Starting phenix.real_space_refine on Sun Sep 13 08:42:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ssa_25406/09_2026/7ssa_25406.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ssa_25406/09_2026/7ssa_25406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ssa_25406/09_2026/7ssa_25406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ssa_25406/09_2026/7ssa_25406.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ssa_25406/09_2026/7ssa_25406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ssa_25406/09_2026/7ssa_25406.map" } resolution = 3.2 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= 0.006 sd= 0.026 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: 6 Type Number sf(0) Gaussians P 273 5.49 5 S 12 5.16 5 C 6974 2.51 5 N 2329 2.21 5 O 2892 1.98 5 H 10277 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s 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: 22757 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1605 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1280 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1518 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1461 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1519 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1351 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1652 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1461 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "K" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1110 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "L" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1111 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "I" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 4325 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "J" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 4364 Classifications: {'DNA': 137} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 136} Time building chain proxies: 3.91, per 1000 atoms: 0.17 Number of scatterers: 22757 At special positions: 0 Unit cell: (115.92, 121.072, 130.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 P 273 15.00 O 2892 8.00 N 2329 7.00 C 6974 6.00 H 10277 1.00 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: 2.21 Conformation dependent library (CDL) restraints added in 433.2 milliseconds 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1638 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 77.7% alpha, 2.8% beta 137 base pairs and 225 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.591A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.566A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.652A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.943A pdb=" N THR D 51 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 87 Processing helix chain 'D' and resid 93 through 105 Processing helix chain 'D' and resid 106 through 126 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.825A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.907A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.509A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.522A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.317A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.563A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.871A pdb=" N LYS G 96 " --> pdb=" O ASP G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 106 through 127 Processing helix chain 'K' and resid 223 through 249 Processing helix chain 'K' and resid 255 through 288 Processing helix chain 'L' and resid 223 through 249 removed outlier: 3.659A pdb=" N HIS L 227 " --> pdb=" O ARG L 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 288 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.918A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.561A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.510A pdb=" N THR B 96 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.205A pdb=" N ARG C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.507A pdb=" N THR C 102 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.135A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.240A pdb=" N ARG G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 505 hydrogen bonds defined for protein. 