Starting phenix.real_space_refine on Thu Jul 2 17:51:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j91_36084/07_2026/8j91_36084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j91_36084/07_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_36084/07_2026/8j91_36084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j91_36084/07_2026/8j91_36084.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j91_36084/07_2026/8j91_36084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j91_36084/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.90, 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: 0.73 Conformation dependent library (CDL) restraints added in 217.4 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: 1.14 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: 1.40 Time building geometry restraints manager: 0.97 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: 15183 6.26 - 12.53: 51 12.53 - 18.79: 3 18.79 - 25.05: 1 25.05 - 31.31: 4 Bond angle restraints: 15242 Sorted by residual: 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 1.50e+00 4.44e-01 3.25e+02 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=" 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: 0.750 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.570 Find NCS groups from input model: 0.090 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- 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= 1.202 Angle : 1.550 31.314 15242 Z= 1.574 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 / 1.20 (10573) covalent geometry : angle 1.54972 / 1.57 (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 : 0.160 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7852 (mmtm) REVERT: D 84 MET cc_start: 0.7773 (mmp) cc_final: 0.7542 (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: 0.8122 time to fit residues: 113.8517 Evaluate side-chains 76 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 7.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.183342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136142 restraints weight = 10675.173| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.26 r_work: 0.3206 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10573 Z= 0.163 Angle : 0.910 35.019 15242 Z= 0.466 Chirality : 0.060 1.123 1749 Planarity : 0.005 0.046 1143 Dihedral : 30.776 166.096 3192 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.44 % Allowed : 9.87 % Favored : 88.69 % 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: 2.07 (0.32), residues: 662 helix: 1.95 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -0.43 (0.43), residues: 162 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 0.007 0.001 PHE F 61 HIS 0.003 0.001 HIS G 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.16 (10573) covalent geometry : angle 0.91013 / 0.47 (15242) hydrogen bonds : bond 0.05930 / 3.97 ( 565) hydrogen bonds : angle 3.34631 / 2.44 ( 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 94 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.158 Fit side-chains REVERT: A 129 ARG cc_start: 0.8205 (ttt180) cc_final: 0.7973 (ttt90) REVERT: B 44 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8383 (mtpp) REVERT: B 79 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8211 (mmtm) REVERT: C 73 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6694 (t0) REVERT: D 104 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7878 (mtmt) REVERT: H 93 ASP cc_start: 0.8361 (t70) cc_final: 0.7883 (t70) REVERT: H 96 GLU cc_start: 0.8258 (tp30) cc_final: 0.7684 (tp30) outliers start: 8 outliers final: 2 residues processed: 89 average time/residue: 0.7382 time to fit residues: 69.1904 Evaluate side-chains 82 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.6164 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.178259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.127976 restraints weight = 10621.506| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.32 r_work: 0.3062 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10573 Z= 0.183 Angle : 0.848 36.216 15242 Z= 0.423 Chirality : 0.050 0.627 1749 Planarity : 0.005 0.043 1143 Dihedral : 31.078 163.702 3192 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.23 % Allowed : 10.59 % Favored : 86.18 % 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: 2.16 (0.32), residues: 662 helix: 2.03 (0.23), residues: 499 sheet: None (None), residues: 0 loop : -0.43 (0.42), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 35 TYR 0.021 0.002 TYR F 51 PHE 0.010 0.002 PHE A 104 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (10573) covalent geometry : angle 0.84791 / 0.42 (15242) hydrogen bonds : bond 0.05599 / 3.77 ( 565) hydrogen bonds : angle 3.15734 / 2.31 ( 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 114 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.284 Fit side-chains REVERT: A 76 GLN cc_start: 0.8119 (tt0) cc_final: 0.7725 (pt0) REVERT: B 79 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8251 (mmtp) REVERT: C 73 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6694 (t0) REVERT: D 137 SER cc_start: 0.8728 (m) cc_final: 0.8499 (m) REVERT: F 79 LYS cc_start: 0.8484 (mtmm) cc_final: 0.8102 (mttm) REVERT: H 63 LYS cc_start: 0.8258 (mptt) cc_final: 0.7017 (ttpp) REVERT: H 65 TYR cc_start: 0.8724 (m-80) cc_final: 0.8467 (m-80) REVERT: H 93 ASP cc_start: 0.8469 (t70) cc_final: 0.8025 (t70) outliers start: 18 outliers final: 6 residues processed: 103 average time/residue: 0.8095 time to fit residues: 87.5894 Evaluate side-chains 95 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.7980 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.177911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.127419 restraints weight = 10646.267| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.33 r_work: 0.3090 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10573 Z= 0.165 Angle : 0.706 27.713 15242 Z= 0.378 Chirality : 0.069 2.083 1749 Planarity : 0.005 0.047 1143 Dihedral : 31.099 164.801 3192 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.33 % Allowed : 14.18 % Favored : 83.48 % 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: 2.30 (0.31), residues: 662 helix: 2.12 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -0.40 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 89 TYR 0.015 0.002 TYR F 51 PHE 0.009 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (10573) covalent geometry : angle 0.70607 / 0.38 (15242) hydrogen bonds : bond 0.05121 / 3.46 ( 565) hydrogen bonds : angle 3.09402 / 2.26 ( 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 103 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8181 (tt0) cc_final: 0.7730 (pt0) REVERT: B 79 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8247 (mmtp) REVERT: C 73 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6739 (t0) REVERT: C 103 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8456 (mm) REVERT: D 108 TYR cc_start: 0.7289 (m-10) cc_final: 0.6791 (t80) REVERT: F 79 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8186 (mttm) REVERT: G 78 ARG cc_start: 0.7679 (mtp85) cc_final: 0.7451 (ttp80) REVERT: H 63 LYS cc_start: 0.8198 (mptt) cc_final: 0.7011 (ttpp) REVERT: H 65 TYR cc_start: 0.8709 (m-80) cc_final: 0.8367 (m-80) REVERT: H 93 ASP cc_start: 0.8469 (t70) cc_final: 0.8030 (t70) outliers start: 13 outliers final: 6 residues processed: 97 average time/residue: 0.8377 time to fit residues: 85.4434 Evaluate side-chains 94 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 H residue 64 ILE 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: 2.9990 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 30.0000 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.177170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126113 restraints weight = 10639.051| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.32 r_work: 0.3068 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10573 Z= 0.168 Angle : 0.624 9.654 15242 Z= 0.357 Chirality : 0.044 0.290 1749 Planarity : 0.005 0.057 1143 Dihedral : 31.179 177.389 3192 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.87 % Allowed : 14.36 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.31), residues: 662 helix: 2.26 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.42 (0.40), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 39 TYR 0.016 0.002 TYR F 51 PHE 0.010 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (10573) covalent geometry : angle 0.62400 / 0.36 (15242) hydrogen bonds : bond 0.05208 / 3.53 ( 565) hydrogen bonds : angle 3.08303 / 2.25 ( 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 109 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8179 (tt0) cc_final: 0.7717 (pt0) REVERT: B 79 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8233 (mmtp) REVERT: C 73 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6703 (t0) REVERT: C 74 ASN cc_start: 0.6849 (m-40) cc_final: 0.6545 (t0) REVERT: C 103 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8492 (mm) REVERT: D 108 TYR cc_start: 0.7350 (m-10) cc_final: 0.6840 (t80) REVERT: H 63 LYS cc_start: 0.8045 (mptt) cc_final: 0.6965 (ttpp) REVERT: H 65 TYR cc_start: 0.8720 (m-80) cc_final: 0.8433 (m-80) REVERT: H 93 ASP cc_start: 0.8482 (t70) cc_final: 0.8028 (t70) outliers start: 16 outliers final: 8 residues processed: 104 average time/residue: 0.7737 time to fit residues: 84.6805 Evaluate side-chains 98 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 65 optimal weight: 30.0000 chunk 34 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 77 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN E 68 GLN F 25 ASN F 93 GLN G 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.175568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126049 restraints weight = 10625.754| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.23 r_work: 0.3066 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3312 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= 0.194 Angle : 0.643 9.773 15242 Z= 0.364 Chirality : 0.045 0.309 1749 Planarity : 0.006 0.058 1143 Dihedral : 31.286 173.932 3192 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.87 % Allowed : 15.80 % 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: 2.21 (0.31), residues: 662 helix: 2.07 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.50 (0.40), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 131 TYR 0.015 0.002 TYR F 51 PHE 0.010 0.002 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (10573) covalent geometry : angle 0.64265 / 0.36 (15242) hydrogen bonds : bond 0.05724 / 3.86 ( 565) hydrogen bonds : angle 3.16807 / 2.31 ( 