Starting phenix.real_space_refine on Wed Aug 5 13:02:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ybk_39120/08_2026/8ybk_39120.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ybk_39120/08_2026/8ybk_39120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ybk_39120/08_2026/8ybk_39120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ybk_39120/08_2026/8ybk_39120.map" model { file = "/net/cci-nas-00/data/ceres_data/8ybk_39120/08_2026/8ybk_39120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ybk_39120/08_2026/8ybk_39120.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 228 5.49 5 S 14 5.16 5 C 5726 2.51 5 N 1932 2.21 5 O 2361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10261 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 632 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 764 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 773 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2321 Classifications: {'DNA': 114} Link IDs: {'rna3p': 113} Chain: "J" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2353 Classifications: {'DNA': 114} Link IDs: {'rna3p': 113} Time building chain proxies: 2.49, per 1000 atoms: 0.24 Number of scatterers: 10261 At special positions: 0 Unit cell: (113.42, 122.96, 109.18, 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 14 16.00 P 228 15.00 O 2361 8.00 N 1932 7.00 C 5726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 211.4 milliseconds 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 73.0% alpha, 3.1% beta 114 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.505A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.736A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) 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 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.375A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.638A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.887A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.486A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.551A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.580A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.916A 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: 7.046A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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: 6.939A 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: 7.051A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 389 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 296 hydrogen bonds 592 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1361 1.32 - 1.44: 3911 1.44 - 1.57: 5143 1.57 - 1.69: 456 1.69 - 1.81: 24 Bond restraints: 10895 Sorted by residual: bond pdb=" C5' DG I -55 " pdb=" C4' DG I -55 " ideal model delta sigma weight residual 1.512 1.548 -0.036 7.00e-03 2.04e+04 2.59e+01 bond pdb=" C5' DT I 15 " pdb=" C4' DT I 15 " ideal model delta sigma weight residual 1.512 1.547 -0.035 7.00e-03 2.04e+04 2.50e+01 bond pdb=" C5' DA I 46 " pdb=" C4' DA I 46 " ideal model delta sigma weight residual 1.512 1.546 -0.034 7.00e-03 2.04e+04 2.41e+01 bond pdb=" C5' DC J -47 " pdb=" C4' DC J -47 " ideal model delta sigma weight residual 1.512 1.546 -0.034 7.00e-03 2.04e+04 2.36e+01 bond pdb=" C5' DC I 35 " pdb=" C4' DC I 35 " ideal model delta sigma weight residual 1.512 1.545 -0.033 7.00e-03 2.04e+04 2.22e+01 ... (remaining 10890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 13962 1.64 - 3.28: 1412 3.28 - 4.93: 254 4.93 - 6.57: 38 6.57 - 8.21: 9 Bond angle restraints: 15675 Sorted by residual: angle pdb=" O5' DC I -27 " pdb=" C5' DC I -27 " pdb=" C4' DC I -27 " ideal model delta sigma weight residual 109.40 115.63 -6.23 8.00e-01 1.56e+00 6.06e+01 angle pdb=" O5' DC I -12 " pdb=" C5' DC I -12 " pdb=" C4' DC I -12 " ideal model delta sigma weight residual 109.40 114.96 -5.56 8.00e-01 1.56e+00 4.84e+01 angle pdb=" O5' DA I -54 " pdb=" C5' DA I -54 " pdb=" C4' DA I -54 " ideal model delta sigma weight residual 109.40 114.52 -5.12 8.00e-01 1.56e+00 4.10e+01 angle pdb=" O5' DA J -43 " pdb=" C5' DA J -43 " pdb=" C4' DA J -43 " ideal model delta sigma weight residual 109.40 114.09 -4.69 8.00e-01 1.56e+00 3.44e+01 angle pdb=" O5' DG I -55 " pdb=" C5' DG I -55 " pdb=" C4' DG I -55 " ideal model delta sigma weight residual 109.40 113.70 -4.30 8.00e-01 1.56e+00 2.89e+01 ... (remaining 15670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.78: 4002 19.78 - 39.55: 945 39.55 - 59.33: 953 59.33 - 79.11: 