1497 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 225 stacking parallelities Total time for adding SS restraints: 5.67 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10273 1.03 - 1.23: 128 1.23 - 1.42: 5870 1.42 - 1.62: 7231 1.62 - 1.81: 20 Bond restraints: 23522 Sorted by residual: bond pdb=" C1' DC I 37 " pdb=" N1 DC I 37 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C1' DC J -49 " pdb=" N1 DC J -49 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.65e+00 bond pdb=" C1' DC I -38 " pdb=" N1 DC I -38 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.37e+00 bond pdb=" C3' DC J -27 " pdb=" C2' DC J -27 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.30e+00 ... (remaining 23517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 39375 1.43 - 2.86: 2987 2.86 - 4.29: 253 4.29 - 5.73: 21 5.73 - 7.16: 1 Bond angle restraints: 42637 Sorted by residual: angle pdb=" N3 DT I 3 " pdb=" C4 DT I 3 " pdb=" O4 DT I 3 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT I 38 " pdb=" C4 DT I 38 " pdb=" O4 DT I 38 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J -24 " pdb=" C4 DT J -24 " pdb=" O4 DT J -24 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT J 22 " pdb=" C4 DT J 22 " pdb=" O4 DT J 22 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 42632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7180 17.85 - 35.70: 1296 35.70 - 53.55: 1012 53.55 - 71.39: 375 71.39 - 89.24: 17 Dihedral angle restraints: 9880 sinusoidal: 7079 harmonic: 2801 Sorted by residual: dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CG ARG A 128 " pdb=" CD ARG A 128 " pdb=" NE ARG A 128 " pdb=" CZ ARG A 128 " ideal model delta sinusoidal sigma weight residual -90.00 -133.92 43.92 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG L 233 " pdb=" CD ARG L 233 " pdb=" NE ARG L 233 " pdb=" CZ ARG L 233 " ideal model delta sinusoidal sigma weight residual -90.00 -133.59 43.59 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 9877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1481 0.041 - 0.082: 375 0.082 - 0.123: 103 0.123 - 0.164: 180 0.164 - 0.205: 42 Chirality restraints: 2181 Sorted by residual: chirality pdb=" C3' DA J -15 " pdb=" C4' DA J -15 " pdb=" O3' DA J -15 " pdb=" C2' DA J -15 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C3' DA I 23 " pdb=" C4' DA I 23 " pdb=" O3' DA I 23 " pdb=" C2' DA I 23 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" C3' DA J 26 " pdb=" C4' DA J 26 " pdb=" O3' DA J 26 " pdb=" C2' DA J 26 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 2178 not shown) Planarity restraints: 2511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I -26 " -0.035 2.00e-02 2.50e+03 1.52e-02 6.90e+00 pdb=" N1 DT I -26 " 0.036 2.00e-02 2.50e+03 pdb=" C2 DT I -26 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DT I -26 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DT I -26 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I -26 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT I -26 " -0.012 2.00e-02 2.50e+03 pdb=" C5 DT I -26 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I -26 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT I -26 " 0.002 2.00e-02 2.50e+03 pdb=" H3 DT I -26 " -0.002 2.00e-02 2.50e+03 pdb=" H6 DT I -26 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 36 " -0.190 9.50e-02 1.11e+02 6.35e-02 4.41e+00 pdb=" NE ARG C 36 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 36 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 36 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 36 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG C 36 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 36 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 36 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG C 36 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -13 " 0.028 2.00e-02 2.50e+03 1.17e-02 4.41e+00 pdb=" N9 DA I -13 " -0.030 2.00e-02 2.50e+03 pdb=" C8 DA I -13 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA I -13 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -13 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -13 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -13 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -13 