Starting phenix.real_space_refine on Sat Aug 23 03:55:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j91_36084/08_2025/8j91_36084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j91_36084/08_2025/8j91_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_2025/8j91_36084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j91_36084/08_2025/8j91_36084.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j91_36084/08_2025/8j91_36084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j91_36084/08_2025/8j91_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-2.0-5787/lib/python3.9/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: 1.83, per 1000 atoms: 0.18 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: 0.78 Conformation dependent library (CDL) restraints added in 172.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.29 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: 1.76 Time building geometry restraints manager: 1.05 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 1.239 1.065 0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C4 DC J 52 " pdb=" N4 DC J 52 " ideal model delta sigma weight residual 1.337 1.187 0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" C1' DA I 24 " pdb=" N9 DA I 24 " ideal model delta sigma weight residual 1.460 1.363 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" CA ALA E 96 " pdb=" CB ALA E 96 " ideal model delta sigma weight residual 1.528 1.462 0.066 1.59e-02 3.96e+03 1.72e+01 bond pdb=" O3' DC J 24 " pdb=" P DT J 25 " ideal model delta sigma weight residual 1.607 1.546 0.061 1.50e-02 4.44e+03 1.66e+01 ... (remaining 10568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.26: 15191 6.26 - 12.53: 43 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=" O3' DA I 24 " pdb=" P DG I 25 " pdb=" OP2 DG I 25 " ideal model delta sigma weight residual 108.00 76.69 31.31 3.00e+00 1.11e-01 1.09e+02 angle pdb=" OP2 DG I 25 " pdb=" P DG I 25 " pdb=" O5' DG I 25 " ideal model delta sigma weight residual 108.00 78.64 29.36 3.00e+00 1.11e-01 9.58e+01 angle pdb=" O3' DC J 24 " pdb=" C3' DC J 24 " pdb=" C2' DC J 24 " ideal model delta sigma weight residual 111.50 96.95 14.55 1.50e+00 4.44e-01 9.41e+01 angle pdb=" O3' DT J 54 " pdb=" C3' DT J 54 " pdb=" C2' DT J 54 " ideal model delta sigma weight residual 111.50 125.27 -13.77 1.50e+00 4.44e-01 8.42e+01 ... (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 - 0.128: 1652 0.128 - 0.257: 84 0.257 - 0.385: 9 0.385 - 0.514: 3 0.514 - 0.642: 1 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 -2.66 -3.30 0.64 2.00e-01 2.50e+01 1.03e+01 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 2.35 -1.86 0.48 2.00e-01 2.50e+01 5.77e+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 -2.66 -2.22 -0.44 2.00e-01 2.50e+01 4.87e+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: 0.030 Process input model: 10.150 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 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 0.174 10573 Z= 0.538 Angle : 1.552 31.314 15242 Z= 0.964 Chirality : 0.069 0.642 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 aren 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 covalent geometry : bond 0.01088 (10573) covalent geometry : angle 1.55243 (15242) hydrogen bonds : bond 0.18380 ( 565) hydrogen bonds : angle 5.31683 ( 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 : 0.218 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: 0.7799 (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: 0.8065 time to fit residues: 112.8650 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 : 0.234 ------------------------------------------------------------------------------- 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: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 G 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.183172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.133519 restraints weight = 10655.632| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.33 r_work: 0.3206 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 10573 Z= 0.174 Angle : 0.770 37.780 15242 Z= 0.388 Chirality : 0.038 0.581 1749 Planarity : 0.005 0.044 1143 Dihedral : 30.378 161.344 3192 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.80 % Allowed : 9.87 % 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 aren not related in a simple way. whole: 2.32 (0.32), residues: 662 helix: 2.16 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.39 (0.42), residues: 164 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 0.008 0.001 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00378 (10573) covalent geometry : angle 0.77002 (15242) hydrogen bonds : bond 0.04481 ( 565) hydrogen bonds : angle 3.08062 ( 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 104 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.248 Fit side-chains REVERT: A 129 ARG cc_start: 0.8364 (ttt180) cc_final: 0.8135 (ttt90) REVERT: B 79 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8208 (mmtp) REVERT: C 73 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6727 (t0) REVERT: C 78 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.7244 (ttm110) REVERT: H 65 TYR cc_start: 0.8743 (m-80) cc_final: 0.8367 (m-80) REVERT: H 79 ILE cc_start: 0.8093 (tp) cc_final: 0.7890 (tt) REVERT: H 93 ASP cc_start: 0.8316 (t70) cc_final: 0.7864 (t70) REVERT: H 141 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8336 (ttmm) outliers start: 10 outliers final: 2 residues processed: 99 average time/residue: 0.7174 time to fit residues: 74.5187 Evaluate side-chains 86 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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: 2.