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 104 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8211 (tt0) cc_final: 0.7751 (pt0) REVERT: B 79 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8223 (mmtp) REVERT: C 73 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6656 (t0) REVERT: C 103 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8542 (mm) REVERT: D 108 TYR cc_start: 0.7347 (m-10) cc_final: 0.6872 (t80) REVERT: E 122 LYS cc_start: 0.8548 (ptmt) cc_final: 0.8328 (ptmt) REVERT: H 63 LYS cc_start: 0.8138 (mptt) cc_final: 0.7168 (ttpp) REVERT: H 65 TYR cc_start: 0.8770 (m-80) cc_final: 0.8463 (m-80) REVERT: H 86 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8212 (mp) REVERT: H 93 ASP cc_start: 0.8568 (t70) cc_final: 0.8153 (t70) outliers start: 16 outliers final: 9 residues processed: 99 average time/residue: 0.8616 time to fit residues: 89.5550 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 : 0.322 ------------------------------------------------------------------------------- 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 73 ASP Chi-restraints excluded: chain C residue 103 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 86 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: 5.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.176216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126931 restraints weight = 10540.719| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.23 r_work: 0.3076 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10573 Z= 0.152 Angle : 0.611 9.772 15242 Z= 0.351 Chirality : 0.044 0.286 1749 Planarity : 0.005 0.059 1143 Dihedral : 31.276 174.754 3192 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.69 % Allowed : 16.52 % Favored : 80.79 % 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: 2.36 (0.31), residues: 662 helix: 2.20 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.50 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 89 TYR 0.014 0.002 TYR F 51 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (10573) covalent geometry : angle 0.61140 / 0.35 (15242) hydrogen bonds : bond 0.05290 / 3.57 ( 565) hydrogen bonds : angle 3.15086 / 2.30 ( 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 100 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8204 (tt0) cc_final: 0.7755 (pt0) REVERT: B 79 LYS cc_start: 0.8694 (mtpt) cc_final: 0.8210 (mmtp) REVERT: C 73 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6661 (t0) REVERT: C 74 ASN cc_start: 0.6913 (m110) cc_final: 0.6478 (t160) REVERT: C 103 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8529 (mm) REVERT: D 108 TYR cc_start: 0.7334 (m-10) cc_final: 0.6900 (t80) REVERT: E 122 LYS cc_start: 0.8492 (ptmt) cc_final: 0.8260 (ptmt) REVERT: H 63 LYS cc_start: 0.8052 (mptt) cc_final: 0.7147 (ttpp) REVERT: H 65 TYR cc_start: 0.8769 (m-80) cc_final: 0.8512 (m-80) REVERT: H 93 ASP cc_start: 0.8531 (t70) cc_final: 0.8097 (t70) outliers start: 15 outliers final: 9 residues processed: 96 average time/residue: 0.8156 time to fit residues: 82.1724 Evaluate side-chains 95 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 ASP Chi-restraints excluded: chain C residue 103 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: 0.6980 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: 4.9990 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 10.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.176215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125143 restraints weight = 10628.330| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.30 r_work: 0.3074 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3389 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= 0.162 Angle : 0.611 9.750 15242 Z= 0.350 Chirality : 0.043 0.286 1749 Planarity : 0.005 0.059 1143 Dihedral : 31.274 175.445 3192 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.69 % Allowed : 16.34 % 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: 2.40 (0.31), residues: 662 helix: 2.23 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.51 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 89 TYR 0.014 0.002 TYR F 51 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (10573) covalent geometry : angle 0.61072 / 0.35 (15242) hydrogen bonds : bond 0.05280 / 3.57 ( 565) hydrogen bonds : angle 3.13265 / 2.28 ( 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 102 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8193 (tt0) cc_final: 0.7713 (pt0) REVERT: B 79 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8162 (mmtp) REVERT: C 73 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6652 (t0) REVERT: C 74 ASN cc_start: 0.6864 (m110) cc_final: 0.6432 (t160) REVERT: C 103 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8524 (mm) REVERT: D 108 TYR cc_start: 0.7373 (m-10) cc_final: 0.6899 (t80) REVERT: E 122 LYS cc_start: 0.8510 (ptmt) cc_final: 0.8271 (ptmt) REVERT: H 63 LYS cc_start: 0.8042 (mptt) cc_final: 0.7031 (ttpp) REVERT: H 65 TYR cc_start: 0.8740 (m-80) cc_final: 0.8470 (m-80) REVERT: H 93 ASP cc_start: 0.8529 (t70) cc_final: 0.8086 (t70) outliers start: 15 outliers final: 9 residues processed: 97 average time/residue: 0.8000 time to fit residues: 81.4680 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 : 0.222 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 2 optimal weight: 0.9980 chunk 