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -13 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -13 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -13 " -0.001 2.00e-02 2.50e+03 pdb=" H8 DA I -13 " -0.002 2.00e-02 2.50e+03 pdb=" H2 DA I -13 " -0.001 2.00e-02 2.50e+03 ... (remaining 2508 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1446 2.21 - 2.81: 41979 2.81 - 3.40: 59662 3.40 - 4.00: 83895 4.00 - 4.60: 125022 Nonbonded interactions: 312004 Sorted by model distance: nonbonded pdb=" OE1 GLU H 116 " pdb="HH22 ARG H 119 " model vdw 1.610 2.450 nonbonded pdb=" H LYS F 79 " pdb=" OP1 DG I 28 " model vdw 1.615 2.450 nonbonded pdb=" HZ3 LYS L 228 " pdb=" OP2 DT I -59 " model vdw 1.623 2.450 nonbonded pdb=" HG1 THR A 45 " pdb=" OP1 DC I 70 " model vdw 1.628 2.450 nonbonded pdb=" OD1 ASP L 225 " pdb=" H SER L 226 " model vdw 1.653 2.450 ... (remaining 311999 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 43 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = (chain 'C' and resid 16 through 110) selection = (chain 'G' and resid 16 through 110) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 222 through 226 or (resid 227 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 228 through 288)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.140 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.850 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.007 0.051 13245 Z= 0.572 Angle : 0.799 7.158 19057 Z= 0.683 Chirality : 0.060 0.205 2181 Planarity : 0.006 0.083 1465 Dihedral : 26.333 89.242 5672 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: 1.86 (0.28), residues: 845 helix: 1.95 (0.20), residues: 641 sheet: None (None), residues: 0 loop : -1.13 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 49 TYR 0.034 0.002 TYR F 88 PHE 0.009 0.002 PHE A 84 TRP 0.017 0.002 TRP L 281 HIS 0.010 0.002 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.57 (13245) covalent geometry : angle 0.79942 / 0.68 (19057) hydrogen bonds : bond 0.09989 / 6.72 ( 855) hydrogen bonds : angle 3.97136 / 3.02 ( 2197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.499 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: C 90 ASN cc_start: 0.8156 (m-40) cc_final: 0.7948 (m-40) REVERT: C 92 ASP cc_start: 0.8081 (t0) cc_final: 0.7761 (t0) REVERT: C 100 ASN cc_start: 0.8292 (p0) cc_final: 0.7967 (p0) REVERT: E 50 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7322 (mt-10) REVERT: E 56 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8736 (tmtt) REVERT: E 87 SER cc_start: 0.9207 (p) cc_final: 0.8936 (p) REVERT: F 64 ASN cc_start: 0.8738 (m-40) cc_final: 0.8436 (m-40) REVERT: G 79 ILE cc_start: 0.8897 (mm) cc_final: 0.8632 (mt) REVERT: K 253 GLU cc_start: 0.5889 (tt0) cc_final: 0.5623 (tt0) REVERT: L 231 GLU cc_start: 0.7918 (tp30) cc_final: 0.7491 (tm-30) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.3994 time to fit residues: 135.1816 Evaluate side-chains 203 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 66 ASN G 16 GLN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.074059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.058182 restraints weight = 97872.204| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.69 r_work: 0.2907 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13245 Z= 0.222 Angle : 0.696 8.444 19057 Z= 0.436 Chirality : 0.042 0.162 2181 Planarity : 0.005 0.055 1465 Dihedral : 29.667 86.768 3952 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.37 % Allowed : 10.00 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.28), residues: 845 helix: 2.05 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -1.19 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 235 TYR 0.010 0.001 TYR D 43 PHE 0.006 0.001 PHE B 61 TRP 0.011 0.001 TRP L 281 HIS 0.004 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.22 (13245) covalent geometry : angle 0.69590 / 0.44 (19057) hydrogen bonds : bond 0.05725 / 3.88 ( 855) hydrogen bonds : angle 3.69403 / 2.82 ( 2197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 203 time to evaluate : 0.441 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: A 120 MET cc_start: 0.9119 (mtp) cc_final: 0.8615 (mtp) REVERT: C 92 ASP cc_start: 0.9027 (t0) cc_final: 0.8776 (t0) REVERT: C 100 ASN