Starting phenix.real_space_refine on Sat Aug 23 13:25:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v28_42901/08_2025/8v28_42901_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v28_42901/08_2025/8v28_42901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v28_42901/08_2025/8v28_42901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v28_42901/08_2025/8v28_42901.map" model { file = "/net/cci-nas-00/data/ceres_data/8v28_42901/08_2025/8v28_42901_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v28_42901/08_2025/8v28_42901_neut.cif" } resolution = 3.36 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= 0.002 sd= 0.019 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 288 5.49 5 S 15 5.16 5 C 7046 2.51 5 N 2380 2.21 5 O 2930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s 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: 12659 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 764 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 3.22, per 1000 atoms: 0.25 Number of scatterers: 12659 At special positions: 0 Unit cell: (100.88, 122.22, 118.34, 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 15 16.00 P 288 15.00 O 2930 8.00 N 2380 7.00 C 7046 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: 1.23 Conformation dependent library (CDL) restraints added in 437.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 67.0% alpha, 4.3% beta 139 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.829A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.772A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.653A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.171A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.562A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.631A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.518A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.657A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.645A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.564A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.717A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.520A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.176A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.551A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.595A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.545A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.576A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 37 through 41 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A 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 42 through 43 removed outlier: 7.330A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.738A 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 42 through 43 removed outlier: 7.385A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 12 through 16 421 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2434 1.33 - 1.45: 4277 1.45 - 1.57: 6155 1.57 - 1.69: 576 1.69 - 1.81: 26 Bond restraints: 13468 Sorted by residual: bond pdb=" C1' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.460 1.384 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1' DG J -70 " pdb=" N9 DG J -70 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C1' DA I 72 " pdb=" N9 DA I 72 " ideal model delta sigma weight residual 1.460 1.390 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N TYR B 98 " pdb=" CA TYR B 98 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.21e-02 6.83e+03 5.20e+00 bond pdb=" N ASP H 65 " pdb=" CA ASP H 65 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.20e+00 ... (remaining 13463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19164 2.13 - 4.26: 239 4.26 - 6.39: 17 6.39 - 8.52: 1 8.52 - 10.65: 5 Bond angle restraints: 19426 Sorted by residual: angle pdb=" C3' DG J 71 " pdb=" O3' DG J 71 " pdb=" P DA J 72 " ideal model delta sigma weight residual 120.20 109.55 10.65 1.50e+00 4.44e-01 5.05e+01 angle pdb=" C3' DC J 70 " pdb=" O3' DC J 70 " pdb=" P DG J 71 " ideal model delta sigma weight residual 120.20 109.76 10.44 1.50e+00 4.44e-01 4.84e+01 angle pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sigma weight residual 120.20 110.58 9.62 1.50e+00 4.44e-01 4.12e+01 angle pdb=" CB ARG K 42 " pdb=" CG ARG K 42 " pdb=" CD ARG K 42 " ideal model delta sigma weight residual 111.30 120.88 -9.58 2.30e+00 1.89e-01 1.73e+01 angle pdb=" CA LYS C 118 " pdb=" CB LYS C 118 " pdb=" CG LYS C 118 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 ... (remaining 