86 optimal weight: 30.0000 chunk 75 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.174233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123167 restraints weight = 10519.880| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.31 r_work: 0.3041 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10573 Z= 0.219 Angle : 0.670 10.449 15242 Z= 0.375 Chirality : 0.047 0.299 1749 Planarity : 0.006 0.069 1143 Dihedral : 31.325 175.658 3192 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.51 % Allowed : 16.70 % Favored : 80.79 % 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: 2.04 (0.31), residues: 662 helix: 1.99 (0.22), residues: 503 sheet: None (None), residues: 0 loop : -0.73 (0.41), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 89 TYR 0.016 0.002 TYR F 51 PHE 0.009 0.002 PHE E 67 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (10573) covalent geometry : angle 0.66963 / 0.38 (15242) hydrogen bonds : bond 0.06141 / 4.11 ( 565) hydrogen bonds : angle 3.26165 / 2.38 ( 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 104 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8218 (tt0) cc_final: 0.7749 (pt0) REVERT: B 79 LYS cc_start: 0.8692 (mtpt) cc_final: 0.8157 (mmtp) REVERT: C 73 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6657 (t0) REVERT: C 74 ASN cc_start: 0.6763 (m110) cc_final: 0.6434 (t160) REVERT: C 103 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8587 (mm) REVERT: D 108 TYR cc_start: 0.7477 (m-10) cc_final: 0.6998 (t80) REVERT: H 65 TYR cc_start: 0.8772 (m-80) cc_final: 0.8455 (m-80) outliers start: 14 outliers final: 8 residues processed: 99 average time/residue: 0.8675 time to fit residues: 90.0739 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 : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 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 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: 0.8980 chunk 67 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 53 optimal weight: 0.0980 chunk 79 optimal weight: 9.9990 chunk 56 optimal weight: 0.0980 chunk 45 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 overall best weight: 0.2338 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.176975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126011 restraints weight = 10487.269| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.30 r_work: 0.3091 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10573 Z= 0.139 Angle : 0.615 9.645 15242 Z= 0.353 Chirality : 0.044 0.285 1749 Planarity : 0.006 0.085 1143 Dihedral : 31.292 174.518 3192 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.97 % Allowed : 17.95 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.31), residues: 662 helix: 2.39 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.47 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 43 TYR 0.022 0.002 TYR B 88 PHE 0.010 0.001 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (10573) covalent geometry : angle 0.61516 / 0.35 (15242) hydrogen bonds : bond 0.04777 / 3.24 ( 565) hydrogen bonds : angle 3.22458 / 2.35 ( 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 100 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.344 Fit side-chains REVERT: A 76 GLN cc_start: 0.8159 (tt0) cc_final: 0.7699 (pt0) REVERT: B 79 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8113 (mmtp) REVERT: C 73 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6660 (t0) REVERT: C 74 ASN cc_start: 0.6704 (m110) cc_final: 0.6356 (t160) REVERT: C 95 SER cc_start: 0.7859 (p) cc_final: 0.7649 (t) REVERT: D 108 TYR cc_start: 0.7413 (m-10) cc_final: 0.7014 (t80) REVERT: F 35 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7939 (mtp180) REVERT: H 65 TYR cc_start: 0.8731 (m-80) cc_final: 0.8452 (m-80) outliers start: 11 outliers final: 8 residues processed: 95 average time/residue: 0.8352 time to fit residues: 83.5132 Evaluate side-chains 92 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP 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=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: 10.0000 chunk 23 optimal weight: 0.0870 chunk 29 optimal weight: 0.0570 chunk 77 optimal weight: 30.0000 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS F 93 GLN H 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.177456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128239 restraints weight = 10595.072| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.23 r_work: 0.3101 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3589 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= 0.131 Angle : 0.584 9.792 15242 Z= 0.339 Chirality : 0.041 0.273 1749 Planarity : 0.005 0.058 1143 Dihedral : 31.238 176.387 3192 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.44 % Allowed : 18.13 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.32), residues: 662 helix: 2.53 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -0.36 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 43 TYR 0.017 0.002 TYR H 108 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.13 (10573) covalent geometry : angle 0.58437 / 0.34 (15242) hydrogen bonds : bond 0.04795 / 3.25 ( 565) hydrogen bonds : angle 3.12182 / 2.27 ( 1485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3034.11 seconds wall clock time: 52 minutes 25.38 seconds (3145.38 seconds total)