Starting phenix.real_space_refine on Wed Aug 5 11:02:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j91_36084/08_2026/8j91_36084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j91_36084/08_2026/8j91_36084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j91_36084/08_2026/8j91_36084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j91_36084/08_2026/8j91_36084.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j91_36084/08_2026/8j91_36084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j91_36084/08_2026/8j91_36084.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 226 5.49 5 S 10 5.16 5 C 5557 2.51 5 N 1843 2.21 5 O 2308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9944 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 598 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 665 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 688 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "D" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "E" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 694 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "I" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2301 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Chain: "J" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2332 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Time building chain proxies: 1.88, per 1000 atoms: 0.19 Number of scatterers: 9944 At special positions: 0 Unit cell: (119.78, 118.72, 101.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 226 15.00 O 2308 8.00 N 1843 7.00 C 5557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 212.7 milliseconds 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 75.2% alpha, 2.9% beta 79 base pairs and 200 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.868A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.605A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.894A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.537A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.776A pdb=" N ALA C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 57 through 74 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.538A pdb=" N LYS C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.724A pdb=" N GLN D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 108 removed outlier: 3.649A pdb=" N LEU D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 128 through 149 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.676A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.902A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.656A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 removed outlier: 3.539A pdb=" N ALA G 22 " --> pdb=" O ARG G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 48 through 74 removed outlier: 3.893A pdb=" N ALA G 54 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 removed outlier: 3.778A pdb=" N ILE G 84 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN G 85 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 99 Processing helix chain 'H' and resid 62 through 74 Processing helix chain 'H' and resid 80 through 109 Processing helix chain 'H' and resid 115 through 127 Processing helix chain 'H' and resid 128 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.075A 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.468A pdb=" N ARG C 43 " --> pdb=" O ILE D 114 " (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 102 through 103 removed outlier: 6.788A 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: 7.073A 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: 7.291A pdb=" N ARG G 43 " --> pdb=" O ILE H 114 " (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 79 367 hydrogen bonds defined for protein. 1089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 198 hydrogen bonds 396 hydrogen bond angles 0 basepair planarities 79 basepair parallelities 200 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 4 1.21 - 1.36: 2977 1.36 - 1.51: 4403 1.51 - 1.66: 3171 1.66 - 1.81: 18 Bond restraints: 10573 Sorted by residual: bond pdb=" C6 DG I -52 " pdb=" O6 DG I -52 " ideal model delta sigma weight residual 1.237 1.065 0.172 9.00e-03 1.23e+04 3.66e+02 bond pdb=" C4 DC J 52 " pdb=" N4 DC J 52 " ideal model delta sigma weight residual 1.335 1.187 0.148 9.00e-03 1.23e+04 2.69e+02 bond pdb=" C3' DA I 24 " pdb=" C2' DA I 24 " ideal model delta sigma weight residual 1.516 1.597 -0.081 8.00e-03 1.56e+04 1.03e+02 bond pdb=" N3 DC J 52 " pdb=" C4 DC J 52 " ideal model delta sigma weight residual 1.335 1.272 0.063 7.00e-03 2.04e+04 8.19e+01 bond pdb=" C3' DC J 24 " pdb=" C2' DC J 24 " ideal model delta sigma weight residual 1.516 1.448 0.068 8.00e-03 1.56e+04 7.29e+01 ... (remaining 10568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.26: 15182 6.26 - 12.53: 52 12.53 - 18.79: 3 18.79 - 25.05: 1 25.05 - 31.31: 4 Bond angle restraints: 15242 Sorted by residual: angle pdb=" C5 DG I -52 " pdb=" C6 DG I -52 " pdb=" O6 DG I -52 " ideal model delta sigma weight residual 128.60 118.85 9.75 6.00e-01 2.78e+00 2.64e+02 angle pdb=" N3 DC J 52 " pdb=" C4 DC J 52 " pdb=" N4 DC J 52 " ideal model delta sigma weight residual 118.00 129.00 -11.00 7.00e-01 2.04e+00 2.47e+02 angle pdb=" N4 DC J 52 " pdb=" C4 DC J 52 " pdb=" C5 DC J 52 " ideal model delta sigma weight residual 120.20 109.45 10.75 7.00e-01 2.04e+00 2.36e+02 angle pdb=" O3' DA I 24 " pdb=" P DG I 25 " pdb=" O5' DG I 25 " ideal model delta sigma weight residual 104.00 131.03 -27.03 1.90e+00 2.77e-01 2.02e+02 angle pdb=" O4' DA I 24 " pdb=" C1' DA I 24 " pdb=" N9 DA I 24 " ideal model delta sigma weight residual 108.00 117.24 -9.24 7.00e-01 2.04e+00 1.74e+02 ... (remaining 15237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.97: 4661 32.97 - 65.95: 1057 65.95 - 98.92: 34 98.92 - 131.89: 2 131.89 - 164.86: 2 Dihedral angle restraints: 5756 sinusoidal: 3800 harmonic: 1956 Sorted by residual: dihedral pdb=" C4' DA I 24 " pdb=" C3' DA I 24 " pdb=" O3' DA I 24 " pdb=" P DG I 25 " ideal model delta sinusoidal sigma weight residual 220.00 55.14 164.86 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 58.65 161.35 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA ASP C 100 " pdb=" CB ASP C 100 " pdb=" CG ASP C 100 " pdb=" OD1 ASP C 100 " ideal model delta sinusoidal sigma weight residual -30.00 -88.66 58.66 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 5753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1526 0.114 - 0.229: 207 0.229 - 0.343: 8 0.343 - 0.458: 5 0.458 - 0.572: 3 Chirality restraints: 1749 Sorted by residual: chirality pdb=" C3' DA I 24 " pdb=" C4' DA I 24 " pdb=" O3' DA I 24 " pdb=" C2' DA I 24 " both_signs ideal model delta sigma weight residual False -2.73 -3.30 0.57 2.00e-01 2.50e+01 8.18e+00 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.22 -0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" P DT J 25 " pdb=" OP1 DT J 25 " pdb=" OP2 DT J 25 " pdb=" O5' DT J 25 " both_signs ideal model delta sigma weight residual True 2.34 -1.86 0.47 2.00e-01 2.50e+01 5.53e+00 ... (remaining 1746 not shown) Planarity restraints: 1143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 57 " -0.174 2.00e-02 2.50e+03 9.24e-02 2.56e+02 pdb=" N9 DG J 57 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DG J 57 " 0.163 2.00e-02 2.50e+03 pdb=" N7 DG J 57 " 0.123 2.00e-02 2.50e+03 pdb=" C5 DG J 57 " -0.034 2.00e-02 2.50e+03 pdb=" C6 DG J 57 " -0.072 2.00e-02 2.50e+03 pdb=" O6 DG J 57 " -0.107 2.00e-02 2.50e+03 pdb=" N1 DG J 57 " -0.021 2.00e-02 2.50e+03 pdb=" C2 DG J 57 " 0.031 2.00e-02 2.50e+03 pdb=" N2 DG J 57 " 0.101 2.00e-02 2.50e+03 pdb=" N3 DG J 57 " 0.024 2.00e-02 2.50e+03 pdb=" C4 DG J 57 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -5 " -0.211 2.00e-02 2.50e+03 9.46e-02 2.46e+02 pdb=" N9 DA I -5 " 0.028 2.00e-02 2.50e+03 pdb=" C8 DA I -5 " 0.102 2.00e-02 2.50e+03 pdb=" N7 DA I -5 " 0.092 2.00e-02 2.50e+03 pdb=" C5 DA I -5 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DA I -5 " -0.051 2.00e-02 2.50e+03 pdb=" N6 DA I -5 " -0.143 2.00e-02 2.50e+03 pdb=" N1 DA I -5 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -5 " 0.081 2.00e-02 2.50e+03 pdb=" N3 DA I -5 " 0.060 2.00e-02 2.50e+03 pdb=" C4 DA I -5 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -21 " -0.144 2.00e-02 2.50e+03 8.09e-02 1.96e+02 pdb=" N9 DG J -21 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG J -21 " 0.136 2.00e-02 2.50e+03 pdb=" N7 DG J -21 " 0.119 2.00e-02 2.50e+03 pdb=" C5 DG J -21 " -0.023 2.00e-02 2.50e+03 pdb=" C6 DG J -21 " -0.060 2.00e-02 2.50e+03 pdb=" O6 DG J -21 " -0.095 2.00e-02 2.50e+03 pdb=" N1 DG J -21 " -0.028 2.00e-02 2.50e+03 pdb=" C2 DG J -21 " 0.035 2.00e-02 2.50e+03 pdb=" N2 DG J -21 " 0.095 2.00e-02 2.50e+03 pdb=" N3 DG J -21 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DG J -21 " -0.021 2.00e-02 2.50e+03 ... (remaining 1140 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 225 2.68 - 3.23: 8262 3.23 - 3.79: 17170 3.79 - 4.34: 23603 4.34 - 4.90: 34329 Nonbonded interactions: 83589 Sorted by model distance: nonbonded pdb=" C2' DA I 24 " pdb=" OP1 DG I 25 " model vdw 2.122 3.440 nonbonded pdb=" C4' DA I 24 " pdb=" OP1 DG I 25 " model vdw 2.163 3.470 nonbonded pdb=" O LEU G 86 " pdb=" ND2 ASN G 90 " model vdw 2.205 3.120 nonbonded pdb=" C3' DA I 24 " pdb=" OP1 DG I 25 " model vdw 2.229 2.776 nonbonded pdb=" NZ LYS G 36 " pdb=" OP2 DA I 39 " model vdw 2.297 3.120 ... (remaining 83584 