Starting phenix.real_space_refine on Thu Mar 5 11:59:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ssa_25406/03_2026/7ssa_25406.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ssa_25406/03_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_25406/03_2026/7ssa_25406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ssa_25406/03_2026/7ssa_25406.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ssa_25406/03_2026/7ssa_25406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ssa_25406/03_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-dev-5986/lib/python3.9/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: 3.86, 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: 1.77 Conformation dependent library (CDL) restraints added in 457.6 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: 3.87 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: 5.15 Time building geometry restraints manager: 2.60 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=" N ALA C 14 " pdb=" CA ALA C 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLN K 222 " pdb=" CA GLN K 222 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLN G 16 " pdb=" CA GLN G 16 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ARG D 36 " pdb=" CA ARG D 36 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N ARG H 36 " pdb=" CA ARG H 36 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 ... (remaining 23517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 39943 1.43 - 2.86: 2598 2.86 - 4.29: 77 4.29 - 5.73: 18 5.73 - 7.16: 1 Bond angle restraints: 42637 Sorted by residual: angle pdb=" N GLU K 229 " pdb=" CA GLU K 229 " pdb=" CB GLU K 229 " ideal model delta sigma weight residual 110.28 115.72 -5.44 1.55e+00 4.16e-01 1.23e+01 angle pdb=" C LEU C 35 " pdb=" N ARG C 36 " pdb=" CA ARG C 36 " ideal model delta sigma weight residual 120.44 116.51 3.93 1.36e+00 5.41e-01 8.37e+00 angle pdb=" CA GLU K 229 " pdb=" CB GLU K 229 " pdb=" CG GLU K 229 " ideal model delta sigma weight residual 114.10 119.60 -5.50 2.00e+00 2.50e-01 7.56e+00 angle pdb=" C3' DA I 23 " pdb=" C2' DA I 23 " pdb=" C1' DA I 23 " ideal model delta sigma weight residual 101.60 105.50 -3.90 1.50e+00 4.44e-01 6.78e+00 angle pdb=" C2' DT I -26 " pdb=" C1' DT I -26 " pdb=" N1 DT I -26 " ideal model delta sigma weight residual 113.50 117.30 -3.80 1.50e+00 4.44e-01 6.42e+00 ... (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 - 0.028: 1182 0.028 - 0.056: 589 0.056 - 0.083: 271 0.083 - 0.111: 115 0.111 - 0.139: 24 Chirality restraints: 2181 Sorted by residual: chirality pdb=" CA VAL F 21 " pdb=" N VAL F 21 " pdb=" C VAL F 21 " pdb=" CB VAL F 21 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.81e-01 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 -2.66 -2.53 -0.13 2.00e-01 2.50e+01 4.54e-01 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 -2.66 -2.53 -0.13 2.00e-01 2.50e+01 4.18e-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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.210 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 0.040 13245 Z= 0.246 Angle : 0.651 7.158 19057 Z= 0.405 Chirality : 0.042 0.139 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 covalent geometry : bond 0.00519 (13245) covalent geometry : angle 0.65091 (19057) hydrogen bonds : bond 0.09989 ( 855) hydrogen bonds : angle 3.97136 ( 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 : 0.481 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: 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: 0.7762 (t0) REVERT: C 100 ASN cc_start: 0.8292 (p0) cc_final: 0.7967 (p0) REVERT: D 91 THR cc_start: 0.8465 (p) cc_final: 0.8233 (p) REVERT: E 50 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7322 (mt-10) REVERT: E 87 SER cc_start: 0.9207 (p) cc_final: 0.8931 (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: 0.7494 (tm-30) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.4271 time to fit residues: 140.8192 Evaluate side-chains 204 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 66 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.056993 restraints weight = 98557.820| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.69 r_work: 0.2886 