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN 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 = 0.3990 r_free = 0.3990 target = 0.178774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129592 restraints weight = 10621.861| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.25 r_work: 0.3128 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2925 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= 0.185 Angle : 0.572 9.526 15242 Z= 0.336 Chirality : 0.036 0.146 1749 Planarity : 0.005 0.045 1143 Dihedral : 30.501 169.728 3192 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.69 % Allowed : 11.49 % Favored : 85.82 % 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 aren not related in a simple way. whole: 2.34 (0.32), residues: 662 helix: 2.19 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.43 (0.41), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 63 TYR 0.018 0.002 TYR F 51 PHE 0.009 0.001 PHE A 104 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00419 (10573) covalent geometry : angle 0.57211 (15242) hydrogen bonds : bond 0.04893 ( 565) hydrogen bonds : angle 3.08757 ( 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 110 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.194 Fit side-chains REVERT: A 76 GLN cc_start: 0.8204 (tt0) cc_final: 0.7806 (pt0) REVERT: B 79 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8280 (mmtp) REVERT: C 73 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6737 (t0) REVERT: D 147 THR cc_start: 0.7933 (m) cc_final: 0.7568 (m) REVERT: H 65 TYR cc_start: 0.8741 (m-80) cc_final: 0.8440 (m-80) REVERT: H 79 ILE cc_start: 0.8100 (tp) cc_final: 0.7899 (tt) REVERT: H 93 ASP cc_start: 0.8445 (t70) cc_final: 0.7999 (t70) outliers start: 15 outliers final: 7 residues processed: 102 average time/residue: 0.7336 time to fit residues: 78.4776 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 : 0.302 ------------------------------------------------------------------------------- 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 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 84 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 82 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN F 25 ASN F 93 GLN G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.177321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128506 restraints weight = 10608.082| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.24 r_work: 0.3107 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10573 Z= 0.184 Angle : 0.562 9.646 15242 Z= 0.331 Chirality : 0.035 0.146 1749 Planarity : 0.005 0.049 1143 Dihedral : 30.479 162.361 3192 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.41 % Allowed : 13.82 % 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 aren not related in a simple way. whole: 2.38 (0.31), residues: 662 helix: 2.18 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -0.35 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 63 TYR 0.016 0.002 TYR F 51 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00418 (10573) covalent geometry : angle 0.56160 (15242) hydrogen bonds : bond 0.04824 ( 565) hydrogen bonds : angle 3.08210 ( 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 108 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8201 (tt0) cc_final: 0.7772 (pt0) REVERT: B 79 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8295 (mmtp) REVERT: C 73 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.7026 (t0) REVERT: C 82 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7466 (ttp80) REVERT: C 103 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8498 (mm) REVERT: D 108 TYR cc_start: 0.7316 (m-10) cc_final: 0.6816 (t80) REVERT: D 147 THR cc_start: 0.7883 (m) cc_final: 0.7555 (m) REVERT: G 78 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6750 (ttp-170) REVERT: G 85 GLN cc_start: 0.8348 (tt0) cc_final: 0.8084 (tp40) REVERT: H 65 TYR cc_start: 0.8730 (m-80) cc_final: 0.8487 (m-80) REVERT: H 93 ASP cc_start: 0.8464 (t70) cc_final: 0.8031 (t70) outliers start: 19 outliers final: 9 residues processed: 101 average time/residue: 0.7599 time to fit residues: 80.3636 Evaluate side-chains 98 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 D residue 64 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 84 MET 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: 10.0000 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 76 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.178006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.129264 restraints weight = 10639.626| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.23 r_work: 0.3121 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3397 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= 0.153 Angle : 0.537 9.407 15242 Z= 0.320 Chirality : 0.034 0.135 1749 Planarity : 0.004 0.054 1143 Dihedral : 30.454 162.556 3192 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.69 % Allowed : 14.54 % 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 aren not related in a simple way. whole: 2.61 (0.31), residues: 662 helix: 2.35 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -0.31 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 39 TYR 0.014 0.002 TYR F 51 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00333 (10573) covalent geometry : angle 0.53708 (15242) hydrogen bonds : bond 0.04410 ( 565) hydrogen bonds : angle 3.04414 ( 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 104 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8197 (tt0) cc_final: 0.7769 (pt0) REVERT: B 79 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8259 (mmtp) REVERT: C 73 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6923 (t0) REVERT: C 78 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7058 (ttm110) REVERT: C 82 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7512 (ttp80) REVERT: C 103 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8499 (mm) REVERT: D 108 TYR cc_start: 0.7291 (m-10) cc_final: 0.6834 (t80) REVERT: D 147 THR cc_start: 0.7877 (m) cc_final: 0.7559 (m) REVERT: E 122 LYS cc_start: 0.8476 (ptmt) cc_final: 0.8258 (ptmt) REVERT: G 78 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6765 (ttp-170) REVERT: H 65 TYR cc_start: 0.8709 (m-80) cc_final: 0.8370 (m-80) REVERT: H 92 ASN cc_start: 0.8854 (m110) cc_final: 0.8566 (m110) REVERT: H 93 ASP cc_start: 0.8472 (t70) cc_final: 0.8021 (t70) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 0.7237 time to fit residues: 76.1308 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 : 0.156 ------------------------------------------------------------------------------- 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 G residue 78 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: 3.