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' selection = (chain 'E' and resid 61 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 106) } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.620 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.011 0.172 10573 Z= 1.206 Angle : 1.559 31.314 15242 Z= 1.579 Chirality : 0.076 0.572 1749 Planarity : 0.015 0.095 1143 Dihedral : 26.616 164.864 4492 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.18 % Allowed : 0.54 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.31), residues: 662 helix: 1.58 (0.23), residues: 488 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 116 TYR 0.017 0.002 TYR D 65 PHE 0.014 0.002 PHE G 26 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01137 / 1.21 (10573) covalent geometry : angle 1.55882 / 1.58 (15242) hydrogen bonds : bond 0.18380 / 12.62 ( 565) hydrogen bonds : angle 5.31683 / 3.87 ( 1485) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7851 (mmtm) REVERT: D 84 MET cc_start: 0.7773 (mmp) cc_final: 0.7543 (mmt) REVERT: H 110 LYS cc_start: 0.8022 (mppt) cc_final: 0.7798 (mmtp) REVERT: H 141 LYS cc_start: 0.8351 (ttpp) cc_final: 0.8140 (ttmm) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.9054 time to fit residues: 127.1128 Evaluate side-chains 78 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 113 HIS B 27 GLN C 74 ASN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.183450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136057 restraints weight = 10682.951| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.26 r_work: 0.3207 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10573 Z= 0.158 Angle : 0.908 33.227 15242 Z= 0.464 Chirality : 0.060 1.007 1749 Planarity : 0.005 0.046 1143 Dihedral : 30.654 164.580 3192 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.62 % Allowed : 10.05 % Favored : 88.33 % 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: 2.11 (0.32), residues: 662 helix: 2.00 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -0.48 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 89 TYR 0.014 0.002 TYR F 51 PHE 0.007 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.16 (10573) covalent geometry : angle 0.90822 / 0.46 (15242) hydrogen bonds : bond 0.05870 / 3.93 ( 565) hydrogen bonds : angle 3.35585 / 2.45 ( 1485) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.276 Fit side-chains REVERT: A 129 ARG cc_start: 0.8199 (ttt180) cc_final: 0.7966 (ttt90) REVERT: B 44 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8380 (mtpp) REVERT: B 79 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8213 (mmtm) REVERT: C 73 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6718 (t0) REVERT: D 104 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7889 (mtmt) REVERT: H 93 ASP cc_start: 0.8370 (t70) cc_final: 0.7898 (t70) REVERT: H 96 GLU cc_start: 0.8265 (tp30) cc_final: 0.7701 (tp30) outliers start: 9 outliers final: 2 residues processed: 86 average time/residue: 0.8272 time to fit residues: 74.9393 Evaluate side-chains 79 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain H residue 64 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 0.0570 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 93 GLN G 74 ASN G 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.177590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.128681 restraints weight = 10634.429| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.23 r_work: 0.3088 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10573 Z= 0.185 Angle : 0.865 36.829 15242 Z= 0.432 Chirality : 0.050 0.434 1749 Planarity : 0.006 0.054 1143 Dihedral : 31.100 162.799 3192 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.41 % Allowed : 10.59 % Favored : 86.00 % 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: 1.98 (0.31), residues: 662 helix: 1.88 (0.23), residues: 501 sheet: None (None), residues: 0 loop : -0.43 (0.42), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 117 TYR 0.023 0.003 TYR F 51 PHE 0.013 0.002 PHE A 104 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (10573) covalent geometry : angle 0.86537 / 0.43 (15242) hydrogen bonds : bond 0.05992 / 4.04 ( 565) hydrogen bonds : angle 3.19826 / 2.33 ( 1485) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.285 Fit side-chains REVERT: A 76 GLN cc_start: 0.8162 (tt0) cc_final: 0.7759 (pt0) REVERT: B 79 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8312 (mmtp) REVERT: C 73 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6724 (t0) REVERT: C 103 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8412 (mm) REVERT: D 137 SER cc_start: 0.8733 (m) cc_final: 0.8508 (m) REVERT: F 79 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8191 (mttm) REVERT: H 63 LYS cc_start: 0.8271 (mptt) cc_final: 0.7106 (ttpp) REVERT: H 93 ASP cc_start: 0.8468 (t70) cc_final: 0.8041 (t70) outliers start: 19 outliers final: 6 residues processed: 107 average time/residue: 0.8264 time to fit residues: 92.8888 Evaluate side-chains 97 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 126 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 82 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN F 93 GLN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.176634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125523 restraints weight = 10643.118| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.31 r_work: 0.3080 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10573 Z= 0.185 Angle : 0.754 30.856 15242 Z= 0.394 Chirality : 0.064 1.830 1749 Planarity : 0.005 0.051 1143 Dihedral : 31.075 164.015 3192 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.51 % Allowed : 14.90 % Favored : 82.59 % 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: 2.09 (0.31), residues: 662 helix: 1.97 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -0.47 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 63 TYR 0.016 0.002 TYR F 51 PHE 0.010 0.002 PHE E 67 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (10573) covalent geometry : angle 0.75378 / 0.39 (15242) hydrogen bonds : bond 0.05488 / 3.70 ( 565) hydrogen bonds : angle 3.15383 / 2.30 ( 1485) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.270 Fit side-chains REVERT: A 76 GLN cc_start: 0.8153 (tt0) cc_final: 0.7709 (pt0) REVERT: B 79 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8260 (mmtp) REVERT: C 73 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6750 (t0) REVERT: C 103 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8369 (mm) REVERT: D 108 TYR cc_start: 0.7275 (m-10) cc_final: 0.6803 (t80) REVERT: H 63 LYS cc_start: 0.8163 (mptt) cc_final: 0.6992 (ttpp) REVERT: H 93 ASP cc_start: 0.8507 (t70) cc_final: 0.8080 (t70) outliers start: 14 outliers final: 10 residues processed: 96 average time/residue: 0.8014 time to fit residues: 80.9965 Evaluate side-chains 99 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 30.0000 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 76 optimal weight: 40.0000 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.177974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.127252 restraints weight = 10653.777| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.37 r_work: 0.3091 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10573 Z= 0.135 Angle : 0.707 27.991 15242 Z= 0.375 Chirality : 0.066 2.027 1749 Planarity : 0.004 0.051 1143 Dihedral : 31.030 163.729 3192 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.69 % Allowed : 15.98 % Favored : 81.33 % 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: 2.48 (0.31), residues: 662 helix: 2.25 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -0.34 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 89 TYR 0.013 0.002 TYR H 108 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.13 (10573) covalent geometry : angle 0.70695 / 0.37 (15242) hydrogen bonds : bond 0.04811 / 3.26 ( 565) hydrogen bonds : angle 3.11022 / 2.27 ( 1485) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8180 (tt0) cc_final: 0.7743 (pt0) REVERT: B 79 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8246 (mmtp) REVERT: C 73 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6815 (t0) REVERT: D 108 TYR cc_start: 0.7292 (m-10) cc_final: 0.6831 (t80) REVERT: D 147 THR cc_start: 0.7929 (m) cc_final: 0.7669 (m) REVERT: H 63 LYS cc_start: 0.8048 (mptt) cc_final: 0.7078 (ttpp) outliers start: 15 outliers final: 6 residues processed: 100 average time/residue: 0.8226 time to fit residues: 86.4023 Evaluate side-chains 96 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 64 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 65 optimal weight: 40.0000 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN E 68 GLN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.174029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122557 restraints weight = 10621.517| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.33 r_work: 0.3036 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10573 Z= 0.254 Angle : 0.775 24.008 15242 Z= 0.409 Chirality : 0.071 2.118 1749 Planarity : 0.007 0.072 1143 Dihedral : 31.157 163.998 3192 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.87 % Allowed : 15.26 % Favored : 81.87 % 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: 1.85 (0.31), residues: 662 helix: 1.85 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -0.73 (0.39), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 89 TYR 