Starting phenix.real_space_refine on Fri Mar 14 04:17:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j91_36084/03_2025/8j91_36084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j91_36084/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j91_36084/03_2025/8j91_36084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j91_36084/03_2025/8j91_36084.map" model { file = "/net/cci-nas-00/data/ceres_data/8j91_36084/03_2025/8j91_36084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j91_36084/03_2025/8j91_36084.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.31, per 1000 atoms: 0.63 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: 2.71 Conformation dependent library (CDL) restraints added in 801.9 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: 5.34 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: 4.38 Time building geometry restraints manager: 3.48 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: 0.380 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 31.040 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:94.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.580 ------------------------------------------------------------------------------- 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= 0.562 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.004 0.001 HIS F 75 PHE 0.014 0.002 PHE G 26 TYR 0.017 0.002 TYR D 65 ARG 0.006 0.001 ARG A 116 *********************** 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 : 1.072 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: 2.5763 time to fit residues: 361.0309 Evaluate side-chains 77 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.182235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132355 restraints weight = 10582.546| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.32 r_work: 0.3189 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 10573 Z= 0.214 Angle : 0.777 37.818 15242 Z= 0.392 Chirality : 0.039 0.586 1749 Planarity : 0.005 0.046 1143 Dihedral : 30.382 161.264 3192 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.80 % Allowed : 10.23 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.32), residues: 662 helix: 2.12 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.42 (0.42), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.015 0.002 TYR F 51 ARG 0.008 0.001 ARG C 89 *********************** 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 106 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.766 Fit side-chains REVERT: A 129 ARG cc_start: 0.8360 (ttt180) cc_final: 0.8129 (ttt90) REVERT: B 79 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8183 (mmtm) REVERT: C 36 LYS cc_start: 0.8123 (mttt) cc_final: 0.7746 (mttp) REVERT: C 73 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6722 (t0) REVERT: C 89 ARG cc_start: 0.6822 (mmt90) cc_final: 0.6554 (mmt90) REVERT: H 65 TYR cc_start: 0.8733 (m-80) cc_final: 0.8355 (m-80) REVERT: H 93 ASP cc_start: 0.8399 (t70) cc_final: 0.7925 (t70) REVERT: H 141 LYS cc_start: 0.8546 (ttpp) cc_final: 0.8344 (ttmm) outliers start: 10 outliers final: 2 residues processed: 101 average time/residue: 1.6093 time to fit residues: 171.3962 Evaluate side-chains 89 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 8 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 30 optimal weight: 0.0980 chunk 47 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.176702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127948 restraints weight = 10659.395| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.24 r_work: 0.3074 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10573 Z= 0.300 Angle : 0.609 10.288 15242 Z= 0.354 Chirality : 0.037 0.143 1749 Planarity : 0.005 0.046 1143 Dihedral : 30.673 171.246 3192 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.23 % Allowed : 10.77 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.32), residues: 662 helix: 1.96 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -0.41 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.010 0.002 PHE A 104 TYR 0.018 0.002 TYR F 51 ARG 0.007 0.001 ARG E 63 *********************** 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 116 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8200 (tt0) cc_final: 0.7768 (pt0) REVERT: B 79 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8283 (mmtp) REVERT: C 36 LYS cc_start: 0.8155 (mttt) cc_final: 0.7728 (mttp) REVERT: C 73 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6681 (t0) REVERT: C 89 ARG cc_start: 0.6917 (mmt90) cc_final: 0.6669 (mmt90) REVERT: C 103 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8442 (mm) REVERT: D 147 THR cc_start: 0.7905 (m) cc_final: 0.7604 (m) REVERT: G 80 VAL cc_start: 0.8611 (m) cc_final: 0.8372 (m) REVERT: H 65 TYR cc_start: 0.8751 (m-80) cc_final: 0.8416 (m-80) REVERT: H 93 ASP cc_start: 0.8524 (t70) cc_final: 0.8121 (t70) outliers start: 18 outliers final: 8 residues processed: 108 average time/residue: 1.7476 time to fit residues: 198.3719 Evaluate side-chains 101 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 84 MET 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 41 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3973 r_free = 0.3973 target = 0.177203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125719 restraints weight = 10530.752| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.24 r_work: 0.3104 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10573 Z= 0.215 Angle : 0.566 9.592 15242 Z= 0.336 Chirality : 0.035 0.157 1749 Planarity : 0.005 0.049 1143 Dihedral : 30.604 163.425 3192 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.23 % Allowed : 13.82 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.31), residues: 662 helix: 2.15 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -0.36 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.015 0.002 TYR F 51 ARG 0.006 0.001 ARG F 39 *********************** 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 109 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.757 Fit side-chains REVERT: A 76 GLN cc_start: 0.8365 (tt0) cc_final: 0.7834 (pt0) REVERT: B 79 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8342 (mmtp) REVERT: C 36 LYS cc_start: 0.8143 (mttt) cc_final: 0.7725 (mttp) REVERT: C 73 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6799 (t0) REVERT: C 74 ASN cc_start: 0.6834 (m110) cc_final: 0.6493 (t0) REVERT: C 95 SER cc_start: 0.7957 (t) cc_final: 0.7692 (p) REVERT: C 103 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8434 (mm) REVERT: D 108 TYR cc_start: 0.7516 (m-10) cc_final: 0.6731 (t80) REVERT: D 147 THR cc_start: 0.7816 (m) cc_final: 0.7526 (m) REVERT: H 65 TYR cc_start: 0.8775 (m-80) cc_final: 0.8470 (m-80) REVERT: H 93 ASP cc_start: 0.8788 (t70) cc_final: 0.8383 (t70) outliers start: 18 outliers final: 7 residues processed: 101 average time/residue: 1.7161 time to fit residues: 182.2453 Evaluate side-chains 97 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 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 35 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN E 68 GLN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.172678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121705 restraints weight = 10450.609| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.32 r_work: 0.3018 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 10573 Z= 0.468 Angle : 0.696 11.576 15242 Z= 0.396 Chirality : 0.043 0.223 1749 Planarity : 0.007 0.078 1143 Dihedral : 31.132 162.714 3192 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.05 % Allowed : 15.26 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.31), residues: 662 helix: 1.60 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -0.61 (0.43), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 113 PHE 0.012 0.002 PHE A 104 TYR 0.015 0.003 TYR F 51 ARG 0.007 0.001 ARG E 131 *********************** 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 112 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8197 (tt0) cc_final: 0.7745 (pt0) REVERT: B 79 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8266 (mmtp) REVERT: C 36 LYS cc_start: 0.8136 (mttt) cc_final: 0.7759 (mttp) REVERT: C 73 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6667 (t0) REVERT: C 103 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8636 (mm) REVERT: D 108 TYR cc_start: 0.7370 (m-10) cc_final: 0.6875 (t80) REVERT: G 57 GLU cc_start: 0.8668 (tt0) cc_final: 0.8378 (tt0) REVERT: H 65 TYR cc_start: 0.8763 (m-80) cc_final: 0.8509 (m-80) outliers start: 17 outliers final: 10 residues processed: 104 average time/residue: 1.7599 time to fit residues: 192.0978 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 : 0.737 ------------------------------------------------------------------------------- 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 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 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 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.175903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.126723 restraints weight = 10416.825| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.25 r_work: 0.3083 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10573 Z= 0.195 Angle : 0.584 9.615 15242 Z= 0.348 Chirality : 0.036 0.138 1749 Planarity : 0.005 0.070 1143 Dihedral : 30.987 162.345 3192 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.05 % Allowed : 17.24 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.31), residues: 662 helix: 2.08 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -0.47 