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.172447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122284 restraints weight = 10601.780| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.28 r_work: 0.3022 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 10573 Z= 0.338 Angle : 0.700 11.584 15242 Z= 0.397 Chirality : 0.044 0.240 1749 Planarity : 0.007 0.088 1143 Dihedral : 31.019 163.260 3192 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.69 % Allowed : 15.80 % Favored : 81.51 % 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 aren not related in a simple way. whole: 1.67 (0.31), residues: 662 helix: 1.66 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -0.65 (0.43), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 131 TYR 0.015 0.003 TYR F 51 PHE 0.012 0.003 PHE A 104 HIS 0.008 0.002 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00810 (10573) covalent geometry : angle 0.70036 (15242) hydrogen bonds : bond 0.06733 ( 565) hydrogen bonds : angle 3.35043 ( 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 108 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8207 (tt0) cc_final: 0.7798 (pt0) REVERT: B 79 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8220 (mmtp) REVERT: C 73 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6899 (t0) REVERT: C 103 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8786 (mm) REVERT: D 108 TYR cc_start: 0.7430 (m-10) cc_final: 0.6935 (t80) REVERT: G 57 GLU cc_start: 0.8637 (tt0) cc_final: 0.8333 (tt0) REVERT: H 65 TYR cc_start: 0.8787 (m-80) cc_final: 0.8509 (m-80) outliers start: 15 outliers final: 10 residues processed: 101 average time/residue: 0.7173 time to fit residues: 75.9644 Evaluate side-chains 98 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 91 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 H residue 64 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 140 THR 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: 0.8980 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.176637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.127380 restraints weight = 10514.752| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.19 r_work: 0.3107 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3734 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= 0.162 Angle : 0.559 9.881 15242 Z= 0.332 Chirality : 0.034 0.143 1749 Planarity : 0.005 0.056 1143 Dihedral : 30.721 162.839 3192 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.44 % Allowed : 19.75 % Favored : 78.82 % 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 aren not related in a simple way. whole: 2.34 (0.31), residues: 662 helix: 2.18 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.49 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 89 TYR 0.011 0.001 TYR F 51 PHE 0.011 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00355 (10573) covalent geometry : angle 0.55886 (15242) hydrogen bonds : bond 0.04680 ( 565) hydrogen bonds : angle 3.10081 ( 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 95 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8389 (tt0) cc_final: 0.7921 (pt0) REVERT: B 79 LYS cc_start: 0.8791 (mtpt) cc_final: 0.8300 (mmtp) REVERT: C 73 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6875 (t0) REVERT: C 82 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7254 (ttt180) REVERT: D 108 TYR cc_start: 0.7584 (m-10) cc_final: 0.6955 (t80) REVERT: E 80 THR cc_start: 0.8754 (p) cc_final: 0.8459 (t) REVERT: H 65 TYR cc_start: 0.8752 (m-80) cc_final: 0.8370 (m-80) REVERT: H 93 ASP cc_start: 0.8735 (t70) cc_final: 0.8300 (t70) REVERT: H 141 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8095 (ttpt) outliers start: 8 outliers final: 6 residues processed: 93 average time/residue: 0.7322 time to fit residues: 71.4439 Evaluate side-chains 90 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 84 MET 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: 0.3980 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 15 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.176559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127502 restraints weight = 10611.608| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.23 r_work: 0.3096 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10573 Z= 0.170 Angle : 0.551 9.409 15242 Z= 0.327 Chirality : 0.034 0.135 1749 Planarity : 0.005 0.057 1143 Dihedral : 30.572 162.595 3192 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.80 % Allowed : 18.85 % Favored : 79.35 % 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 aren not related in a simple way. whole: 2.65 (0.31), residues: 662 helix: 2.40 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.35 (0.44), residues: 160 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 0.011 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00381 (10573) covalent geometry : angle 0.55142 (15242) hydrogen bonds : bond 0.04621 ( 565) hydrogen bonds : angle 3.03814 ( 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 96 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8215 (tt0) cc_final: 0.7763 (pt0) REVERT: B 79 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8195 (mmtp) REVERT: C 25 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7594 (mp10) REVERT: C 73 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.6939 (t0) REVERT: C 78 ARG cc_start: 0.7619 (mtm-85) cc_final: 0.7252 (ttm110) REVERT: C 82 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7188 (ttt180) REVERT: D 108 TYR