Starting phenix.real_space_refine on Sat Sep 12 03:48:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dbp_30161/09_2026/7dbp_30161.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dbp_30161/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7dbp_30161/09_2026/7dbp_30161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dbp_30161/09_2026/7dbp_30161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dbp_30161/09_2026/7dbp_30161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dbp_30161/09_2026/7dbp_30161.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.90, per 1000 atoms: 0.21 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: 1.20 Conformation dependent library (CDL) restraints added in 438.8 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: 1.54 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: 1.66 Time building geometry restraints manager: 1.61 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: 19648 1.15 - 2.29: 1491 2.29 - 3.44: 273 3.44 - 4.59: 9 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: 0.960 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.020 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.650 ------------------------------------------------------------------------------- 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 : 0.661 5.734 21429 Z= 0.622 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 0.66091 / 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 : 0.292 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: 0.1594 time to fit residues: 44.0337 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 : 0.206 ------------------------------------------------------------------------------- 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: 30.0000 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 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 = 0.3234 r_free = 0.3234 target = 0.040325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.031134 restraints weight = 213024.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.032011 restraints weight = 116159.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.032595 restraints weight = 78532.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.032985 restraints weight = 60258.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.033196 restraints weight = 50294.623| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 14760 Z= 0.246 Angle : 0.764 8.529 21429 Z= 0.426 Chirality : 0.047 0.287 2434 Planarity : 0.006 0.038 1497 Dihedral : 31.530 173.716 4757 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.95 % Favored : 97.80 % Rotamer: Outliers : 0.72 % Allowed : 1.86 % Favored : 97.42 % 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: 0.10 (0.28), residues: 819 helix: 1.03 (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 0.014 0.001 ARG K 27 TYR 0.037 0.003 TYR B 88 PHE 0.021 0.002 PHE B 100 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.25 (14760) covalent geometry : angle 0.76432 / 0.43 (21429) hydrogen bonds : bond 0.09807 / 6.60 ( 484) hydrogen bonds : angle 4.10311 / 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 106 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.388 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: 0.7055 (m-10) cc_final: 0.6772 (m-10) REVERT: E 94 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8689 (tp30) REVERT: G 38 ASN cc_start: 0.9152 (m-40) cc_final: 0.8866 (t0) REVERT: H 73 GLU cc_start: 0.8561 (tp30) cc_final: 0.8272 (tp30) outliers start: 5 outliers final: 0 residues processed: 103 average time/residue: 0.1448 time to fit residues: 20.6534 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 : 0.371 ------------------------------------------------------------------------------- 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: 40.0000 chunk 78 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 97 optimal weight: 50.0000 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 93 optimal weight: 40.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** D 44 GLN E 68 GLN G 31 HIS ** 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 = 0.3195 r_free = 0.3195 target = 0.038945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.029735 restraints weight = 216455.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.030589 restraints weight = 115743.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.031160 restraints weight = 77838.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.031478 restraints weight = 59756.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.031746 restraints weight = 50777.733| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14760 Z= 0.180 Angle : 0.587 7.248 21429 Z= 0.351 Chirality : 0.040 0.260 2434 Planarity : 0.004 0.067 1497 Dihedral : 31.629 169.998 4757 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.81 % Favored : 96.95 % Rotamer: Outliers : 0.29 % Allowed : 3.15 % Favored : 96.56 % 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: 1.02 (0.29), residues: 819 helix: 1.71 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.99 (0.33), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 134 TYR 0.018 0.002 TYR B 88 PHE 0.009 0.001 PHE C 25 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.18 (14760) covalent geometry : angle 0.58746 / 0.35 (21429) hydrogen bonds : bond 0.06107 / 4.19 ( 484) hydrogen bonds : angle 3.59913 / 2.54 ( 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 92 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.325 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: A 97 GLU cc_start: 0.8970 (pp20) cc_final: 0.8765 (pp20) REVERT: B 98 TYR cc_start: 0.6949 (m-10) cc_final: 0.6642 (m-10) REVERT: D 68 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8512 (mp0) REVERT: E 94 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8771 (tp30) REVERT: F 97 LEU cc_start: 0.7625 (tt) cc_final: 0.6977 (tt) REVERT: G 38 ASN cc_start: 