19421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 6009 35.66 - 71.32: 1362 71.32 - 106.98: 13 106.98 - 142.65: 4 142.65 - 178.31: 1 Dihedral angle restraints: 7389 sinusoidal: 4936 harmonic: 2453 Sorted by residual: 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 -140.00 38.31 -178.31 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 91.35 128.65 1 3.50e+01 8.16e-04 1.27e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 95.57 124.43 1 3.50e+01 8.16e-04 1.23e+01 ... (remaining 7386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2164 0.093 - 0.186: 48 0.186 - 0.279: 0 0.279 - 0.373: 0 0.373 - 0.466: 3 Chirality restraints: 2215 Sorted by residual: chirality pdb=" P DC J 70 " pdb=" OP1 DC J 70 " pdb=" OP2 DC J 70 " pdb=" O5' DC J 70 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" P DG J 71 " pdb=" OP1 DG J 71 " pdb=" OP2 DG J 71 " pdb=" O5' DG J 71 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" P DA J 72 " pdb=" OP1 DA J 72 " pdb=" OP2 DA J 72 " pdb=" O5' DA J 72 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 2212 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ASP F 24 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 24 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" CG ASP F 24 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP F 24 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP F 24 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.024 2.00e-02 2.50e+03 1.00e-02 3.01e+00 pdb=" N9 DG I 47 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2842 2.82 - 3.34: 10531 3.34 - 3.86: 22604 3.86 - 4.38: 26544 4.38 - 4.90: 38192 Nonbonded interactions: 100713 Sorted by model distance: nonbonded pdb=" O THR E 58 " pdb=" OG1 THR E 58 " model vdw 2.295 3.040 nonbonded pdb=" O GLN K 2 " pdb=" N GLU K 64 " model vdw 2.347 3.120 nonbonded pdb=" O ARG A 129 " pdb=" NH1 ARG A 129 " model vdw 2.361 3.120 nonbonded pdb=" N ASP F 85 " pdb=" OD1 ASP F 85 " model vdw 2.362 3.120 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.376 3.040 ... (remaining 100708 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 37 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 26 through 121) 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.450 Find NCS groups from input model: 0.160 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 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 : 0.004 0.076 13468 Z= 0.196 Angle : 0.582 10.654 19426 Z= 0.351 Chirality : 0.038 0.466 2215 Planarity : 0.004 0.037 1457 Dihedral : 27.274 178.308 5803 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.56 % Allowed : 19.15 % Favored : 80.28 % 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: 2.83 (0.30), residues: 827 helix: 3.33 (0.22), residues: 530 sheet: 1.37 (1.73), residues: 12 loop : -1.10 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.017 0.001 TYR H 80 PHE 0.010 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00422 (13468) covalent geometry : angle 0.58220 (19426) hydrogen bonds : bond 0.11556 ( 778) hydrogen bonds : angle 3.58914 ( 1950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.368 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 114 average time/residue: 0.1828 time to fit residues: 27.1800 Evaluate side-chains 110 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.059272 restraints weight = 30130.438| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.08 r_work: 0.2621 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13468 Z= 0.232 Angle : 0.572 7.649 19426 Z= 0.344 Chirality : 0.036 0.136 2215 Planarity : 0.004 0.035 1457 Dihedral : 29.412 178.287 4112 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.83 % Allowed : 19.44 % Favored : 78.73 % 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: 2.83 (0.30), residues: 827 helix: 3.30 (0.22), residues: 532 sheet: 1.24 (1.32), residues: 20 loop : -1.13 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.017 0.001 TYR B 98 PHE 0.011 0.001 PHE D 67 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00528 (13468) covalent geometry : angle 0.57174 (19426) hydrogen bonds : bond 0.07002 ( 778) hydrogen bonds : angle 3.20143 ( 1950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.371 Fit side-chains REVERT: A 83 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8381 (mtp180) REVERT: D 73 GLU cc_start: 0.9165 (tp30) cc_final: 0.8781 (tp30) REVERT: E 118 THR cc_start: 0.9484 (m) cc_final: 0.9261 (p) REVERT: F 24 ASP cc_start: 0.8520 (p0) cc_final: 0.8283 (p0) REVERT: H 65 ASP cc_start: 0.8815 (t0) cc_final: 0.8579 (t0) outliers start: 13 outliers final: 5 residues processed: 123 average time/residue: 0.1841 time to fit residues: 29.2806 Evaluate side-chains 113 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 0.0010 chunk 101 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.094065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.062909 restraints weight = 30415.812| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.16 r_work: 0.2704 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13468 Z= 0.149 Angle : 0.520 7.289 19426 Z= 0.314 Chirality : 0.032 0.128 2215 Planarity : 0.004 0.053 1457 Dihedral : 29.360 178.385 4110 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.39 % Allowed : 20.70 % Favored : 76.90 % 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: 3.17 (0.30), residues: 827 helix: 3.56 (0.22), residues: 530 sheet: 1.35 (1.32), residues: 20 loop : -0.94 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.009 0.001 TYR H 80 PHE 0.006 0.001 PHE F 61 HIS 0.002 0.001 HIS K 68 Details of bonding type rmsd covalent geometry : bond 0.00304 (13468) covalent geometry : angle 0.51953 (19426) hydrogen bonds : bond 0.04969 ( 778) hydrogen bonds : angle 2.83056 ( 1950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.327 Fit side-chains REVERT: A 83 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8641 (mtp85) REVERT: B 24 ASP cc_start: 0.8543 (t0) cc_final: 0.8329 (t0) REVERT: D 73 GLU cc_start: 0.9166 (tp30) cc_final: 0.8947 (tp30) REVERT: F 24 ASP cc_start: 0.8571 (p0) cc_final: 0.8286 (p0) REVERT: H 65 ASP cc_start: 0.8798 (t0) cc_final: 0.8539 (t0) outliers start: 17 outliers final: 6 residues processed: 134 average time/residue: 0.1653 time to fit residues: 29.3150 Evaluate side-chains 113 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 35 optimal weight: 0.0020 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.094166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.063265 restraints weight = 30249.961| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.11 r_work: 0.2712 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13468 Z= 0.151 Angle : 0.509 5.602 19426 Z= 0.310 Chirality : 0.032 0.128 2215 Planarity : 0.004 0.035 1457 Dihedral : 29.399 178.286 4110 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.41 % Allowed : 21.83 % Favored : 76.76 % 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: 3.21 (0.30), residues: 827 helix: 3.61 (0.22), residues: 532 sheet: 1.24 (1.30), residues: 20 loop : -1.00 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.008 0.001 TYR H 80 PHE 0.008 0.001 PHE F 61 HIS 0.002 0.000 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00318 (13468) covalent geometry : angle 0.50929 (19426) hydrogen bonds : bond 0.04840 ( 778) hydrogen bonds : angle 2.76744 ( 1950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.378 Fit side-chains REVERT: A 59 GLU cc_start: 0.8261 (pm20) cc_final: 0.7909 (pm20) REVERT: D 73 GLU cc_start: 0.9223 (tp30) cc_final: 0.8905 (tp30) REVERT: F 24 ASP cc_start: 0.8592 (p0) cc_final: 0.8285 (p0) REVERT: H 65 ASP cc_start: 0.8809 (t0) cc_final: 0.8586 (t0) outliers start: 10 outliers final: 6 residues processed: 120 average time/residue: 0.1685 time to fit residues: 26.3763 Evaluate side-chains 114 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.063299 restraints weight = 30403.330| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.14 r_work: 0.2715 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13468 Z= 0.148 Angle : 0.506 5.447 19426 Z= 0.307 Chirality : 0.032 0.127 2215 Planarity : 0.003 0.035 1457 Dihedral : 29.395 178.323 4110 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.55 % Allowed : 21.69 % Favored : 76.76 % 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: 3.23 (0.30), residues: 827 helix: 3.64 (0.22), residues: 532 sheet: 1.19 (1.30), residues: 20 loop : -1.02 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.009 0.001 TYR H 80 PHE 0.007 0.001 PHE F 61 HIS 0.001 0.000 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00310 (13468) covalent geometry : angle 0.50647 (19426) hydrogen bonds : bond 0.04750 ( 778) hydrogen bonds : angle 2.73655 ( 1950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.351 Fit side-chains REVERT: A 59 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: D 73 GLU cc_start: 0.9186 (tp30) cc_final: 0.8811 (tp30) REVERT: F 24 ASP cc_start: 