56 79.11 - 98.88: 7 Dihedral angle restraints: 5963 sinusoidal: 3921 harmonic: 2042 Sorted by residual: dihedral pdb=" CA LEU E 61 " pdb=" C LEU E 61 " pdb=" N ILE E 62 " pdb=" CA ILE E 62 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA LEU A 61 " pdb=" C LEU A 61 " pdb=" N ILE A 62 " pdb=" CA ILE A 62 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA VAL G 107 " pdb=" C VAL G 107 " pdb=" N LEU G 108 " pdb=" CA LEU G 108 " ideal model delta harmonic sigma weight residual 180.00 -154.21 -25.79 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 5960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1416 0.062 - 0.124: 323 0.124 - 0.186: 38 0.186 - 0.248: 10 0.248 - 0.310: 2 Chirality restraints: 1789 Sorted by residual: chirality pdb=" CA ARG B 40 " pdb=" N ARG B 40 " pdb=" C ARG B 40 " pdb=" CB ARG B 40 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA LYS C 36 " pdb=" N LYS C 36 " pdb=" C LYS C 36 " pdb=" CB LYS C 36 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA GLU H 71 " pdb=" N GLU H 71 " pdb=" C GLU H 71 " pdb=" CB GLU H 71 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1786 not shown) Planarity restraints: 1195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -7 " -0.099 2.00e-02 2.50e+03 6.11e-02 1.12e+02 pdb=" N9 DG I -7 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DG I -7 " 0.117 2.00e-02 2.50e+03 pdb=" N7 DG I -7 " 0.077 2.00e-02 2.50e+03 pdb=" C5 DG I -7 " -0.024 2.00e-02 2.50e+03 pdb=" C6 DG I -7 " -0.037 2.00e-02 2.50e+03 pdb=" O6 DG I -7 " -0.076 2.00e-02 2.50e+03 pdb=" N1 DG I -7 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG I -7 " 0.015 2.00e-02 2.50e+03 pdb=" N2 DG I -7 " 0.080 2.00e-02 2.50e+03 pdb=" N3 DG I -7 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DG I -7 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -11 " 0.089 2.00e-02 2.50e+03 5.96e-02 1.07e+02 pdb=" N9 DG I -11 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG I -11 " -0.105 2.00e-02 2.50e+03 pdb=" N7 DG I -11 " -0.085 2.00e-02 2.50e+03 pdb=" C5 DG I -11 " 0.013 2.00e-02 2.50e+03 pdb=" C6 DG I -11 " 0.040 2.00e-02 2.50e+03 pdb=" O6 DG I -11 " 0.069 2.00e-02 2.50e+03 pdb=" N1 DG I -11 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DG I -11 " -0.020 2.00e-02 2.50e+03 pdb=" N2 DG I -11 " -0.087 2.00e-02 2.50e+03 pdb=" N3 DG I -11 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DG I -11 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -13 " 0.111 2.00e-02 2.50e+03 5.95e-02 9.75e+01 pdb=" N9 DA I -13 " 0.008 2.00e-02 2.50e+03 pdb=" C8 DA I -13 " -0.102 2.00e-02 2.50e+03 pdb=" N7 DA I -13 " -0.050 2.00e-02 2.50e+03 pdb=" C5 DA I -13 " 0.022 2.00e-02 2.50e+03 pdb=" C6 DA I -13 " 0.027 2.00e-02 2.50e+03 pdb=" N6 DA I -13 " 0.087 2.00e-02 2.50e+03 pdb=" N1 DA I -13 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DA I -13 " -0.055 2.00e-02 2.50e+03 pdb=" N3 DA I -13 " -0.032 2.00e-02 2.50e+03 pdb=" C4 DA I -13 " 0.010 2.00e-02 2.50e+03 ... (remaining 1192 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 3137 2.87 - 3.38: 8636 3.38 - 3.89: 20259 3.89 - 4.39: 23298 4.39 - 4.90: 32409 Nonbonded interactions: 87739 Sorted by model distance: nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.369 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NE ARG E 131 " model vdw 2.423 3.120 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.427 3.040 nonbonded pdb=" NH1 ARG A 72 " pdb=" OP1 DC I -23 " model vdw 2.440 3.120 nonbonded pdb=" O ALA D 124 " pdb=" OXT LYS D 125 " model vdw 2.446 3.040 ... (remaining 87734 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 58 through 135) } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 108) } ncs_group { reference = (chain 'D' and resid 32 through 125) 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=0.00 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: 1.130 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.900 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.008 0.047 10895 Z= 0.734 Angle : 1.069 8.212 15675 Z= 0.924 Chirality : 0.054 0.310 1789 Planarity : 0.014 0.125 1195 Dihedral : 27.854 98.881 4647 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 14.78 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.30), residues: 692 helix: 1.85 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -1.32 (0.36), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG E 131 TYR 0.068 0.005 TYR H 42 PHE 0.054 0.004 PHE H 70 HIS 0.012 0.002 