rms_B_bonded: 2.77 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: 0.8646 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13245 Z= 0.239 Angle : 0.635 4.848 19057 Z= 0.391 Chirality : 0.043 0.133 2181 Planarity : 0.005 0.043 1465 Dihedral : 29.645 85.172 3952 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.78 % Allowed : 9.59 % 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: 2.54 (0.29), residues: 845 helix: 2.40 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.04 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 235 TYR 0.011 0.001 TYR G 58 PHE 0.007 0.001 PHE E 67 TRP 0.011 0.002 TRP L 281 HIS 0.007 0.002 HIS K 227 Details of bonding type rmsd covalent geometry : bond 0.00510 (13245) covalent geometry : angle 0.63470 (19057) hydrogen bonds : bond 0.04532 ( 855) hydrogen bonds : angle 3.38260 ( 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 218 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 0.465 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: A 73 GLU cc_start: 0.9190 (tt0) cc_final: 0.8971 (tt0) REVERT: A 120 MET cc_start: 0.8884 (mtp) cc_final: 0.8487 (mtp) REVERT: C 100 ASN cc_start: 0.9133 (p0) cc_final: 0.8772 (p0) REVERT: E 50 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8441 (mt-10) REVERT: E 59 GLU cc_start: 0.7393 (pm20) cc_final: 0.7175 (pm20) REVERT: F 64 ASN cc_start: 0.9341 (m-40) cc_final: 0.8848 (m-40) REVERT: G 57 GLU cc_start: 0.9249 (tt0) cc_final: 0.9002 (tt0) REVERT: G 72 ARG cc_start: 0.9163 (mtp-110) cc_final: 0.8810 (ttp80) REVERT: K 232 ARG cc_start: 0.7255 (mmt90) cc_final: 0.6489 (mmp-170) REVERT: K 265 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7964 (tm-30) REVERT: K 270 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6977 (mt) REVERT: L 231 GLU cc_start: 0.8675 (tp30) cc_final: 0.7887 (tm-30) outliers start: 13 outliers final: 8 residues processed: 215 average time/residue: 0.4147 time to fit residues: 110.0477 Evaluate side-chains 202 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 66 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.071806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.056138 restraints weight = 98726.186| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.66 r_work: 0.2871 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13245 Z= 0.237 Angle : 0.621 4.688 19057 Z= 0.383 Chirality : 0.042 0.138 2181 Planarity : 0.004 0.036 1465 Dihedral : 29.699 84.196 3952 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.19 % Allowed : 11.10 % Favored : 86.71 % 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: 2.73 (0.29), residues: 845 helix: 2.54 (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 0.006 0.001 ARG C 37 TYR 0.010 0.001 TYR F 88 PHE 0.008 0.001 PHE B 61 TRP 0.011 0.001 TRP L 281 HIS 0.005 0.001 HIS K 227 Details of bonding type rmsd covalent geometry : bond 0.00505 (13245) covalent geometry : angle 0.62137 (19057) hydrogen bonds : bond 0.04368 ( 855) hydrogen bonds : angle 3.33696 ( 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 207 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.471 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: A 120 MET cc_start: 0.8940 (mtp) cc_final: 0.8523 (mtp) REVERT: B 54 THR cc_start: 0.9245 (m) cc_final: 0.8911 (p) REVERT: B 92 ARG cc_start: 0.9423 (OUTLIER) cc_final: 0.8795 (ttp80) REVERT: C 91 ASP cc_start: 0.8743 (t0) cc_final: 0.8501 (t0) REVERT: C 100 ASN cc_start: 0.9174 (p0) cc_final: 0.8813 (p0) REVERT: E 50 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8351 (mt-10) REVERT: E 55 GLN cc_start: 0.9180 (tt0) cc_final: 0.8969 (tt0) REVERT: E 59 GLU cc_start: 0.7472 (pm20) cc_final: 0.7201 (pm20) REVERT: E 68 GLN cc_start: 0.8992 (tt0) cc_final: 0.8773 (tt0) REVERT: F 64 ASN cc_start: 0.9383 (m-40) cc_final: 0.8868 (m-40) REVERT: G 72 ARG cc_start: 0.9163 (mtp-110) cc_final: 0.8798 (ttp80) REVERT: G 114 GLN cc_start: 0.9032 (mp10) cc_final: 0.8786 (mp10) REVERT: K 232 ARG cc_start: 0.7042 (mmt90) cc_final: 0.6401 (mmp-170) REVERT: K 270 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6863 (mt) REVERT: L 231 GLU cc_start: 0.8639 (tp30) cc_final: 0.8410 (tp30) outliers start: 16 outliers final: 10 