0.9209 (m-40) cc_final: 0.8840 (t0) REVERT: H 30 ARG cc_start: 0.8485 (mpp-170) cc_final: 0.7942 (mtm180) REVERT: H 73 GLU cc_start: 0.8598 (tp30) cc_final: 0.8327 (tp30) outliers start: 2 outliers final: 0 residues processed: 92 average time/residue: 0.1326 time to fit residues: 17.0097 Evaluate side-chains 47 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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: 7.9990 chunk 13 optimal weight: 0.9980 chunk 82 optimal weight: 50.0000 chunk 39 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 99 optimal weight: 40.0000 chunk 110 optimal weight: 40.0000 chunk 19 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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 38 ASN ** 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 = 0.3141 r_free = 0.3141 target = 0.036648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.027903 restraints weight = 228680.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.028741 restraints weight = 119379.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.029285 restraints weight = 79402.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.029629 restraints weight = 60663.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.029813 restraints weight = 50853.387| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4442 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= 0.188 Angle : 0.640 8.791 21429 Z= 0.370 Chirality : 0.040 0.278 2434 Planarity : 0.005 0.074 1497 Dihedral : 31.796 167.299 4757 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.56 % Favored : 97.31 % Rotamer: Outliers : 0.43 % Allowed : 2.87 % Favored : 96.70 % 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: 1.04 (0.29), residues: 819 helix: 1.64 (0.21), residues: 577 sheet: None (None), residues: 0 loop : -1.70 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 128 TYR 0.016 0.002 TYR D 34 PHE 0.014 0.002 PHE C 25 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.19 (14760) covalent geometry : angle 0.64011 / 0.37 (21429) hydrogen bonds : bond 0.07219 / 5.00 ( 484) hydrogen bonds : angle 3.73940 / 2.65 ( 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 87 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.282 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: 0.6719 (m-10) cc_final: 0.6294 (m-10) REVERT: E 94 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8729 (tp30) REVERT: F 97 LEU cc_start: 0.7775 (tt) cc_final: 0.7362 (tt) REVERT: G 38 ASN cc_start: 0.9218 (m110) cc_final: 0.8879 (t0) REVERT: H 30 ARG cc_start: 0.8496 (mpp-170) cc_final: 0.7913 (mtm180) REVERT: H 73 GLU cc_start: 0.8721 (tp30) cc_final: 0.8474 (tp30) outliers start: 3 outliers final: 1 residues processed: 86 average time/residue: 0.1252 time to fit residues: 15.4155 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 : 0.259 ------------------------------------------------------------------------------- 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: 1.9990 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 81 optimal weight: 50.0000 chunk 65 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** 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 = 0.3154 r_free = 0.3154 target = 0.036824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.028025 restraints weight = 230596.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.028885 restraints weight = 121277.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.029436 restraints weight = 80723.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.029759 restraints weight = 61654.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.030003 restraints weight = 52081.064| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14760 Z= 0.141 Angle : 0.559 7.421 21429 Z= 0.333 Chirality : 0.038 0.270 2434 Planarity : 0.004 0.068 1497 Dihedral : 31.868 166.615 4757 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.93 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: 1.39 (0.29), residues: 819 helix: 1.90 (0.21), residues: 577 sheet: None (None), residues: 0 loop : -1.58 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 92 TYR 0.018 0.001 TYR K 8 PHE 0.014 0.001 PHE D 62 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.14 (14760) covalent geometry : angle 0.55875 / 0.33 (21429) hydrogen bonds : bond 0.05570 / 3.87 ( 484) hydrogen bonds : angle 3.50315 / 2.48 ( 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 81 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9118 (pp20) cc_final: 0.8893 (pp20) REVERT: B 43 VAL cc_start: 0.3326 (t) cc_final: 0.2885 (t) REVERT: B 98 TYR cc_start: 0.6491 (m-10) cc_final: 0.6069 (m-10) REVERT: D 31 LYS cc_start: 0.8087 (mmpt) cc_final: 0.7612 (tmtt) REVERT: E 94 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8786 (tp30) REVERT: F 97 LEU cc_start: 0.7881 (tt) cc_final: 0.7413 (tt) REVERT: G 38 ASN cc_start: 0.9155 (m110) cc_final: 0.8745 (t0) REVERT: H 30 ARG cc_start: 0.8549 (mpp-170) cc_final: 0.7997 (mtm180) REVERT: H 73 GLU cc_start: 0.8693 (tp30) cc_final: 0.8408 (tp30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1225 time to fit residues: 14.1820 Evaluate side-chains 51 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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: 20.0000 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 chunk 91 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 chunk 108 optimal weight: 40.0000 chunk 84 optimal weight: 40.0000 chunk 67 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3059 r_free = 0.3059 target = 0.035202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.026106 restraints weight = 227128.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.026818 restraints weight = 120001.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.027284 restraints weight = 81722.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.027579 restraints weight = 63726.