0.015 0.003 TYR F 51 PHE 0.009 0.002 PHE G 26 HIS 0.005 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (10573) covalent geometry : angle 0.77488 / 0.41 (15242) hydrogen bonds : bond 0.06476 / 4.35 ( 565) hydrogen bonds : angle 3.27569 / 2.39 ( 1485) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8194 (tt0) cc_final: 0.7738 (pt0) REVERT: B 79 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8188 (mmtp) REVERT: C 73 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6674 (t0) REVERT: C 95 SER cc_start: 0.7949 (t) cc_final: 0.7743 (p) REVERT: C 103 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8536 (mm) REVERT: D 108 TYR cc_start: 0.7436 (m-10) cc_final: 0.6842 (t80) REVERT: D 111 LYS cc_start: 0.7612 (tttt) cc_final: 0.7357 (tttt) REVERT: E 122 LYS cc_start: 0.8581 (ptmt) cc_final: 0.8344 (ptmt) REVERT: H 63 LYS cc_start: 0.8107 (mptt) cc_final: 0.6996 (ttpp) outliers start: 16 outliers final: 12 residues processed: 99 average time/residue: 0.8642 time to fit residues: 89.6378 Evaluate side-chains 100 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN F 93 GLN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.175968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124759 restraints weight = 10529.845| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.31 r_work: 0.3068 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10573 Z= 0.148 Angle : 0.721 25.800 15242 Z= 0.383 Chirality : 0.067 2.037 1749 Planarity : 0.005 0.055 1143 Dihedral : 31.150 163.080 3192 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.69 % Allowed : 16.70 % Favored : 80.61 % 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: 2.23 (0.31), residues: 662 helix: 2.13 (0.22), residues: 500 sheet: None (None), residues: 0 loop : -0.62 (0.40), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 117 TYR 0.015 0.002 TYR F 51 PHE 0.010 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (10573) covalent geometry : angle 0.72061 / 0.38 (15242) hydrogen bonds : bond 0.05294 / 3.58 ( 565) hydrogen bonds : angle 3.24341 / 2.36 ( 1485) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8172 (tt0) cc_final: 0.7703 (pt0) REVERT: B 79 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8159 (mmtp) REVERT: C 73 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6719 (t0) REVERT: C 74 ASN cc_start: 0.6913 (m110) cc_final: 0.6428 (t0) REVERT: C 103 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8489 (mm) REVERT: D 108 TYR cc_start: 0.7335 (m-10) cc_final: 0.6859 (t80) REVERT: E 122 LYS cc_start: 0.8492 (ptmt) cc_final: 0.8244 (ptmt) REVERT: H 63 LYS cc_start: 0.8017 (mptt) cc_final: 0.7037 (ttpp) outliers start: 15 outliers final: 9 residues processed: 97 average time/residue: 0.8350 time to fit residues: 85.2335 Evaluate side-chains 97 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.176100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.126701 restraints weight = 10622.497| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.22 r_work: 0.3060 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10573 Z= 0.155 Angle : 0.705 25.625 15242 Z= 0.375 Chirality : 0.066 2.043 1749 Planarity : 0.005 0.056 1143 Dihedral : 31.130 164.281 3192 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.33 % Allowed : 16.70 % Favored : 80.97 % 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: 2.37 (0.31), residues: 662 helix: 2.21 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.49 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 63 TYR 0.015 0.002 TYR H 108 PHE 0.010 0.001 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (10573) covalent geometry : angle 0.70516 / 0.37 (15242) hydrogen bonds : bond 0.05320 / 3.59 ( 565) hydrogen bonds : angle 3.17737 / 2.31 ( 1485) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8199 (tt0) cc_final: 0.7764 (pt0) REVERT: B 79 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8204 (mmtp) REVERT: C 73 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6743 (t0) REVERT: C 74 ASN cc_start: 0.6844 (m110) cc_final: 0.6419 (t160) REVERT: C 95 SER cc_start: 0.7950 (p) cc_final: 0.7716 (t) REVERT: C 103 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8513 (mm) REVERT: D 108 TYR cc_start: 0.7350 (m-10) cc_final: 0.6862 (t80) REVERT: E 122 LYS cc_start: 0.8454 (ptmt) cc_final: 0.8209 (ptmt) outliers start: 13 outliers final: 8 residues processed: 92 average time/residue: 0.7750 time to fit residues: 75.1373 Evaluate side-chains 95 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 64 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 2 optimal weight: 0.9990 chunk 86 optimal weight: 30.0000 chunk 75 optimal weight: 30.0000 chunk 66 