0.8559 (p0) cc_final: 0.8242 (p0) outliers start: 11 outliers final: 8 residues processed: 115 average time/residue: 0.1605 time to fit residues: 24.5525 Evaluate side-chains 115 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.061842 restraints weight = 30059.013| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.10 r_work: 0.2681 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13468 Z= 0.173 Angle : 0.519 5.861 19426 Z= 0.315 Chirality : 0.033 0.130 2215 Planarity : 0.004 0.040 1457 Dihedral : 29.435 178.196 4110 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.54 % Allowed : 21.41 % Favored : 76.06 % 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: 3.14 (0.30), residues: 827 helix: 3.60 (0.22), residues: 532 sheet: 1.57 (1.28), residues: 19 loop : -1.17 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.011 0.001 TYR H 80 PHE 0.009 0.001 PHE F 61 HIS 0.002 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00379 (13468) covalent geometry : angle 0.51907 (19426) hydrogen bonds : bond 0.05448 ( 778) hydrogen bonds : angle 2.82621 ( 1950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.333 Fit side-chains REVERT: D 73 GLU cc_start: 0.9190 (tp30) cc_final: 0.8815 (tp30) REVERT: F 24 ASP cc_start: 0.8548 (p0) cc_final: 0.8209 (p0) REVERT: H 32 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7674 (mm-30) outliers start: 18 outliers final: 10 residues processed: 122 average time/residue: 0.1581 time to fit residues: 25.7699 Evaluate side-chains 118 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 82 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 50.0000 chunk 24 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.089567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.057156 restraints weight = 29593.560| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.10 r_work: 0.2564 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 13468 Z= 0.293 Angle : 0.620 6.814 19426 Z= 0.369 Chirality : 0.039 0.144 2215 Planarity : 0.004 0.041 1457 Dihedral : 29.658 179.239 4110 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.68 % Allowed : 21.13 % Favored : 76.20 % 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: 2.62 (0.30), residues: 827 helix: 3.20 (0.22), residues: 533 sheet: 1.66 (1.36), residues: 19 loop : -1.43 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 96 TYR 0.016 0.002 TYR H 80 PHE 0.014 0.002 PHE D 67 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00680 (13468) covalent geometry : angle 0.61998 (19426) hydrogen bonds : bond 0.08044 ( 778) hydrogen bonds : angle 3.32046 ( 1950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.366 Fit side-chains REVERT: D 32 GLU cc_start: 0.8527 (mp0) cc_final: 0.8233 (mp0) REVERT: D 73 GLU cc_start: 0.9172 (tp30) cc_final: 0.8728 (tp30) REVERT: F 24 ASP cc_start: 0.8634 (p0) cc_final: 0.8398 (p0) REVERT: F 74 GLU cc_start: 0.9075 (tp30) cc_final: 0.8789 (mt-10) REVERT: H 32 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7696 (mm-30) outliers start: 19 outliers final: 15 residues processed: 123 average time/residue: 0.1563 time to fit residues: 25.7643 Evaluate side-chains 122 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.061137 restraints weight = 29279.545| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.10 r_work: 0.2658 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13468 Z= 0.157 Angle : 0.555 9.793 19426 Z= 0.333 Chirality : 0.035 0.131 2215 Planarity : 0.004 0.036 1457 Dihedral : 29.517 178.947 4110 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.11 % Allowed : 22.54 % Favored : 75.35 % 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: 2.80 (0.30), residues: 827 helix: 3.37 (0.22), residues: 532 sheet: 1.52 (1.35), residues: 19 loop : -1.37 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 96 TYR 0.016 0.001 TYR H 80 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00320 (13468) covalent geometry : angle 0.55531 (19426) hydrogen bonds : bond 0.05758 ( 778) hydrogen bonds : angle 2.85160 ( 1950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.339 Fit side-chains REVERT: B 74 GLU cc_start: 0.8368 (tp30) cc_final: 0.8070 (tp30) REVERT: D 73 GLU cc_start: 0.9170 (tp30) cc_final: 0.8890 (tp30) REVERT: F 24 ASP cc_start: 0.8593 (p0) cc_final: 0.8244 (p0) REVERT: H 32 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7462 (mm-30) REVERT: H 65 ASP cc_start: 0.8823 (t0) cc_final: 0.8583 (t0) outliers start: 15 outliers final: 10 residues