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.027799 restraints weight = 54580.077| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14760 Z= 0.188 Angle : 0.651 7.476 21429 Z= 0.371 Chirality : 0.040 0.278 2434 Planarity : 0.005 0.071 1497 Dihedral : 32.165 166.319 4757 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.29 % Allowed : 2.44 % 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: 1.25 (0.28), residues: 819 helix: 1.76 (0.21), residues: 577 sheet: None (None), residues: 0 loop : -1.50 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 131 TYR 0.024 0.002 TYR C 50 PHE 0.017 0.002 PHE C 25 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.19 (14760) covalent geometry : angle 0.65087 / 0.37 (21429) hydrogen bonds : bond 0.07560 / 5.23 ( 484) hydrogen bonds : angle 3.73978 / 2.63 ( 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 75 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9052 (pp20) cc_final: 0.8821 (pp20) REVERT: B 98 TYR cc_start: 0.6672 (m-10) cc_final: 0.6302 (m-10) REVERT: D 68 GLU cc_start: 0.8482 (mp0) cc_final: 0.8221 (mp0) REVERT: D 73 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8052 (pm20) REVERT: E 94 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8820 (tp30) REVERT: F 97 LEU cc_start: 0.7954 (tt) cc_final: 0.7505 (tt) REVERT: G 38 ASN cc_start: 0.9180 (m110) cc_final: 0.8807 (t0) REVERT: H 30 ARG cc_start: 0.8606 (mpp-170) cc_final: 0.8082 (mtm180) REVERT: H 73 GLU cc_start: 0.8656 (tp30) cc_final: 0.8427 (tp30) outliers start: 2 outliers final: 0 residues processed: 75 average time/residue: 0.1266 time to fit residues: 13.7104 Evaluate side-chains 48 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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: 10.0000 chunk 14 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 107 optimal weight: 40.0000 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 50.0000 chunk 53 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3083 r_free = 0.3083 target = 0.034192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.025706 restraints weight = 243505.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.026478 restraints weight = 127211.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.026990 restraints weight = 85481.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.027314 restraints weight = 65796.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.027477 restraints weight = 55439.050| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 14760 Z= 0.187 Angle : 0.623 8.954 21429 Z= 0.365 Chirality : 0.040 0.273 2434 Planarity : 0.005 0.050 1497 Dihedral : 32.454 167.078 4757 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.69 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: 1.01 (0.28), residues: 819 helix: 1.59 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -1.61 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 89 TYR 0.014 0.002 TYR E 54 PHE 0.016 0.001 PHE D 62 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.19 (14760) covalent geometry : angle 0.62333 / 0.36 (21429) hydrogen bonds : bond 0.06488 / 4.55 ( 484) hydrogen bonds : angle 3.82255 / 2.72 ( 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 68 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9123 (pp20) cc_final: 0.8922 (pp20) REVERT: B 98 TYR cc_start: 0.6404 (m-10) cc_final: 0.6032 (m-10) REVERT: E 94 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8740 (tp30) REVERT: F 97 LEU cc_start: 0.7853 (tt) cc_final: 0.7581 (tt) REVERT: G 38 ASN cc_start: 0.9092 (m110) cc_final: 0.8758 (t0) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1315 time to fit residues: 12.5144 Evaluate side-chains 44 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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: 7.9990 chunk 92 optimal weight: 50.0000 chunk 102 optimal weight: 40.0000 chunk 42 optimal weight: 5.9990 chunk 103 optimal weight: 40.0000 chunk 72 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 96 optimal weight: 50.0000 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3085 r_free = 0.3085 target = 0.034157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.025621 restraints weight = 243078.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.026394 restraints weight = 127047.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.026908 restraints weight = 85133.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.027186 restraints weight = 65539.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.027436 restraints weight = 55985.378| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14760 Z= 0.155 Angle : 0.600 7.835 21429 Z= 0.350 Chirality : 0.039 0.260 2434 Planarity : 0.004 0.041 1497 Dihedral : 32.491 167.084 4757 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: 1.81 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -1.58 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 128 TYR 0.011 0.001 TYR K 8 PHE 0.020 0.002 PHE B 100 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (14760) covalent geometry : angle 0.59960 / 0.35 (21429) hydrogen bonds : bond 0.06015 / 4.22 ( 484) hydrogen bonds : angle 3.74429 / 2.62 ( 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 68 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9119 (pp20) cc_final: 0.8908 (pp20) REVERT: B 98 TYR cc_start: 0.6574 (m-10) cc_final: 0.6223 (m-10) REVERT: D 68 GLU cc_start: 0.8323 (mp0) cc_final: 0.8085 (mp0) REVERT: E 94 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8722 (tp30) REVERT: F 97 LEU cc_start: 0.7834 (tt) cc_final: 0.7541 (tt) REVERT: G 38 ASN cc_start: 0.9097 (m110) cc_final: 0.8751 (t0) REVERT: H 73 GLU cc_start: 0.8881 (tp30) cc_final: 0.8458 (tp30) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1215 time to fit residues: 11.7353 Evaluate side-chains 44 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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: 5.9990 chunk 82 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 0.1980 chunk 44 optimal weight: 7.9990 chunk 83 optimal weight: 50.0000 chunk 19 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 97 optimal weight: 50.0000 chunk 28 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 HIS ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 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 = 0.3029 r_free = 0.3029 target = 0.033455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.024551 restraints weight = 233558.