bonds : angle 3.38747 / 2.40 ( 1362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.6521 (m-10) cc_final: 0.6099 (m-10) REVERT: D 31 LYS cc_start: 0.8087 (mmpt) cc_final: 0.7662 (tmtt) REVERT: D 68 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8562 (mp0) REVERT: E 94 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8777 (tp30) REVERT: F 97 LEU cc_start: 0.7893 (tt) cc_final: 0.7469 (tt) REVERT: G 38 ASN cc_start: 0.9160 (m110) cc_final: 0.8794 (t0) REVERT: H 30 ARG cc_start: 0.8527 (mpp-170) cc_final: 0.7975 (ttt180) REVERT: H 73 GLU cc_start: 0.8653 (tp30) cc_final: 0.8421 (tp30) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1350 time to fit residues: 15.0937 Evaluate side-chains 50 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 91 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 chunk 108 optimal weight: 40.0000 chunk 84 optimal weight: 50.0000 chunk 67 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 overall best weight: 5.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** 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 = 0.3076 r_free = 0.3076 target = 0.035933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.026723 restraints weight = 223133.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.027478 restraints weight = 118310.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.027957 restraints weight = 80126.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.028300 restraints weight = 62429.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.028479 restraints weight = 52736.428| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14760 Z= 0.176 Angle : 0.596 8.406 21429 Z= 0.352 Chirality : 0.038 0.246 2434 Planarity : 0.004 0.059 1497 Dihedral : 32.082 165.720 4757 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.56 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 1.38 (0.29), residues: 819 helix: 1.88 (0.21), residues: 579 sheet: None (None), residues: 0 loop : -1.56 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 35 TYR 0.016 0.002 TYR C 50 PHE 0.024 0.002 PHE D 62 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.18 (14760) covalent geometry : angle 0.59613 / 0.35 (21429) hydrogen bonds : bond 0.06614 / 4.58 ( 484) hydrogen bonds : angle 3.69995 / 2.66 ( 1362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.6679 (m-10) cc_final: 0.6265 (m-10) REVERT: E 94 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8763 (tp30) REVERT: F 97 LEU cc_start: 0.7898 (tt) cc_final: 0.7446 (tt) REVERT: G 38 ASN cc_start: 0.9156 (m110) cc_final: 0.8792 (t0) REVERT: H 30 ARG cc_start: 0.8603 (mpp-170) cc_final: 0.8098 (ttt180) REVERT: H 77 LEU cc_start: 0.8810 (mt) cc_final: 0.8600 (mt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1250 time to fit residues: 12.6221 Evaluate side-chains 49 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 36 optimal weight: 0.0980 chunk 51 optimal weight: 7.9990 chunk 107 optimal weight: 40.0000 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 50.0000 chunk 53 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** 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 = 0.3089 r_free = 0.3089 target = 0.036653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.027387 restraints weight = 223239.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.028135 restraints weight = 120044.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.028616 restraints weight = 81669.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.028946 restraints weight = 63937.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.029136 restraints weight = 54485.154| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14760 Z= 0.141 Angle : 0.560 7.446 21429 Z= 0.333 Chirality : 0.038 0.243 2434 Planarity : 0.004 0.053 1497 Dihedral : 32.152 165.163 4757 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: 1.58 (0.29), residues: 819 helix: 2.02 (0.21), residues: 577 sheet: None (None), residues: 0 loop : -1.43 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 69 TYR 0.011 0.001 TYR K 8 PHE 0.026 0.002 PHE D 62 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.14 (14760) covalent geometry : angle 0.56017 / 0.33 (21429) hydrogen bonds : bond 0.05373 / 3.74 ( 484) hydrogen bonds : angle 3.46945 / 2.49 ( 1362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.6518 (m-10) cc_final: 0.6151 (m-10) REVERT: D 31 LYS cc_start: 0.7890 (mmpt) cc_final: 0.7399 (tmtt) REVERT: E 94 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8824 (tp30) REVERT: F 97 LEU cc_start: 0.7701 (tt) cc_final: 0.7360 (tt) REVERT: G 38 ASN cc_start: 0.9148 (m110) cc_final: 0.8773 (t0) REVERT: H 30 ARG cc_start: 0.8545 (mpp-170) cc_final: 0.8012 (ttt180) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1455 time to fit residues: 15.0757 Evaluate side-chains 46 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 1.9990 chunk 92 optimal weight: 50.0000 chunk 102 optimal weight: 40.0000 chunk 42 optimal weight: 8.9990 chunk 103 optimal weight: 50.0000 chunk 72 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 96 optimal weight: 50.0000 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** 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 = 0.3067 r_free = 0.3067 target = 0.035530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.026369 restraints weight = 224080.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.027104 restraints weight = 119128.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.027580 restraints weight = 80585.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.027901 restraints weight = 62967.