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.173583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121826 restraints weight = 10508.247| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.31 r_work: 0.2972 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10573 Z= 0.244 Angle : 0.774 24.942 15242 Z= 0.407 Chirality : 0.069 2.028 1749 Planarity : 0.007 0.076 1143 Dihedral : 31.202 164.341 3192 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.69 % Allowed : 16.70 % Favored : 80.61 % 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: 1.88 (0.31), residues: 662 helix: 1.88 (0.22), residues: 503 sheet: None (None), residues: 0 loop : -0.82 (0.40), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 89 TYR 0.015 0.002 TYR F 51 PHE 0.010 0.002 PHE E 67 HIS 0.005 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 (10573) covalent geometry : angle 0.77419 / 0.41 (15242) hydrogen bonds : bond 0.06517 / 4.37 ( 565) hydrogen bonds : angle 3.32433 / 2.42 ( 1485) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8194 (tt0) cc_final: 0.7743 (pt0) REVERT: B 79 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8142 (mmtp) REVERT: C 73 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6639 (t0) REVERT: C 74 ASN cc_start: 0.6860 (m110) cc_final: 0.6394 (t0) REVERT: C 103 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8546 (mm) REVERT: D 108 TYR cc_start: 0.7386 (m-10) cc_final: 0.6818 (t80) REVERT: D 111 LYS cc_start: 0.7719 (tttt) cc_final: 0.7483 (tttt) REVERT: H 63 LYS cc_start: 0.8125 (mptt) cc_final: 0.7042 (ttpp) outliers start: 15 outliers final: 10 residues processed: 97 average time/residue: 0.8920 time to fit residues: 90.7465 Evaluate side-chains 95 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 27 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 67 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 53 optimal weight: 0.1980 chunk 79 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.176416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125346 restraints weight = 10483.441| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.31 r_work: 0.3078 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10573 Z= 0.137 Angle : 0.702 25.451 15242 Z= 0.374 Chirality : 0.066 2.027 1749 Planarity : 0.005 0.060 1143 Dihedral : 31.164 164.029 3192 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.80 % Allowed : 17.95 % Favored : 80.25 % 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: 2.41 (0.31), residues: 662 helix: 2.26 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.60 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 89 TYR 0.023 0.002 TYR B 88 PHE 0.010 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (10573) covalent geometry : angle 0.70202 / 0.37 (15242) hydrogen bonds : bond 0.05012 / 3.40 ( 565) hydrogen bonds : angle 3.22557 / 2.34 ( 1485) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8161 (tt0) cc_final: 0.7701 (pt0) REVERT: B 79 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8120 (mmtp) REVERT: C 43 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8012 (mtp180) REVERT: C 73 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6674 (t0) REVERT: C 74 ASN cc_start: 0.6752 (m110) cc_final: 0.6387 (t160) REVERT: D 108 TYR cc_start: 0.7400 (m-10) cc_final: 0.6978 (t80) REVERT: F 79 LYS cc_start: 0.8520 (mttp) cc_final: 0.8144 (mttm) outliers start: 10 outliers final: 8 residues processed: 93 average time/residue: 0.8918 time to fit residues: 87.0060 Evaluate side-chains 91 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 67 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 23 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN H 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.176955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.127413 restraints weight = 10578.849| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.21 r_work: 0.3094 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10573 Z= 0.143 Angle : 0.685 25.186 15242 Z= 0.366 Chirality : 0.064 2.012 1749 Planarity : 0.005 0.075 1143 Dihedral : 31.086 164.542 3192 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.80 % Allowed : 18.49 % Favored : 79.71 % 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: 2.63 (0.31), residues: 662 helix: 2.41 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.46 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 89 TYR 0.013 0.002 TYR H 108 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (10573) covalent geometry : angle 0.68492 / 0.37 (15242) hydrogen bonds : bond 0.05001 / 3.39 ( 565) hydrogen bonds : angle 3.16248 / 2.30 ( 1485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3014.22 seconds wall clock time: 52 minutes 6.71 seconds (3126.71 seconds total)