cc_start: 0.9045 (p0) cc_final: 0.8677 (p0) REVERT: E 50 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8300 (mt-10) REVERT: E 56 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8446 (tmtt) REVERT: E 59 GLU cc_start: 0.7277 (pm20) cc_final: 0.7032 (pm20) REVERT: E 60 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8643 (mm) REVERT: F 64 ASN cc_start: 0.9314 (m-40) cc_final: 0.8861 (m-40) REVERT: G 72 ARG cc_start: 0.9250 (mtp-110) cc_final: 0.8922 (ttp80) REVERT: L 231 GLU cc_start: 0.8698 (tp30) cc_final: 0.7886 (tm-30) outliers start: 10 outliers final: 5 residues processed: 211 average time/residue: 0.3767 time to fit residues: 100.7157 Evaluate side-chains 201 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 273 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN ** K 227 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 = 0.3395 r_free = 0.3395 target = 0.072528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056899 restraints weight = 98161.329| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.67 r_work: 0.2882 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13245 Z= 0.244 Angle : 0.674 7.994 19057 Z= 0.422 Chirality : 0.041 0.172 2181 Planarity : 0.005 0.047 1465 Dihedral : 29.860 86.475 3952 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.51 % Allowed : 10.82 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.28), residues: 845 helix: 2.16 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.16 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 234 TYR 0.010 0.001 TYR F 51 PHE 0.008 0.001 PHE E 67 TRP 0.011 0.002 TRP L 281 HIS 0.005 0.001 HIS D 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.24 (13245) covalent geometry : angle 0.67441 / 0.42 (19057) hydrogen bonds : bond 0.05222 / 3.54 ( 855) hydrogen bonds : angle 3.58756 / 2.73 ( 2197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.488 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 120 MET cc_start: 0.8914 (mtp) cc_final: 0.8394 (mtp) REVERT: C 92 ASP cc_start: 0.9077 (t0) cc_final: 0.8782 (t0) REVERT: C 100 ASN cc_start: 0.9118 (p0) cc_final: 0.8744 (p0) REVERT: E 50 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8369 (mt-10) REVERT: E 56 LYS cc_start: 0.9061 (ttpt) cc_final: 0.8452 (tmtt) REVERT: E 59 GLU cc_start: 0.7314 (pm20) cc_final: 0.6992 (pm20) REVERT: E 60 LEU cc_start: 0.8937 (mt) cc_final: 0.8713 (mt) REVERT: E 68 GLN cc_start: 0.8981 (tt0) cc_final: 0.8714 (tt0) REVERT: F 64 ASN cc_start: 0.9335 (m-40) cc_final: 0.8854 (m-40) REVERT: G 57 GLU cc_start: 0.9228 (tt0) cc_final: 0.8988 (tt0) REVERT: G 72 ARG cc_start: 0.9225 (mtp-110) cc_final: 0.8907 (ttp80) REVERT: G 114 GLN cc_start: 0.8951 (mp10) cc_final: 0.8676 (mp10) REVERT: K 256 LYS cc_start: 0.9118 (mttm) cc_final: 0.8901 (mttm) REVERT: L 231 GLU cc_start: 0.8679 (tp30) cc_final: 0.7920 (tm-30) outliers start: 11 outliers final: 7 residues processed: 203 average time/residue: 0.3800 time to fit residues: 98.2470 Evaluate side-chains 192 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 185 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 273 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 107 optimal weight: 10.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 227 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 = 0.3400 r_free = 0.3400 target = 0.072561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056765 restraints weight = 99111.023| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.68 r_work: 0.2888 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13245 Z= 0.195 Angle : 0.646 7.664 19057 Z= 0.406 Chirality : 0.040 0.174 2181 Planarity : 0.005 0.044 1465 Dihedral : 29.926 85.879 3952 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.10 % Allowed : 13.84 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.29), residues: 845 helix: 2.35 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.15 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 30 TYR 0.009 0.001 TYR D 43 PHE 0.008 0.001 PHE E 67 TRP 0.010 0.001 TRP L 281 HIS 0.009 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.19 (13245) covalent geometry : angle 0.64626 / 0.41 (19057) hydrogen bonds : bond 0.04858 / 3.29 ( 855) hydrogen bonds : angle 3.44400 / 2.63 ( 2197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 193 time to evaluate : 0.515 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 120 MET cc_start: 0.8871 (mtp) cc_final: 0.8359 (mtp) REVERT: B 92 ARG cc_start: 0.9396 (OUTLIER) cc_final: 0.8787 (ttp80) REVERT: C 100 ASN cc_start: 0.9145 (p0) cc_final: 0.8780 (p0) REVERT: E 50 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8375 (mt-10) REVERT: E 56 LYS cc_start: 0.9062 (ttpt) cc_final: 0.8453 (tmtt) REVERT: E 59 GLU cc_start: 0.7325 (pm20) cc_final: 0.6973 (pm20) REVERT: E 60 LEU cc_start: 0.8926 (mt) cc_final: 0.8630 (mt) REVERT: E 68 GLN cc_start: 0.8999 (tt0) cc_final: 0.8734 (tt0) REVERT: F 64 ASN cc_start: 0.9338 (m-40) cc_final: 0.8847 (m-40) REVERT: G 72 ARG cc_start: 0.9198 (mtp-110) cc_final: 0.8869 (ttp80) REVERT: G 114 GLN cc_start: 0.8975 (mp10) cc_final: 0.8693 (mp10) REVERT: L 231 GLU cc_start: 0.8627 (tp30) cc_final: 0.7853 (tm-30) outliers start: 8 outliers final: 6 residues processed: 200 average time/residue: 0.3740 time to fit residues: 94.8725 Evaluate side-chains 195 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 188 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 270 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN K 222 GLN ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 227 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 = 0.3386 r_free = 0.3386 target = 0.071810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.055961 restraints weight = 98296.717| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.64 r_work: 0.2860 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13245 Z= 0.248 Angle : 0.676 8.234 19057 Z= 0.418 Chirality : 0.041 0.173 2181 Planarity : 0.004 0.040 1465 Dihedral : 29.992 85.400 3952 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.05 % Allowed : 13.42 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.29), residues: 845 helix: 2.33 (0.20), residues: 659 sheet: None (None), residues: 0 loop : -1.17 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 89 TYR 0.009 0.001 TYR F 51 PHE 0.010 0.001 PHE E 67 TRP 0.011 0.001 TRP L 281 HIS 0.008 0.002 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.25 (13245) covalent geometry : angle 0.67605 / 0.42 (19057) hydrogen bonds : bond 0.04997 / 3.38 ( 855) hydrogen bonds : angle 3.55338 / 2.70 ( 2197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.550 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: A 120 MET cc_start: 0.8924 (mtp) cc_final: 0.8555 (mtp) REVERT: A 125 GLN cc_start: 0.9285 (mt0) cc_final: 0.8821 (mt0) REVERT: C 100 ASN cc_start: 0.9160 (p0) cc_final: 0.8807 (p0) REVERT: E 50 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8427 (mt-10) REVERT: E 56 LYS cc_start: 0.9091 (ttpt) cc_final: 0.8512 (tmtt) REVERT: E 59 GLU cc_start: 0.7369 (pm20) cc_final: 0.7017 (pm20) REVERT: E 60 LEU cc_start: 0.8890 (mt) cc_final: 0.8688 (mt) REVERT: E 68 GLN cc_start: 0.9020 (tt0) cc_final: 0.8773 (tt0) REVERT: F 64 ASN cc_start: 0.9369 (m-40) cc_final: 0.8874 (m-40) REVERT: G 65 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8588 (tm-30) REVERT: G 72 ARG cc_start: 0.9168 (mtp-110) cc_final: 0.8817 (ttp80) REVERT: G 114 GLN cc_start: 0.8972 (mp10) cc_final: 0.8641 (mp10) REVERT: K 270 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6962 (mt) REVERT: L 231 GLU cc_start: 0.8659 (tp30) cc_final: 0.7906 (tm-30) outliers start: 15 outliers final: 10 residues processed: 199 average time/residue: 0.3783 time to fit residues: 95.5771 Evaluate side-chains 198 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 282 THR Chi-restraints excluded: chain L residue 283 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 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 = 0.3404 r_free = 0.3404 target = 0.072469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.056774 restraints weight = 98387.216| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.64 r_work: 0.2890 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13245 Z= 0.166 Angle : 0.629 7.916 19057 Z= 0.396 Chirality : 0.039 0.170 2181 Planarity : 0.004 0.053 1465 Dihedral : 30.028 86.458 3952 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.78 % Allowed : 14.52 % Favored : 83.70 % 