processed: 120 average time/residue: 0.1504 time to fit residues: 24.3514 Evaluate side-chains 118 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 106 optimal weight: 0.2980 chunk 89 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN K 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.091183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.059085 restraints weight = 29673.181| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.10 r_work: 0.2612 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13468 Z= 0.219 Angle : 0.568 8.103 19426 Z= 0.341 Chirality : 0.035 0.138 2215 Planarity : 0.004 0.035 1457 Dihedral : 29.588 178.808 4110 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.97 % Allowed : 22.68 % Favored : 75.35 % 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: 2.78 (0.30), residues: 827 helix: 3.37 (0.22), residues: 533 sheet: 1.32 (1.35), residues: 19 loop : -1.44 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 96 TYR 0.025 0.001 TYR H 80 PHE 0.010 0.001 PHE F 61 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00499 (13468) covalent geometry : angle 0.56824 (19426) hydrogen bonds : bond 0.06605 ( 778) hydrogen bonds : angle 3.05232 ( 1950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.374 Fit side-chains REVERT: C 91 GLU cc_start: 0.8101 (tp30) cc_final: 0.7850 (tp30) REVERT: D 32 GLU cc_start: 0.8519 (mp0) cc_final: 0.8233 (mp0) REVERT: D 73 GLU cc_start: 0.9189 (tp30) cc_final: 0.8832 (tp30) REVERT: F 24 ASP cc_start: 0.8606 (p0) cc_final: 0.8362 (p0) REVERT: F 39 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8957 (tpp-160) REVERT: H 32 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7513 (mm-30) outliers start: 14 outliers final: 12 residues processed: 115 average time/residue: 0.1569 time to fit residues: 24.2704 Evaluate side-chains 119 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 18 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.092539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.060593 restraints weight = 29715.816| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.11 r_work: 0.2644 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13468 Z= 0.153 Angle : 0.542 7.715 19426 Z= 0.328 Chirality : 0.033 0.130 2215 Planarity : 0.004 0.035 1457 Dihedral : 29.565 178.881 4110 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.41 % Allowed : 23.24 % Favored : 75.35 % 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: 2.81 (0.30), residues: 827 helix: 3.38 (0.22), residues: 533 sheet: 1.27 (1.34), residues: 19 loop : -1.38 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.019 0.001 TYR H 80 PHE 0.008 0.001 PHE F 61 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00312 (13468) covalent geometry : angle 0.54192 (19426) hydrogen bonds : bond 0.05772 ( 778) hydrogen bonds : angle 2.87767 ( 1950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.343 Fit side-chains REVERT: C 91 GLU cc_start: 0.8032 (tp30) cc_final: 0.7789 (tp30) REVERT: D 73 GLU cc_start: 0.9170 (tp30) cc_final: 0.8809 (tp30) REVERT: F 24 ASP cc_start: 0.8601 (p0) cc_final: 0.8254 (p0) REVERT: H 65 ASP cc_start: 0.8846 (t0) cc_final: 0.8637 (t0) outliers start: 10 outliers final: 9 residues processed: 114 average time/residue: 0.1347 time to fit residues: 20.9282 Evaluate side-chains 115 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN K 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.091117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.058980 restraints weight = 29599.694| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.11 r_work: 0.2613 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13468 Z= 0.219 Angle : 0.569 7.034 19426 Z= 0.342 Chirality : 0.035 0.137 2215 Planarity : 0.004 0.035 1457 Dihedral : 29.600 178.713 4110 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.55 % Allowed : 23.10 % Favored : 75.35 % 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: 2.74 (0.30), residues: 827 helix: 3.33 (0.22), residues: 533 sheet: 1.22 (1.35), residues: 19 loop : -1.43 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 96 TYR 0.024 0.002 TYR H 80 PHE 0.010 0.001 PHE F 61 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00496 (13468) covalent geometry : angle 0.56910 (19426) hydrogen bonds : bond 0.06620 ( 778) hydrogen bonds : angle 3.05644 ( 1950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2587.59 seconds wall clock time: 45 minutes 0.48 seconds (2700.48 seconds total)