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.025277 restraints weight = 122138.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.025785 restraints weight = 82288.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.026108 restraints weight = 63419.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.026289 restraints weight = 53409.344| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14760 Z= 0.174 Angle : 0.628 8.052 21429 Z= 0.364 Chirality : 0.039 0.255 2434 Planarity : 0.004 0.041 1497 Dihedral : 32.660 168.366 4757 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.93 % Favored : 96.95 % Rotamer: Outliers : 0.14 % Allowed : 1.00 % 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: 1.00 (0.28), residues: 819 helix: 1.60 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -1.64 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.026 0.002 TYR G 50 PHE 0.015 0.002 PHE C 25 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.17 (14760) covalent geometry : angle 0.62847 / 0.36 (21429) hydrogen bonds : bond 0.06492 / 4.54 ( 484) hydrogen bonds : angle 3.86228 / 2.72 ( 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 68 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9095 (pp20) cc_final: 0.8891 (pp20) REVERT: E 94 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8776 (tp30) REVERT: E 120 MET cc_start: 0.7244 (mmp) cc_final: 0.7034 (mmp) REVERT: F 97 LEU cc_start: 0.7960 (tt) cc_final: 0.7707 (tt) REVERT: H 73 GLU cc_start: 0.8737 (tp30) cc_final: 0.8402 (tp30) outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.1284 time to fit residues: 12.2252 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 : 0.283 ------------------------------------------------------------------------------- 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: 9.9990 chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 110 optimal weight: 50.0000 chunk 64 optimal weight: 8.9990 chunk 96 optimal weight: 50.0000 chunk 84 optimal weight: 50.0000 chunk 50 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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** F 75 HIS ** 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 = 0.3057 r_free = 0.3057 target = 0.033332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.024938 restraints weight = 246742.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.025660 restraints weight = 131650.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.026137 restraints weight = 89075.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.026430 restraints weight = 68880.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.026612 restraints weight = 58368.879| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.7137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14760 Z= 0.211 Angle : 0.681 10.280 21429 Z= 0.391 Chirality : 0.042 0.263 2434 Planarity : 0.005 0.038 1497 Dihedral : 32.985 170.071 4757 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 0.85 (0.28), residues: 819 helix: 1.47 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -1.67 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.016 0.002 TYR E 99 PHE 0.018 0.002 PHE C 25 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.21 (14760) covalent geometry : angle 0.68126 / 0.39 (21429) hydrogen bonds : bond 0.07406 / 5.21 ( 484) hydrogen bonds : angle 4.20837 / 2.98 ( 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 61 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9137 (pp20) cc_final: 0.8919 (pp20) REVERT: B 98 TYR cc_start: 0.6539 (m-10) cc_final: 0.6187 (m-10) REVERT: E 94 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8790 (tp30) REVERT: E 107 THR cc_start: 0.8810 (p) cc_final: 0.8607 (t) REVERT: E 120 MET cc_start: 0.7352 (mmp) cc_final: 0.7083 (mmp) REVERT: F 97 LEU cc_start: 0.8000 (tt) cc_final: 0.7733 (tt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1180 time to fit residues: 10.3409 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 : 0.346 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 50.0000 chunk 66 optimal weight: 0.5980 chunk 85 optimal weight: 50.0000 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 30.0000 chunk 4 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.3073 r_free = 0.3073 target = 0.033517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.024983 restraints weight = 245734.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.025743 restraints weight = 129111.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.026239 restraints weight = 86805.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.026517 restraints weight = 67028.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.026752 restraints weight = 57345.088| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.7008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14760 Z= 0.142 Angle : 0.597 8.058 21429 Z= 0.349 Chirality : 0.040 0.238 2434 Planarity : 0.004 0.039 1497 Dihedral : 32.884 170.089 4757 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.14 (0.28), residues: 819 helix: 1.71 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.023 0.002 TYR G 50 PHE 0.022 0.002 PHE H 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.14 (14760) covalent geometry : angle 0.59686 / 0.35 (21429) hydrogen bonds : bond 0.05225 / 3.66 ( 484) hydrogen bonds : angle 3.75670 / 2.64 ( 1362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2340.73 seconds wall clock time: 41 minutes 3.35 seconds (2463.35 seconds total)