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.007 0.001 PHE E 67 TYR 0.014 0.002 TYR D 62 ARG 0.009 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8230 (mmtp) REVERT: C 36 LYS cc_start: 0.8098 (mttt) cc_final: 0.7714 (mttp) REVERT: C 43 ARG cc_start: 0.8323 (mtp85) cc_final: 0.8062 (mtp180) REVERT: C 73 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6677 (t0) REVERT: C 74 ASN cc_start: 0.6647 (m110) cc_final: 0.6329 (t0) REVERT: C 103 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8672 (mm) REVERT: D 108 TYR cc_start: 0.7320 (m-10) cc_final: 0.6939 (t80) REVERT: H 65 TYR cc_start: 0.8694 (m-80) cc_final: 0.8412 (m-80) REVERT: H 84 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.8024 (mmm) REVERT: H 141 LYS cc_start: 0.8423 (ttmm) cc_final: 0.8043 (ttpp) outliers start: 17 outliers final: 7 residues processed: 101 average time/residue: 1.7396 time to fit residues: 184.9817 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 : 0.722 ------------------------------------------------------------------------------- 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 84 MET 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 9 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN H 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.174175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125609 restraints weight = 10631.557| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.20 r_work: 0.3060 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10573 Z= 0.315 Angle : 0.605 9.802 15242 Z= 0.353 Chirality : 0.038 0.151 1749 Planarity : 0.005 0.057 1143 Dihedral : 30.876 161.849 3192 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.69 % Allowed : 16.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.31), residues: 662 helix: 2.09 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -0.54 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.010 0.002 PHE E 67 TYR 0.016 0.002 TYR F 51 ARG 0.007 0.001 ARG C 89 *********************** 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 98 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8403 (tt0) cc_final: 0.7867 (pt0) REVERT: B 79 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8288 (mmtp) REVERT: C 25 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7693 (mp10) REVERT: C 36 LYS cc_start: 0.8126 (mttt) cc_final: 0.7716 (mttp) REVERT: C 73 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6749 (t0) REVERT: C 74 ASN cc_start: 0.6705 (m110) cc_final: 0.6335 (t160) REVERT: C 103 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8677 (mm) REVERT: D 108 TYR cc_start: 0.7696 (m-10) cc_final: 0.7044 (t80) REVERT: G 57 GLU cc_start: 0.8814 (tt0) cc_final: 0.8562 (tt0) REVERT: H 65 TYR cc_start: 0.8788 (m-80) cc_final: 0.8562 (m-80) REVERT: H 141 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8067 (ttpp) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 1.9153 time to fit residues: 187.3105 Evaluate side-chains 94 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 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 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3947 r_free = 0.3947 target = 0.175053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126530 restraints weight = 10525.008| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.21 r_work: 0.3077 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3776 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= 0.217 Angle : 0.578 9.377 15242 Z= 0.342 Chirality : 0.036 0.238 1749 Planarity : 0.005 0.058 1143 Dihedral : 30.866 161.692 3192 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.51 % Allowed : 17.77 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.31), residues: 662 helix: 2.27 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.55 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.011 0.001 PHE E 67 TYR 0.015 0.002 TYR F 51 ARG 0.005 0.001 ARG E 63 *********************** 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 95 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8192 (tt0) cc_final: 0.7751 (pt0) REVERT: B 79 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8184 (mmtp) REVERT: C 25 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7627 (mp10) REVERT: C 36 LYS cc_start: 0.8080 (mttt) cc_final: 0.7690 (mttp) REVERT: C 73 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6678 (t0) REVERT: C 74 ASN cc_start: 0.6675 (m110) cc_final: 0.6354 (t160) REVERT: C 103 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8667 (mm) REVERT: D 108 TYR cc_start: 0.7460 (m-10) cc_final: 0.7058 (t80) REVERT: H 65 TYR cc_start: 0.8702 (m-80) cc_final: 0.8461 (m-80) REVERT: H 141 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8051 (ttpp) outliers start: 14 outliers final: 