residues processed: 204 average time/residue: 0.4183 time to fit residues: 105.1886 Evaluate side-chains 195 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 E residue 87 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 Chi-restraints excluded: chain L residue 283 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.073347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.057696 restraints weight = 99112.133| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.67 r_work: 0.2912 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13245 Z= 0.169 Angle : 0.591 6.128 19057 Z= 0.366 Chirality : 0.039 0.138 2181 Planarity : 0.004 0.041 1465 Dihedral : 29.592 85.671 3952 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.51 % Allowed : 12.19 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.29), residues: 845 helix: 2.85 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.91 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 36 TYR 0.010 0.001 TYR F 88 PHE 0.008 0.001 PHE A 67 TRP 0.008 0.001 TRP L 281 HIS 0.007 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00359 (13245) covalent geometry : angle 0.59087 (19057) hydrogen bonds : bond 0.03751 ( 855) hydrogen bonds : angle 3.08677 ( 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 203 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.472 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: A 120 MET cc_start: 0.8938 (mtp) cc_final: 0.8470 (mtp) REVERT: A 125 GLN cc_start: 0.9316 (mt0) cc_final: 0.8913 (mt0) REVERT: B 54 THR cc_start: 0.9210 (m) cc_final: 0.8948 (p) REVERT: B 92 ARG cc_start: 0.9373 (OUTLIER) cc_final: 0.8802 (ttp80) REVERT: C 91 ASP cc_start: 0.8699 (t0) cc_final: 0.8348 (t0) REVERT: C 100 ASN cc_start: 0.9181 (p0) cc_final: 0.8855 (p0) REVERT: D 60 LYS cc_start: 0.9292 (mmmm) cc_final: 0.9085 (mmmt) REVERT: E 50 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8357 (mt-10) REVERT: E 55 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8960 (tt0) REVERT: E 59 GLU cc_start: 0.7528 (pm20) cc_final: 0.7219 (pm20) REVERT: E 68 GLN cc_start: 0.8991 (tt0) cc_final: 0.8758 (tt0) REVERT: E 94 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8665 (mm-30) REVERT: F 64 ASN cc_start: 0.9357 (m-40) cc_final: 0.8842 (m-40) REVERT: G 114 GLN cc_start: 0.8996 (mp10) cc_final: 0.8720 (mp10) REVERT: K 232 ARG cc_start: 0.7136 (mmt90) cc_final: 0.6397 (mmp-170) REVERT: K 235 ARG cc_start: 0.6738 (tpt170) cc_final: 0.6515 (tpt170) REVERT: K 239 ASN cc_start: 0.7917 (m-40) cc_final: 0.7653 (m-40) REVERT: K 259 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8078 (tp) REVERT: L 231 GLU cc_start: 0.8622 (tp30) cc_final: 0.8415 (tp30) outliers start: 11 outliers final: 6 residues processed: 199 average time/residue: 0.4287 time to fit residues: 105.2623 Evaluate side-chains 196 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 187 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 55 GLN Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 259 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 66 ASN G 16 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 = 0.3374 r_free = 0.3374 target = 0.071395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.056041 restraints weight = 98462.486| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.67 r_work: 0.2858 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 13245 Z= 0.237 Angle : 0.613 5.182 19057 Z= 0.378 Chirality : 0.042 0.140 2181 Planarity : 0.004 0.033 1465 Dihedral : 29.682 90.283 3952 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.47 % Allowed : 11.64 % Favored : 85.89 % 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: 3.00 (0.29), residues: 845 helix: 2.73 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.93 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 36 TYR 0.012 0.001 TYR F 88 PHE 0.008 0.001 PHE B 61 TRP 0.010 0.001 TRP L 281 HIS 0.008 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00506 (13245) covalent geometry : angle 0.61296 (19057) hydrogen bonds : bond 0.04248 ( 855) hydrogen bonds : angle 3.29529 ( 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 202 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.501 