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00811 / 0.73 (10895) covalent geometry : angle 1.06909 / 0.92 (15675) hydrogen bonds : bond 0.11763 / 7.58 ( 685) hydrogen bonds : angle 3.94742 / 2.77 ( 1744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.311 Fit side-chains REVERT: C 75 LYS cc_start: 0.8227 (mttp) cc_final: 0.7562 (tmtt) REVERT: C 95 LYS cc_start: 0.8838 (tttt) cc_final: 0.8233 (ttpt) REVERT: E 94 GLU cc_start: 0.8407 (tp30) cc_final: 0.8166 (mm-30) REVERT: F 39 ARG cc_start: 0.8046 (mpt180) cc_final: 0.7800 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.9854 time to fit residues: 144.0193 Evaluate side-chains 126 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 104 GLN D 82 HIS D 84 ASN E 76 GLN F 25 ASN G 24 GLN H 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116038 restraints weight = 11164.690| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.26 r_work: 0.3232 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10895 Z= 0.139 Angle : 0.653 6.701 15675 Z= 0.380 Chirality : 0.047 0.222 1789 Planarity : 0.004 0.039 1195 Dihedral : 30.275 107.944 3267 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.55 % Allowed : 15.64 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.31), residues: 692 helix: 2.75 (0.22), residues: 511 sheet: None (None), residues: 0 loop : -1.14 (0.38), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 72 TYR 0.009 0.001 TYR F 51 PHE 0.008 0.001 PHE H 70 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.14 (10895) covalent geometry : angle 0.65304 / 0.38 (15675) hydrogen bonds : bond 0.05122 / 3.34 ( 685) hydrogen bonds : angle 3.07858 / 2.19 ( 1744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8430 (tt0) cc_final: 0.8154 (tt0) REVERT: A 133 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8485 (mt-10) REVERT: B 35 ARG cc_start: 0.8826 (mtp85) cc_final: 0.8522 (mtp180) REVERT: C 75 LYS cc_start: 0.8005 (mttp) cc_final: 0.7285 (tptt) REVERT: C 95 LYS cc_start: 0.8532 (tttt) cc_final: 0.7796 (ttpt) REVERT: E 94 GLU cc_start: 0.8360 (tp30) cc_final: 0.8147 (mm-30) REVERT: H 113 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8310 (mm-30) outliers start: 9 outliers final: 1 residues processed: 134 average time/residue: 0.9258 time to fit residues: 129.9192 Evaluate side-chains 127 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 74 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 104 GLN D 82 HIS D 84 ASN E 76 GLN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.148829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113716 restraints weight = 11281.165| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.27 r_work: 0.3192 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10895 Z= 0.161 Angle : 0.631 6.159 15675 Z= 0.368 Chirality : 0.046 0.204 1789 Planarity : 0.005 0.038 1195 Dihedral : 30.460 110.141 3267 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.55 % Allowed : 16.84 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.31), residues: 692 helix: 2.85 (0.22), residues: 511 sheet: None (None), residues: 0 loop : -1.21 (0.37), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 72 TYR 0.010 0.002 TYR B 51 PHE 0.009 0.002 PHE B 61 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (10895) covalent geometry : angle 0.63060 / 0.37 (15675) hydrogen bonds : bond 0.05491 / 3.56 ( 685) hydrogen bonds : angle 2.97308 / 2.11 ( 1744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.219 Fit side-chains REVERT: A 133 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8450 (mt-10) REVERT: B 25 ASN cc_start: 0.8188 (m-40) cc_final: 0.7860 (m-40) REVERT: B 35 ARG cc_start: 0.8756 (mtp85) cc_final: 0.8505 (mtp180) REVERT: C 75 LYS cc_start: 0.8103 (mttp) cc_final: 0.7395 (tptt) REVERT: C 95 LYS cc_start: 0.8543 (tttt) cc_final: 0.7815 (ttpt) REVERT: E 94 GLU cc_start: 0.8420 (tp30) cc_final: 0.8180 (mm-30) outliers start: 9 outliers final: 3 residues processed: 132 average time/residue: 0.8929 time to fit residues: 123.3060 Evaluate side-chains 126 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 82 HIS E 76 GLN G 104 GLN H 63 ASN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.147972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112860 restraints weight = 11289.429| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.26 r_work: 0.3196 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10895 Z= 0.175 Angle : 0.643 6.499 15675 Z= 0.368 Chirality : 0.046 0.214 1789 