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.028083 restraints weight = 53494.781| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14760 Z= 0.154 Angle : 0.587 7.559 21429 Z= 0.346 Chirality : 0.038 0.239 2434 Planarity : 0.004 0.041 1497 Dihedral : 32.245 165.153 4757 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.29), residues: 819 helix: 1.78 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.47 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.012 0.001 TYR K 8 PHE 0.022 0.001 PHE D 62 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (14760) covalent geometry : angle 0.58680 / 0.35 (21429) hydrogen bonds : bond 0.05829 / 4.05 ( 484) hydrogen bonds : angle 3.74326 / 2.67 ( 1362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.6608 (m-10) cc_final: 0.6194 (m-10) REVERT: D 68 GLU cc_start: 0.8665 (pp20) cc_final: 0.8420 (pt0) REVERT: E 94 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8774 (tp30) REVERT: F 97 LEU cc_start: 0.7720 (tt) cc_final: 0.7500 (tt) REVERT: G 38 ASN cc_start: 0.9181 (m110) cc_final: 0.8785 (t0) REVERT: H 30 ARG cc_start: 0.8551 (mpp-170) cc_final: 0.7996 (mtt180) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1289 time to fit residues: 12.6224 Evaluate side-chains 49 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 8.9990 chunk 82 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 83 optimal weight: 50.0000 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 97 optimal weight: 50.0000 chunk 28 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** 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 = 0.3058 r_free = 0.3058 target = 0.033318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.024860 restraints weight = 250211.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.025609 restraints weight = 133608.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.026100 restraints weight = 89843.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.026378 restraints weight = 69245.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.026611 restraints weight = 59044.167| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14760 Z= 0.209 Angle : 0.667 9.829 21429 Z= 0.383 Chirality : 0.040 0.261 2434 Planarity : 0.005 0.042 1497 Dihedral : 32.690 166.851 4757 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 0.98 (0.28), residues: 819 helix: 1.56 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -1.61 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 69 TYR 0.021 0.002 TYR K 8 PHE 0.030 0.003 PHE D 67 HIS 0.015 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.21 (14760) covalent geometry : angle 0.66708 / 0.38 (21429) hydrogen bonds : bond 0.07563 / 5.29 ( 484) hydrogen bonds : angle 4.15994 / 2.99 ( 1362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.6610 (m-10) cc_final: 0.6224 (m-10) REVERT: E 94 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8780 (tp30) REVERT: E 120 MET cc_start: 0.7205 (mmp) cc_final: 0.6923 (mmm) REVERT: F 97 LEU cc_start: 0.8011 (tt) cc_final: 0.7557 (tt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1260 time to fit residues: 12.2081 Evaluate side-chains 42 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 40.0000 chunk 8 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 68 optimal weight: 0.0980 chunk 11 optimal weight: 5.9990 chunk 110 optimal weight: 50.0000 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 50.0000 chunk 84 optimal weight: 50.0000 chunk 50 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** 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 = 0.3079 r_free = 0.3079 target = 0.033845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.025330 restraints weight = 245085.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.026084 restraints weight = 129055.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.026589 restraints weight = 86693.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.026906 restraints weight = 66738.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.027072 restraints weight = 56535.436| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14760 Z= 0.158 Angle : 0.607 8.674 21429 Z= 0.358 Chirality : 0.039 0.241 2434 Planarity : 0.004 0.038 1497 Dihedral : 32.749 167.867 4757 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.13 (0.29), residues: 819 helix: 1.66 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -1.53 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 128 TYR 0.017 0.001 TYR K 8 PHE 0.026 0.002 PHE D 62 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.16 (14760) covalent geometry : angle 0.60693 / 0.36 (21429) hydrogen bonds : bond 0.05777 / 4.07 ( 484) hydrogen bonds : angle 3.93999 / 2.83 ( 1362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8807 (mp0) cc_final: 0.8603 (pm20) REVERT: B 91 LYS cc_start: 0.8068 (ptpp) cc_final: 0.7832 (ptpp) REVERT: B 98 TYR cc_start: 0.6571 (m-10) cc_final: 0.6366 (m-10) REVERT: D 68 GLU cc_start: 0.8831 (pp20) cc_final: 0.8614 (mt-10) REVERT: E 94 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8765 (tp30) REVERT: F 97 LEU cc_start: 0.7837 (tt) cc_final: 0.7526 (tt) REVERT: G 38 ASN cc_start: 0.9027 (m110) cc_final: 0.8708 (t0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1177 time to fit residues: 11.6372 Evaluate side-chains 50 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 50.0000 chunk 11 optimal weight: 20.0000 chunk 81 optimal weight: 40.0000 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 40.0000 chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 5.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** 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 = 0.3065 r_free = 0.3065 target = 0.033407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.024926 restraints weight = 249015.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.025689 restraints weight = 131686.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.026169 restraints weight = 87919.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.026461 restraints weight = 67895.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.026678 restraints weight = 57958.835| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.6860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 14760 Z= 0.177 Angle : 0.622 9.410 21429 Z= 0.362 Chirality : 0.039 0.222 2434 Planarity : 0.004 0.038 1497 Dihedral : 32.793 168.150 4757 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.29), residues: 819 helix: 1.62 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -1.54 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 92 TYR 0.013 0.002 TYR E 99 PHE 0.022 0.002 PHE D 62 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.18 (14760) covalent geometry : angle 0.62223 / 0.36 (21429) hydrogen bonds : bond 0.06269 / 4.39 ( 484) hydrogen bonds : angle 4.02546 / 2.88 ( 1362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.06 seconds wall clock time: 40 minutes 8.45 seconds (2408.45 seconds total)