8 residues processed: 92 average time/residue: 1.8345 time to fit residues: 177.2161 Evaluate side-chains 90 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.174013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124913 restraints weight = 10491.864| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.23 r_work: 0.3055 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10573 Z= 0.311 Angle : 0.602 9.664 15242 Z= 0.352 Chirality : 0.038 0.140 1749 Planarity : 0.005 0.056 1143 Dihedral : 30.855 162.092 3192 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.33 % Allowed : 17.95 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.31), residues: 662 helix: 2.18 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.64 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.010 0.002 PHE E 67 TYR 0.016 0.002 TYR F 51 ARG 0.009 0.001 ARG C 89 *********************** 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 93 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8244 (tt0) cc_final: 0.7764 (pt0) REVERT: B 79 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8181 (mmtp) REVERT: C 25 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7619 (mp10) REVERT: C 36 LYS cc_start: 0.8108 (mttt) cc_final: 0.7714 (mttp) REVERT: C 73 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6645 (t0) REVERT: C 74 ASN cc_start: 0.6637 (m110) cc_final: 0.6307 (t160) REVERT: C 78 ARG cc_start: 0.7670 (mmm-85) cc_final: 0.7322 (ttm110) REVERT: C 103 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8682 (mm) REVERT: D 108 TYR cc_start: 0.7457 (m-10) cc_final: 0.6911 (t80) REVERT: H 65 TYR cc_start: 0.8728 (m-80) cc_final: 0.8510 (m-80) REVERT: H 141 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8056 (ttpp) outliers start: 13 outliers final: 7 residues processed: 88 average time/residue: 2.0688 time to fit residues: 191.7288 Evaluate side-chains 89 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 0.3980 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 72 GLN H 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.174753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125590 restraints weight = 10503.511| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.24 r_work: 0.3064 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3898 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= 0.225 Angle : 0.580 9.538 15242 Z= 0.343 Chirality : 0.036 0.140 1749 Planarity : 0.005 0.057 1143 Dihedral : 30.854 161.944 3192 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.62 % Allowed : 19.21 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.32), residues: 662 helix: 2.29 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.61 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.011 0.002 PHE E 67 TYR 0.016 0.002 TYR F 51 ARG 0.008 0.001 ARG C 89 ********************** 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 90 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8246 (tt0) cc_final: 0.7778 (pt0) REVERT: B 79 LYS cc_start: 0.8672 (mtpt) cc_final: 0.8182 (mmtp) REVERT: C 25 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7618 (mp10) REVERT: C 36 LYS cc_start: 0.8106 (mttt) cc_final: 0.7707 (mttp) REVERT: C 73 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6641 (t0) REVERT: C 74 ASN cc_start: 0.6610 (m110) cc_final: 0.6288 (t160) REVERT: C 78 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7315 (ttm110) REVERT: C 103 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8680 (mm) REVERT: D 108 TYR cc_start: 0.7459 (m-10) cc_final: 0.6912 (t80) REVERT: H 65 TYR cc_start: 0.8712 (m-80) cc_final: 0.8486 (m-80) REVERT: H 101 GLU cc_start: 0.7979 (tp30) cc_final: 0.7743 (tm-30) REVERT: H 141 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8057 (ttpp) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 1.7555 time to fit residues: 160.7535 Evaluate side-chains 88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.174884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125805 restraints weight = 10520.539| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.24 r_work: 0.3067 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3906 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= 0.220 Angle : 0.575 9.626 15242 Z= 0.341 Chirality : 0.036 0.135 1749 Planarity : 0.005 0.057 1143 Dihedral : 30.840 162.033 3192 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.44 % Allowed : 19.57 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.32), residues: 662 helix: 2.31 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -0.60 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.015 0.002 TYR F 51 ARG 0.010 0.001 ARG C 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6742.32 seconds wall clock time: 119 minutes 25.22 seconds (7165.22 seconds total)