cc_start: 0.7359 (m-10) cc_final: 0.6919 (t80) REVERT: E 80 THR cc_start: 0.8705 (p) cc_final: 0.8433 (t) REVERT: F 93 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: H 65 TYR cc_start: 0.8683 (m-80) cc_final: 0.8274 (m-80) REVERT: H 93 ASP cc_start: 0.8454 (t70) cc_final: 0.8012 (t70) REVERT: H 141 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8104 (ttpt) outliers start: 10 outliers final: 5 residues processed: 93 average time/residue: 0.6945 time to fit residues: 67.7618 Evaluate side-chains 90 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 84 MET 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: 2.9990 chunk 86 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.172503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122406 restraints weight = 10511.214| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.29 r_work: 0.3003 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 10573 Z= 0.318 Angle : 0.679 10.934 15242 Z= 0.388 Chirality : 0.043 0.287 1749 Planarity : 0.006 0.080 1143 Dihedral : 31.020 163.201 3192 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.97 % Allowed : 19.21 % Favored : 78.82 % 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 aren not related in a simple way. whole: 1.84 (0.31), residues: 662 helix: 1.80 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -0.65 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 131 TYR 0.016 0.003 TYR F 51 PHE 0.011 0.002 PHE E 67 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00760 (10573) covalent geometry : angle 0.67917 (15242) hydrogen bonds : bond 0.06454 ( 565) hydrogen bonds : angle 3.31273 ( 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 96 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8253 (tt0) cc_final: 0.7801 (pt0) REVERT: B 79 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8206 (mmtp) REVERT: C 25 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7651 (mp10) REVERT: C 73 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6836 (t0) REVERT: C 82 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7276 (tpt170) REVERT: D 108 TYR cc_start: 0.7525 (m-10) cc_final: 0.6938 (t80) REVERT: F 93 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7993 (mt0) REVERT: G 57 GLU cc_start: 0.8659 (tt0) cc_final: 0.8361 (tt0) REVERT: H 65 TYR cc_start: 0.8768 (m-80) cc_final: 0.8555 (m-80) REVERT: H 141 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8069 (ttpm) outliers start: 11 outliers final: 7 residues processed: 93 average time/residue: 0.7932 time to fit residues: 77.2254 Evaluate side-chains 93 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 D residue 64 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 84 MET 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: 0.7980 chunk 59 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 62 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3953 r_free = 0.3953 target = 0.175604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125962 restraints weight = 10437.339| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.24 r_work: 0.3078 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10573 Z= 0.155 Angle : 0.582 9.622 15242 Z= 0.347 Chirality : 0.036 0.197 1749 Planarity : 0.005 0.055 1143 Dihedral : 30.926 162.611 3192 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.80 % Allowed : 19.93 % Favored : 78.28 % 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 aren not related in a simple way. whole: 2.47 (0.32), residues: 662 helix: 2.28 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -0.51 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 89 TYR 0.018 0.002 TYR B 88 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00331 (10573) covalent geometry : angle 0.58163 (15242) hydrogen bonds : bond 0.04826 ( 565) hydrogen bonds : angle 3.17650 ( 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 93 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8175 (tt0) cc_final: 0.7759 (pt0) REVERT: B 79 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8159 (mmtp) REVERT: C 25 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7616 (mp10) REVERT: C 73 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6691 (t0) REVERT: C 78 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.7291 (ttm110) REVERT: C 82 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7239 (tpt170) REVERT: D 108 TYR cc_start: 0.7457 (m-10) cc_final: 0.6930 (t80) REVERT: H 65 TYR cc_start: 0.8719 (m-80) cc_final: 0.8474 (m-80) REVERT: H 141 LYS cc_start: 0.8400 (ttmm) cc_final: 0.7996 (ttpp) outliers start: 10 outliers final: 6 residues processed: 88 average time/residue: 0.7909 time to fit residues: 72.9840 Evaluate side-chains 87 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain H residue 84 MET 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: 7.9990 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 85 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.174792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125285 restraints weight = 10557.968| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.22 r_work: 0.3066 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10573 Z= 0.204 Angle : 0.591 9.873 15242 Z= 0.346 Chirality : 0.037 0.240 1749 Planarity : 0.005 0.056 1143 Dihedral : 30.763 162.364 3192 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.44 % Allowed : 20.47 % Favored : 78.10 % 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 aren not related in a simple way. whole: 2.45 (0.32), residues: 662 helix: 2.30 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.61 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 89 TYR 0.017 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 covalent geometry : bond 0.00470 (10573) covalent geometry : angle 0.59094 (15242) hydrogen bonds : bond 0.05220 ( 565) hydrogen bonds : angle 3.14596 ( 1485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.45 seconds wall clock time: 45 minutes 8.87 seconds (2708.87 seconds total)