Planarity : 0.005 0.051 1195 Dihedral : 30.554 113.417 3267 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.06 % Allowed : 17.01 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.31), residues: 692 helix: 2.78 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.31 (0.37), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.010 0.002 TYR B 51 PHE 0.008 0.002 PHE B 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (10895) covalent geometry : angle 0.64335 / 0.37 (15675) hydrogen bonds : bond 0.05518 / 3.59 ( 685) hydrogen bonds : angle 2.94563 / 2.10 ( 1744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.277 Fit side-chains REVERT: A 133 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8471 (mt-10) REVERT: B 35 ARG cc_start: 0.8721 (mtp85) cc_final: 0.8483 (mtp180) REVERT: B 93 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8075 (mm-40) REVERT: C 75 LYS cc_start: 0.8120 (mttp) cc_final: 0.7378 (tptt) REVERT: C 95 LYS cc_start: 0.8559 (tttt) cc_final: 0.7829 (ttpt) REVERT: D 85 LYS cc_start: 0.9170 (mmtp) cc_final: 0.8967 (mptt) REVERT: G 73 ASN cc_start: 0.7671 (t0) cc_final: 0.7435 (t0) REVERT: G 75 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7181 (tptt) outliers start: 12 outliers final: 5 residues processed: 135 average time/residue: 0.9432 time to fit residues: 132.9896 Evaluate side-chains 130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 4 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 40.0000 chunk 24 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 82 HIS E 76 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.148574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113496 restraints weight = 11241.448| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.26 r_work: 0.3202 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10895 Z= 0.154 Angle : 0.631 6.518 15675 Z= 0.362 Chirality : 0.045 0.213 1789 Planarity : 0.004 0.038 1195 Dihedral : 30.541 114.225 3267 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.06 % Allowed : 17.53 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.31), residues: 692 helix: 2.84 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.29 (0.37), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 72 TYR 0.010 0.001 TYR B 51 PHE 0.008 0.001 PHE B 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (10895) covalent geometry : angle 0.63104 / 0.36 (15675) hydrogen bonds : bond 0.05266 / 3.42 ( 685) hydrogen bonds : angle 2.92443 / 2.08 ( 1744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.287 Fit side-chains REVERT: A 133 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8449 (mt-10) REVERT: B 29 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7439 (mm) REVERT: B 35 ARG cc_start: 0.8740 (mtp85) cc_final: 0.8475 (mtp180) REVERT: B 93 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8057 (mm-40) REVERT: C 75 LYS cc_start: 0.8124 (mttp) cc_final: 0.7388 (tptt) REVERT: C 95 LYS cc_start: 0.8562 (tttt) cc_final: 0.7839 (ttpt) REVERT: E 133 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8379 (mt-10) REVERT: G 75 LYS cc_start: 0.8014 (mmmt) cc_final: 0.7231 (tmtt) REVERT: H 71 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8019 (mt-10) outliers start: 12 outliers final: 4 residues processed: 132 average time/residue: 0.9610 time to fit residues: 132.4402 Evaluate side-chains 130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 76 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 82 HIS E 76 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108812 restraints weight = 11421.761| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.26 r_work: 0.3153 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10895 Z= 0.272 Angle : 0.717 6.995 15675 Z= 0.398 Chirality : 0.051 0.220 1789 Planarity : 0.006 0.055 1195 Dihedral : 30.745 114.800 3267 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.06 % Allowed : 17.87 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.31), residues: 692 helix: 2.48 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.51 (0.36), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 72 TYR 0.012 0.002 TYR D 83 PHE 0.009 0.002 PHE B 100 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.27 (10895) covalent geometry : angle 0.71651 / 0.40 (15675) hydrogen bonds : bond 0.06994 / 4.54 ( 685) hydrogen bonds : angle 3.06959 / 2.18 ( 1744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.284 Fit side-chains REVERT: A 133 