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: 2.73 (0.29), residues: 845 helix: 2.55 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.10 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 252 TYR 0.009 0.001 TYR F 51 PHE 0.007 0.001 PHE E 67 TRP 0.009 0.001 TRP L 281 HIS 0.006 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.17 (13245) covalent geometry : angle 0.62928 / 0.40 (19057) hydrogen bonds : bond 0.04602 / 3.10 ( 855) hydrogen bonds : angle 3.36784 / 2.57 ( 2197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.493 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 125 GLN cc_start: 0.9253 (mt0) cc_final: 0.8665 (mt0) REVERT: B 53 GLU cc_start: 0.8727 (tp30) cc_final: 0.8495 (tp30) REVERT: B 92 ARG cc_start: 0.9401 (OUTLIER) cc_final: 0.8809 (ttp80) REVERT: C 100 ASN cc_start: 0.9147 (p0) cc_final: 0.8822 (p0) REVERT: E 50 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8314 (mt-10) REVERT: E 56 LYS cc_start: 0.9085 (ttpt) cc_final: 0.8479 (tmtt) REVERT: E 59 GLU cc_start: 0.7350 (pm20) cc_final: 0.6977 (pm20) REVERT: E 60 LEU cc_start: 0.8896 (mt) cc_final: 0.8644 (mt) REVERT: E 68 GLN cc_start: 0.8986 (tt0) cc_final: 0.8748 (tt0) REVERT: F 64 ASN cc_start: 0.9348 (m-40) cc_final: 0.8828 (m-40) REVERT: G 114 GLN cc_start: 0.8982 (mp10) cc_final: 0.8659 (mp10) REVERT: H 96 GLU cc_start: 0.9082 (mp0) cc_final: 0.8833 (mp0) REVERT: K 270 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7002 (mt) REVERT: L 231 GLU cc_start: 0.8598 (tp30) cc_final: 0.7827 (tm-30) outliers start: 13 outliers final: 8 residues processed: 205 average time/residue: 0.3772 time to fit residues: 98.5045 Evaluate side-chains 198 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain L residue 282 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 227 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 = 0.3385 r_free = 0.3385 target = 0.071525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.055827 restraints weight = 99022.322| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.64 r_work: 0.2867 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13245 Z= 0.231 Angle : 0.667 7.942 19057 Z= 0.410 Chirality : 0.040 0.169 2181 Planarity : 0.005 0.054 1465 Dihedral : 30.050 86.626 3952 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.64 % Allowed : 13.84 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.29), residues: 845 helix: 2.48 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.16 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 72 TYR 0.012 0.002 TYR F 88 PHE 0.010 0.001 PHE E 67 TRP 0.010 0.001 TRP L 281 HIS 0.011 0.002 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.23 (13245) covalent geometry : angle 0.66653 / 0.41 (19057) hydrogen bonds : bond 0.04820 / 3.26 ( 855) hydrogen bonds : angle 3.46882 / 2.64 ( 2197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.494 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: B 92 ARG cc_start: 0.9431 (OUTLIER) cc_final: 0.8818 (ttp80) REVERT: C 100 ASN cc_start: 0.9174 (p0) cc_final: 0.8806 (p0) REVERT: E 50 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8371 (mt-10) REVERT: E 56 LYS cc_start: 0.9103 (ttpt) cc_final: 0.8500 (tmtt) REVERT: E 59 GLU cc_start: 0.7416 (pm20) cc_final: 0.7060 (pm20) REVERT: E 65 LEU cc_start: 0.9274 (mt) cc_final: 0.8989 (tt) REVERT: E 68 GLN cc_start: 0.9023 (tt0) cc_final: 0.8798 (tt0) REVERT: F 64 ASN cc_start: 0.9371 (m-40) cc_final: 0.8865 (m-40) REVERT: G 65 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8610 (tm-30) REVERT: G 72 ARG cc_start: 0.9094 (mtp-110) cc_final: 0.8814 (ttp80) REVERT: G 114 GLN cc_start: 0.9012 (mp10) cc_final: 0.8705 (mp10) REVERT: K 270 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7006 (mt) REVERT: L 231 GLU cc_start: 0.8639 (tp30) cc_final: 0.7888 (tm-30) outliers start: 12 outliers final: 8 residues processed: 196 average time/residue: 0.3778 time to fit residues: 94.6936 Evaluate side-chains 194 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 184 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain L residue 282 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 31 optimal weight: 0.4980 chunk 96 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 66 ASN ** K 227 