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: A 120 MET cc_start: 0.9064 (mtp) cc_final: 0.8704 (mtp) REVERT: B 54 THR cc_start: 0.9220 (m) cc_final: 0.8908 (p) REVERT: C 91 ASP cc_start: 0.8750 (t0) cc_final: 0.8394 (t0) REVERT: C 100 ASN cc_start: 0.9244 (p0) cc_final: 0.8916 (p0) REVERT: E 50 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8419 (mt-10) REVERT: E 55 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8988 (tt0) REVERT: E 59 GLU cc_start: 0.7481 (pm20) cc_final: 0.7149 (pm20) REVERT: E 68 GLN cc_start: 0.9054 (tt0) cc_final: 0.8827 (tt0) REVERT: E 94 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8644 (mm-30) REVERT: F 64 ASN cc_start: 0.9368 (m-40) cc_final: 0.8828 (m-40) REVERT: F 79 LYS cc_start: 0.8900 (mmtp) cc_final: 0.8699 (mttp) REVERT: G 72 ARG cc_start: 0.9084 (mtp-110) cc_final: 0.8803 (ttp80) REVERT: G 114 GLN cc_start: 0.9067 (mp10) cc_final: 0.8736 (mp10) REVERT: K 232 ARG cc_start: 0.7059 (mmt90) cc_final: 0.6403 (mmp-170) REVERT: K 259 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8116 (tp) REVERT: K 270 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7113 (mt) REVERT: L 231 GLU cc_start: 0.8628 (tp30) cc_final: 0.8419 (tp30) outliers start: 18 outliers final: 11 residues processed: 197 average time/residue: 0.4419 time to fit residues: 107.6649 Evaluate side-chains 193 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 D residue 44 ILE Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain L residue 237 ASN Chi-restraints excluded: chain L residue 282 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 1.9990 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: 0.7980 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 227 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 = 0.3390 r_free = 0.3390 target = 0.072092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.056799 restraints weight = 98780.807| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.65 r_work: 0.2880 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13245 Z= 0.192 Angle : 0.600 6.601 19057 Z= 0.370 Chirality : 0.040 0.140 2181 Planarity : 0.004 0.036 1465 Dihedral : 29.692 91.378 3952 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.64 % Allowed : 12.19 % Favored : 86.16 % 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: 3.17 (0.29), residues: 845 helix: 2.87 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.93 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 36 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 0.008 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00408 (13245) covalent geometry : angle 0.59967 (19057) hydrogen bonds : bond 0.03947 ( 855) hydrogen bonds : angle 3.17709 ( 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 200 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.738 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 59 GLU cc_start: 0.8842 (pm20) cc_final: 0.8435 (pm20) REVERT: A 120 MET cc_start: 0.9050 (mtp) cc_final: 0.8694 (mtp) REVERT: A 125 GLN cc_start: 0.9330 (mt0) cc_final: 0.8811 (mt0) REVERT: B 54 THR cc_start: 0.9234 (m) cc_final: 0.8966 (p) REVERT: B 92 ARG cc_start: 0.9394 (OUTLIER) cc_final: 0.8798 (ttp80) REVERT: C 91 ASP cc_start: 0.8721 (t0) cc_final: 0.8325 (t0) REVERT: C 100 ASN cc_start: 0.9241 (p0) cc_final: 0.8920 (p0) REVERT: E 50 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8428 (mt-10) REVERT: E 59 GLU cc_start: 0.7514 (pm20) cc_final: 0.7166 (pm20) REVERT: E 68 GLN cc_start: 0.9037 (tt0) cc_final: 0.8805 (tt0) REVERT: E 94 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8658 (mm-30) REVERT: F 64 ASN cc_start: 0.9370 (m-40) cc_final: 0.8845 (m-40) REVERT: F 79 LYS cc_start: 0.8909 (mmtp) cc_final: 0.8707 (mttp) REVERT: G 114 GLN cc_start: 0.9086 (mp10) cc_final: 0.8722 (mp10) REVERT: K 259 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8067 (tp) REVERT: K 270 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7084 (mt) REVERT: L 231 GLU cc_start: 0.8616 (tp30) cc_final: 0.8412 (tp30) outliers start: 12 outliers final: 7 residues processed: 196 average time/residue: 0.4280 time to fit residues: 104.3347 Evaluate side-chains 196 