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: B 93 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8250 (mm-40) REVERT: C 75 LYS cc_start: 0.8193 (mttp) cc_final: 0.7468 (tptt) REVERT: C 95 LYS cc_start: 0.8622 (tttt) cc_final: 0.7919 (ttpt) REVERT: E 131 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.7114 (mtp180) REVERT: E 133 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: G 75 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7290 (tmtt) outliers start: 12 outliers final: 6 residues processed: 131 average time/residue: 1.0021 time to fit residues: 136.9140 Evaluate side-chains 132 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 82 HIS E 76 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109981 restraints weight = 11257.057| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.25 r_work: 0.3174 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10895 Z= 0.184 Angle : 0.676 6.614 15675 Z= 0.380 Chirality : 0.048 0.224 1789 Planarity : 0.005 0.040 1195 Dihedral : 30.741 116.205 3267 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.55 % Allowed : 18.73 % Favored : 79.73 % 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 are not related in a simple way. whole: 2.44 (0.31), residues: 692 helix: 2.61 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.52 (0.36), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 72 TYR 0.010 0.002 TYR F 51 PHE 0.009 0.001 PHE B 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (10895) covalent geometry : angle 0.67557 / 0.38 (15675) hydrogen bonds : bond 0.06082 / 3.94 ( 685) hydrogen bonds : angle 3.02608 / 2.16 ( 1744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.256 Fit side-chains REVERT: A 133 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8498 (mt-10) REVERT: B 93 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8197 (mm-40) REVERT: C 75 LYS cc_start: 0.8124 (mttp) cc_final: 0.7370 (tptt) REVERT: C 95 LYS cc_start: 0.8602 (tttt) cc_final: 0.7894 (ttpt) REVERT: D 108 LYS cc_start: 0.8324 (mtpp) cc_final: 0.7868 (mmtp) REVERT: E 133 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8431 (mt-10) REVERT: G 75 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7279 (tmtt) outliers start: 9 outliers final: 5 residues processed: 129 average time/residue: 0.9589 time to fit residues: 129.2222 Evaluate side-chains 130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 4 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 82 HIS E 76 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.145810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110494 restraints weight = 11278.537| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.26 r_work: 0.3177 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10895 Z= 0.146 Angle : 0.659 6.696 15675 Z= 0.374 Chirality : 0.047 0.224 1789 Planarity : 0.004 0.038 1195 Dihedral : 30.723 116.213 3267 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.72 % Allowed : 18.56 % Favored : 79.73 % 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 are not related in a simple way. whole: 2.54 (0.31), residues: 692 helix: 2.68 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.48 (0.36), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 72 TYR 0.011 0.002 TYR F 51 PHE 0.008 0.002 PHE D 65 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.15 (10895) covalent geometry : angle 0.65912 / 0.37 (15675) hydrogen bonds : bond 0.05764 / 3.74 ( 685) hydrogen bonds : angle 3.00912 / 2.15 ( 1744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.270 Fit side-chains REVERT: B 93 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8175 (mm-40) REVERT: C 75 LYS cc_start: 0.8119 (mttp) cc_final: 0.7367 (tptt) REVERT: C 95 LYS cc_start: 0.8594 (tttt) cc_final: 0.7883 (ttpt) REVERT: E 133 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8420 (mt-10) REVERT: G 75 LYS cc_start: 0.8086 (mmmt) cc_final: 0.7271 (tmtt) REVERT: H 71 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8020 (mt-10) outliers start: 10 outliers final: 5 residues processed: 126 average time/residue: 0.9686 time to fit residues: 127.5462 Evaluate side-chains 128 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 46 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 67 optimal weight: 40.0000 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 82 HIS E 76 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110364 restraints weight = 