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 = 0.3407 r_free = 0.3407 target = 0.072600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.056822 restraints weight = 97855.819| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.64 r_work: 0.2889 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13245 Z= 0.155 Angle : 0.623 8.338 19057 Z= 0.391 Chirality : 0.038 0.165 2181 Planarity : 0.004 0.045 1465 Dihedral : 30.072 88.604 3952 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.64 % Allowed : 13.84 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.29), residues: 845 helix: 2.68 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.08 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 37 TYR 0.011 0.001 TYR F 88 PHE 0.008 0.001 PHE E 67 TRP 0.009 0.001 TRP L 281 HIS 0.005 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.16 (13245) covalent geometry : angle 0.62251 / 0.39 (19057) hydrogen bonds : bond 0.04452 / 3.00 ( 855) hydrogen bonds : angle 3.28816 / 2.51 ( 2197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.490 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 125 GLN cc_start: 0.9270 (mt0) cc_final: 0.8691 (mt0) REVERT: B 54 THR cc_start: 0.9201 (m) cc_final: 0.8921 (p) REVERT: B 92 ARG cc_start: 0.9378 (OUTLIER) cc_final: 0.8766 (ttp80) REVERT: C 100 ASN cc_start: 0.9169 (p0) cc_final: 0.8851 (p0) REVERT: D 60 LYS cc_start: 0.9288 (mmmm) cc_final: 0.9071 (mmmt) REVERT: E 50 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8347 (mt-10) REVERT: E 56 LYS cc_start: 0.9041 (ttpt) cc_final: 0.8451 (tmtt) REVERT: E 59 GLU cc_start: 0.7405 (pm20) cc_final: 0.7032 (pm20) REVERT: E 68 GLN cc_start: 0.8996 (tt0) cc_final: 0.8746 (tt0) REVERT: F 64 ASN cc_start: 0.9340 (m-40) cc_final: 0.8816 (m-40) REVERT: G 91 ASP cc_start: 0.8949 (t0) cc_final: 0.8712 (t0) REVERT: G 114 GLN cc_start: 0.9025 (mp10) cc_final: 0.8731 (mp10) REVERT: H 96 GLU cc_start: 0.9063 (mp0) cc_final: 0.8810 (mp0) REVERT: K 270 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6984 (mt) REVERT: L 231 GLU cc_start: 0.8611 (tp30) cc_final: 0.7825 (tm-30) outliers start: 12 outliers final: 7 residues processed: 204 average time/residue: 0.3828 time to fit residues: 99.9930 Evaluate side-chains 198 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 270 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN G 42 GLN ** K 227 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 = 0.3390 r_free = 0.3390 target = 0.071685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.056123 restraints weight = 99788.479| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.63 r_work: 0.2869 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13245 Z= 0.241 Angle : 0.662 7.435 19057 Z= 0.409 Chirality : 0.040 0.164 2181 Planarity : 0.005 0.046 1465 Dihedral : 30.080 88.602 3952 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.51 % Allowed : 14.93 % Favored : 83.56 % 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: 2.68 (0.29), residues: 845 helix: 2.52 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.12 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 72 TYR 0.010 0.001 TYR F 88 PHE 0.008 0.001 PHE E 67 TRP 0.010 0.001 TRP L 281 HIS 0.007 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.24 (13245) covalent geometry : angle 0.66161 / 0.41 (19057) hydrogen bonds : bond 0.04703 / 3.18 ( 855) hydrogen bonds : angle 3.46709 / 2.64 ( 2197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.489 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: A 125 GLN cc_start: 0.9302 (mt0) cc_final: 0.8720 (mt0) REVERT: B 92 ARG cc_start: 0.9410 (OUTLIER) cc_final: 0.8779 (ttp80) REVERT: C 100 ASN cc_start: 0.9182 (p0) cc_final: 0.8865 (p0) REVERT: D 60 LYS cc_start: 0.9343 (mmmm) cc_final: 0.9125 (mmmt) REVERT: E 50 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8382 (mt-10) REVERT: E 56 LYS cc_start: 0.9075 (ttpt) cc_final: 0.8483 (tmtt) REVERT: E 59 GLU cc_start: 0.7553 (pm20) cc_final: 0.7200 (pm20) REVERT: E 65 LEU cc_start: 0.9272 (mt) cc_final: 0.8993 (tt) REVERT: E 68 GLN cc_start: 0.9030 (tt0) cc_final: 0.8793 (tt0) REVERT: F 64 ASN cc_start: 0.9342 (m-40) cc_final: 0.8845 (m-40) REVERT: G 65 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8606 (tm-30) REVERT: G 