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER 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 65 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 270 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 0.0060 chunk 59 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3389 r_free = 0.3389 target = 0.071953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.056798 restraints weight = 98763.867| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.63 r_work: 0.2881 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13245 Z= 0.197 Angle : 0.601 6.154 19057 Z= 0.370 Chirality : 0.040 0.141 2181 Planarity : 0.004 0.034 1465 Dihedral : 29.706 92.897 3952 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.78 % Allowed : 12.47 % Favored : 85.75 % 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: 3.20 (0.29), residues: 845 helix: 2.90 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.96 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 37 TYR 0.011 0.001 TYR F 88 PHE 0.007 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 covalent geometry : bond 0.00420 (13245) covalent geometry : angle 0.60083 (19057) hydrogen bonds : bond 0.03912 ( 855) hydrogen bonds : angle 3.17112 ( 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 202 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 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: 0.9046 (mtp) cc_final: 0.8687 (mtp) REVERT: A 125 GLN cc_start: 0.9331 (mt0) cc_final: 0.8803 (mt0) REVERT: B 54 THR cc_start: 0.9218 (m) cc_final: 0.8938 (p) REVERT: B 92 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.8803 (ttp80) REVERT: C 91 ASP cc_start: 0.8668 (t0) cc_final: 0.8207 (t0) REVERT: C 100 ASN cc_start: 0.9258 (p0) cc_final: 0.8951 (p0) REVERT: E 50 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8422 (mt-10) REVERT: E 59 GLU cc_start: 0.7495 (pm20) cc_final: 0.7141 (pm20) REVERT: E 68 GLN cc_start: 0.9038 (tt0) cc_final: 0.8822 (tt0) REVERT: E 94 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8699 (mm-30) REVERT: F 64 ASN cc_start: 0.9354 (m-40) cc_final: 0.8831 (m-40) REVERT: F 79 LYS cc_start: 0.8906 (mmtp) cc_final: 0.8683 (mttp) REVERT: G 72 ARG cc_start: 0.9177 (mtp-110) cc_final: 0.8827 (ttp80) REVERT: G 91 ASP cc_start: 0.9045 (t0) cc_final: 0.8519 (t0) REVERT: G 114 GLN cc_start: 0.9093 (mp10) cc_final: 0.8756 (mp10) REVERT: K 232 ARG cc_start: 0.7109 (mmt90) cc_final: 0.6428 (mmp-170) outliers start: 13 outliers final: 10 residues processed: 200 average time/residue: 0.4251 time to fit residues: 105.9481 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 : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER 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 E residue 65 LEU Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain L residue 237 ASN 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: 2.9990 chunk 75 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 227 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 = 0.3380 r_free = 0.3380 target = 0.071496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.056313 restraints weight = 98532.058| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.64 r_work: 0.2871 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3649 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= 0.213 Angle : 0.608 6.413 19057 Z= 0.374 Chirality : 0.041 0.142 2181 Planarity : 0.004 0.034 1465 Dihedral : 29.743 93.096 3952 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.64 % Allowed : 12.74 % Favored : 85.62 % 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: 3.18 (0.29), residues: 845 helix: 2.89 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.99 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 235 TYR 0.011 0.001 TYR F 88 PHE 0.007 0.001 PHE E 67 TRP 0.010 0.001 TRP L 281 HIS 0.004 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00454 (13245) covalent geometry : angle 0.60820 (19057) hydrogen bonds : bond 0.04019 ( 855) hydrogen bonds : angle 3.20185 ( 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 198 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.502 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 59 GLU cc_start: 0.8866 (pm20) cc_final: 0.8562 (pm20) REVERT: A 120 MET cc_start: 0.9040 (mtp) cc_final: 0.8708 (mtp) REVERT: A 125 GLN cc_start: 0.9351 (mt0) cc_final: 0.8823 (mt0) REVERT: B 54 THR cc_start: 0.9207 (m) cc_final: 0.8889 (p) REVERT: B 92 ARG cc_start: 0.9403 (OUTLIER) cc_final: 0.8801 (ttp80) REVERT: C 91 ASP cc_start: 0.8674 (t0) cc_final: 0.8213 (t0) REVERT: C 100 ASN cc_start: 0.9260 (p0) cc_final: 0.8963 (p0) REVERT: E 50 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8397 (mt-10) REVERT: E 59 GLU cc_start: 0.7524 (pm20) cc_final: 0.7160 (pm20) REVERT: E 68 GLN cc_start: 0.9044 (tt0) cc_final: 0.8826 (tt0) REVERT: E 94 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8710 (mm-30) REVERT: F 79 LYS cc_start: 0.8866 (mmtp) cc_final: 0.8650 (mttp) REVERT: G 65 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8587 (tm-30) REVERT: G 91 ASP cc_start: 0.9053 (t0) cc_final: 0.8689 (t0) REVERT: G 114 GLN cc_start: 0.9089 (mp10) cc_final: 0.8766 (mp10) REVERT: K 232 ARG cc_start: 0.7247 (mmt90) cc_final: 0.6515 (mmp-170) REVERT: K 259 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8090 (tp) outliers start: 12 outliers final: 10 residues processed: 196 average time/residue: 0.4101 time to fit residues: 100.1315 Evaluate side-chains 196 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER 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 E residue 65 LEU Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain L residue 237 ASN Chi-restraints excluded: chain L residue 282 THR 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: 5.9990 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 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 = 0.3361 r_free = 0.3361 target = 0.070617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.055374 restraints weight = 99743.032| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.65 r_work: 0.2846 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13245 Z= 0.249 Angle : 0.629 5.863 19057 Z= 0.384 Chirality : 0.043 0.141 2181 Planarity : 0.004 0.034 1465 Dihedral : 29.850 92.807 3952 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.64 % Allowed : 13.70 % Favored : 84.66 % 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: 2.99 (0.29), residues: 845 helix: 2.76 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.11 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 37 TYR 0.016 0.002 TYR L 266 PHE 0.007 0.001 PHE E 67 TRP 0.011 0.001 TRP L 281 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00532 (13245) covalent geometry : angle 0.62872 (19057) hydrogen bonds : bond 0.04297 ( 855) hydrogen bonds : angle 3.32715 ( 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 197 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 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: A 59 GLU cc_start: 0.8810 (pm20) cc_final: 0.8467 (pm20) REVERT: A 120 MET cc_start: 0.9063 (mtp) cc_final: 0.8672 (mtp) REVERT: A 125 GLN cc_start: 0.9353 (mt0) cc_final: 0.8915 (mt0) REVERT: B 54 THR cc_start: 0.9254 (m) cc_final: 0.8906 (p) REVERT: B 92 ARG cc_start: 0.9420 (OUTLIER) cc_final: 0.8801 (ttp80) REVERT: C 91 ASP cc_start: 0.8697 (t0) cc_final: 0.8305 (t0) REVERT: C 100 ASN cc_start: 0.9266 (p0) cc_final: 0.8968 (p0) REVERT: E 50 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8380 (mt-10) REVERT: E 59 GLU cc_start: 0.7538 (pm20) cc_final: 0.7169 (pm20) REVERT: E 68 GLN cc_start: 0.9117 (tt0) cc_final: 0.8910 (tt0) REVERT: E 94 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8763 (mm-30) REVERT: F 79 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8625 (mttp) REVERT: G 65 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8560 (tm-30) REVERT: G 72 ARG cc_start: 0.9197 (mtp-110) cc_final: 0.8842 (ttp80) REVERT: G 91 ASP cc_start: 0.9055 (t0) cc_final: 0.8719 (t0) REVERT: G 114 GLN cc_start: 0.9104 (mp10) cc_final: 0.8774 (mp10) REVERT: K 232 ARG cc_start: 0.7275 (mmt90) cc_final: 0.6608 (mmp-170) REVERT: K 266 TYR cc_start: 0.7690 (t80) cc_final: 0.7415 (t80) outliers start: 12 outliers final: 11 residues processed: 195 average time/residue: 0.4432 time to fit residues: 106.8925 Evaluate side-chains 195 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER 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 E residue 65 LEU Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain L residue 237 ASN 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: 3.9990 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 227 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 = 0.3412 r_free = 0.3412 target = 0.072920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.057739 restraints weight = 98424.887| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.64 r_work: 0.2904 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13245 Z= 0.158 Angle : 0.599 6.641 19057 Z= 0.368 Chirality : 0.038 0.140 2181 Planarity : 0.004 0.067 1465 Dihedral : 29.737 91.401 3952 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.37 % Allowed : 13.97 % Favored : 84.66 % 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: 3.41 (0.29), residues: 845 helix: 3.08 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.03 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 102 TYR 0.012 0.001 TYR L 266 PHE 0.009 0.001 PHE A 67 TRP 0.007 0.001 TRP L 281 HIS 0.004 0.001 HIS K 227 Details of bonding type rmsd covalent geometry : bond 0.00344 (13245) covalent geometry : angle 0.59907 (19057) hydrogen bonds : bond 0.03639 ( 855) hydrogen bonds : angle 3.05404 ( 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: 10 poor density : 194 time to evaluate : 0.522 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 59 GLU cc_start: 0.8792 (pm20) cc_final: 0.8413 (pm20) REVERT: A 120 MET cc_start: 0.9000 (mtp) cc_final: 0.8659 (mtp) REVERT: A 125 GLN cc_start: 0.9314 (mt0) cc_final: 0.8864 (mt0) REVERT: B 54 THR cc_start: 0.9180 (m) cc_final: 0.8908 (p) REVERT: B 92 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.8818 (ttp80) REVERT: C 91 ASP cc_start: 0.8575 (t0) cc_final: 0.8096 (t0) REVERT: C 100 ASN cc_start: 0.9244 (p0) cc_final: 0.8966 (p0) REVERT: C 105 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8711 (mm-40) REVERT: E 59 GLU cc_start: 0.7636 (pm20) cc_final: 0.7269 (pm20) REVERT: E 68 GLN cc_start: 0.9018 (tt0) cc_final: 0.8800 (tt0) REVERT: E 94 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8687 (mm-30) REVERT: F 64 ASN cc_start: 0.9330 (m-40) cc_final: 0.8817 (m-40) REVERT: G 72 ARG cc_start: 0.9168 (mtp-110) cc_final: 0.8822 (ttp80) REVERT: G 91 ASP cc_start: 0.9055 (t0) cc_final: 0.8683 (t0) REVERT: G 114 GLN cc_start: 0.9088 (mp10) cc_final: 0.8779 (mp10) REVERT: H 37 LYS cc_start: 0.9149 (mttp) cc_final: 0.8825 (ptpp) REVERT: K 259 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8015 (tp) REVERT: K 266 TYR cc_start: 0.7657 (t80) cc_final: 0.7397 (t80) outliers start: 10 outliers final: 7 residues processed: 202 average time/residue: 0.4265 time to fit residues: 107.6508 Evaluate side-chains 201 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER 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 65 LEU Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain L residue 237 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 67 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.073437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.058127 restraints weight = 98941.265| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.67 r_work: 0.2921 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13245 Z= 0.160 Angle : 0.596 6.106 19057 Z= 0.366 Chirality : 0.038 0.139 2181 Planarity : 0.004 0.063 1465 Dihedral : 29.643 88.969 3952 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.37 % Allowed : 14.38 % Favored : 84.25 % 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: 3.52 (0.29), residues: 845 helix: 3.15 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.99 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 102 TYR 0.015 0.001 TYR H 86 PHE 0.007 0.001 PHE E 67 TRP 0.007 0.001 TRP L 281 HIS 0.003 0.001 HIS K 227 Details of bonding type rmsd covalent geometry : bond 0.00345 (13245) covalent geometry : angle 0.59572 (19057) hydrogen bonds : bond 0.03605 ( 855) hydrogen bonds : angle 3.02043 ( 2197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6504.83 seconds wall clock time: 110 minutes 40.24 seconds (6640.24 seconds total)