11264.770| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.27 r_work: 0.3176 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10895 Z= 0.186 Angle : 0.667 6.732 15675 Z= 0.375 Chirality : 0.047 0.222 1789 Planarity : 0.004 0.039 1195 Dihedral : 30.707 117.578 3267 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.72 % Allowed : 18.73 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.31), residues: 692 helix: 2.65 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.47 (0.36), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 72 TYR 0.010 0.002 TYR H 121 PHE 0.008 0.002 PHE B 61 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (10895) covalent geometry : angle 0.66676 / 0.38 (15675) hydrogen bonds : bond 0.05811 / 3.77 ( 685) hydrogen bonds : angle 2.98297 / 2.13 ( 1744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.289 Fit side-chains REVERT: A 133 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8488 (mt-10) REVERT: B 93 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8181 (mm-40) REVERT: C 75 LYS cc_start: 0.8129 (mttp) cc_final: 0.7370 (tptt) REVERT: C 95 LYS cc_start: 0.8615 (tttt) cc_final: 0.7905 (ttpt) REVERT: E 133 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: G 75 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7284 (tmtt) REVERT: H 71 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8018 (mt-10) outliers start: 10 outliers final: 4 residues processed: 126 average time/residue: 0.8540 time to fit residues: 112.3845 Evaluate side-chains 129 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 15 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 82 HIS E 76 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109324 restraints weight = 11462.435| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.27 r_work: 0.3159 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10895 Z= 0.136 Angle : 0.644 6.761 15675 Z= 0.367 Chirality : 0.046 0.224 1789 Planarity : 0.004 0.038 1195 Dihedral : 30.685 118.488 3267 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.37 % Allowed : 19.24 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.31), residues: 692 helix: 2.82 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.42 (0.37), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 72 TYR 0.010 0.002 TYR F 51 PHE 0.009 0.002 PHE D 65 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (10895) covalent geometry : angle 0.64431 / 0.37 (15675) hydrogen bonds : bond 0.05351 / 3.47 ( 685) hydrogen bonds : angle 2.97838 / 2.13 ( 1744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.168 Fit side-chains REVERT: A 133 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: B 93 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8147 (mm-40) REVERT: C 75 LYS cc_start: 0.8038 (mttp) cc_final: 0.7315 (tptt) REVERT: C 95 LYS cc_start: 0.8524 (tttt) cc_final: 0.7793 (ttpt) REVERT: E 133 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8422 (mt-10) REVERT: G 75 LYS cc_start: 0.8065 (mmmt) cc_final: 0.7236 (tmtt) REVERT: H 71 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7957 (mt-10) outliers start: 8 outliers final: 4 residues processed: 129 average time/residue: 0.8567 time to fit residues: 115.4217 Evaluate side-chains 130 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 0.0000 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 68 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 82 HIS E 76 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.145238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109590 restraints weight = 11554.495| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.28 r_work: 0.3165 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10895 Z= 0.139 Angle : 0.649 7.701 15675 Z= 0.368 Chirality : 0.046 0.226 1789 Planarity : 0.004 0.039 1195 Dihedral : 30.659 119.490 3267 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.20 % Allowed : 20.10 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.31), residues: 692 helix: 2.79 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.43 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 79 TYR 0.010 0.001 TYR F 51 PHE 0.009 0.001 PHE D 65 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (10895) covalent geometry : angle 0.64863 / 0.37 (15675) hydrogen bonds : bond 0.05228 / 3.40 ( 685) hydrogen bonds : angle 2.94865 / 2.11 ( 1744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4159.04 seconds wall clock time: 71 minutes 15.51 seconds (4275.51 seconds total)