72 ARG cc_start: 0.9093 (mtp-110) cc_final: 0.8797 (ttp80) REVERT: G 91 ASP cc_start: 0.8983 (t0) cc_final: 0.8752 (t0) REVERT: G 114 GLN cc_start: 0.9032 (mp10) cc_final: 0.8714 (mp10) REVERT: K 270 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7028 (mt) REVERT: L 231 GLU cc_start: 0.8629 (tp30) cc_final: 0.7882 (tm-30) outliers start: 11 outliers final: 9 residues processed: 193 average time/residue: 0.3868 time to fit residues: 95.1313 Evaluate side-chains 195 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain L residue 282 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 89 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** K 227 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 = 0.3400 r_free = 0.3400 target = 0.072231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.056578 restraints weight = 98466.705| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.63 r_work: 0.2886 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13245 Z= 0.167 Angle : 0.631 8.456 19057 Z= 0.394 Chirality : 0.038 0.161 2181 Planarity : 0.004 0.049 1465 Dihedral : 30.103 89.941 3952 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.64 % Allowed : 14.52 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.29), residues: 845 helix: 2.64 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.06 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 37 TYR 0.012 0.001 TYR F 88 PHE 0.009 0.001 PHE E 67 TRP 0.009 0.001 TRP L 281 HIS 0.005 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.17 (13245) covalent geometry : angle 0.63058 / 0.39 (19057) hydrogen bonds : bond 0.04459 / 3.00 ( 855) hydrogen bonds : angle 3.32689 / 2.54 ( 2197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.486 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: A 125 GLN cc_start: 0.9282 (mt0) cc_final: 0.8716 (mt0) REVERT: B 92 ARG cc_start: 0.9390 (OUTLIER) cc_final: 0.8786 (ttp80) REVERT: C 100 ASN cc_start: 0.9174 (p0) cc_final: 0.8848 (p0) REVERT: D 60 LYS cc_start: 0.9288 (mmmm) cc_final: 0.9084 (mmmt) REVERT: E 50 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8288 (mt-10) REVERT: E 56 LYS cc_start: 0.9068 (ttpt) cc_final: 0.8470 (tmtt) REVERT: E 59 GLU cc_start: 0.7553 (pm20) cc_final: 0.7202 (pm20) REVERT: E 68 GLN cc_start: 0.9000 (tt0) cc_final: 0.8750 (tt0) REVERT: F 64 ASN cc_start: 0.9360 (m-40) cc_final: 0.8842 (m-40) REVERT: G 65 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8623 (tm-30) REVERT: G 91 ASP cc_start: 0.8956 (t0) cc_final: 0.8719 (t0) REVERT: G 114 GLN cc_start: 0.9048 (mp10) cc_final: 0.8727 (mp10) REVERT: H 96 GLU cc_start: 0.9077 (mp0) cc_final: 0.8830 (mp0) REVERT: K 270 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6955 (mt) REVERT: L 231 GLU cc_start: 0.8597 (tp30) cc_final: 0.7761 (tm-30) outliers start: 12 outliers final: 9 residues processed: 202 average time/residue: 0.3612 time to fit residues: 93.6966 Evaluate side-chains 200 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain L residue 282 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 66 ASN ** K 227 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 = 0.3386 r_free = 0.3386 target = 0.071858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.056318 restraints weight = 98779.057| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.68 r_work: 0.2873 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13245 Z= 0.183 Angle : 0.636 8.270 19057 Z= 0.395 Chirality : 0.038 0.156 2181 Planarity : 0.004 0.050 1465 Dihedral : 30.102 89.263 3952 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.64 % Allowed : 14.79 % Favored : 83.56 % 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: 2.92 (0.29), residues: 845 helix: 2.70 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.04 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 37 TYR 0.012 0.001 TYR F 88 PHE 0.008 0.001 PHE A 67 TRP 0.009 0.001 TRP L 281 HIS 0.006 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.18 (13245) covalent geometry : angle 0.63575 / 0.40 (19057) hydrogen bonds : bond 0.04461 / 3.02 ( 855) hydrogen bonds : angle 3.31551 / 2.53 ( 2197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6258.12 seconds wall clock time: 106 minutes 45.92 seconds (6405.92 seconds total)