Starting phenix.real_space_refine on Thu Jul 2 19:42:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ybk_39120/07_2026/8ybk_39120.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ybk_39120/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ybk_39120/07_2026/8ybk_39120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ybk_39120/07_2026/8ybk_39120.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ybk_39120/07_2026/8ybk_39120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ybk_39120/07_2026/8ybk_39120.map" } 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-dev-6108/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: 2.02, per 1000 atoms: 0.20 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: 0.89 Conformation dependent library (CDL) restraints added in 237.7 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: 1.50 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: 1.64 Time building geometry restraints manager: 1.19 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: 13982 1.64 - 3.28: 1397 3.28 - 4.93: 250 4.93 - 6.57: 37 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: 1.000 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.290 Find NCS groups from input model: 0.100 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:5.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- 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= 0.733 Angle : 1.061 8.212 15675 Z= 0.917 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 1.06095 / 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 : 0.249 Fit side-chains REVERT: C 75 LYS cc_start: 0.8227 (mttp) cc_final: 0.7490 (tptt) 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: 0.8371 time to fit residues: 122.5733 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 : 0.240 ------------------------------------------------------------------------------- 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: 9.9990 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 = 0.3868 r_free = 0.3868 target = 0.148356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114760 restraints weight = 11768.482| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.24 r_work: 0.3239 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0933 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= 0.140 Angle : 0.639 6.761 15675 Z= 0.377 Chirality : 0.047 0.218 1789 Planarity : 0.004 0.044 1195 Dihedral : 30.343 109.149 3267 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.55 % Allowed : 15.81 % Favored : 82.65 % 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: 2.73 (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 0.009 0.001 PHE H 70 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.14 (10895) covalent geometry : angle 0.63907 / 0.38 (15675) hydrogen bonds : bond 0.05204 / 3.39 ( 685) hydrogen bonds : angle 3.09413 / 2.21 ( 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 138 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8502 (tt0) cc_final: 0.8294 (tt0) REVERT: A 133 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8510 (mt-10) REVERT: B 35 ARG cc_start: 0.8840 (mtp85) cc_final: 0.8540 (mtp180) REVERT: C 75 LYS cc_start: 0.8025 (mttp) cc_final: 0.7309 (tptt) REVERT: C 95 LYS cc_start: 0.8679 (tttt) cc_final: 0.7979 (ttpt) REVERT: E 94 GLU cc_start: 0.8402 (tp30) cc_final: 0.8198 (mm-30) REVERT: H 113 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8336 (mm-30) outliers start: 9 outliers final: 1 residues processed: 133 average time/residue: 0.8159 time to fit residues: 113.5742 Evaluate side-chains 126 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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: 10.0000 chunk 5 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.150408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115526 restraints weight = 11317.007| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.27 r_work: 0.3224 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10895 Z= 0.140 Angle : 0.594 5.698 15675 Z= 0.355 Chirality : 0.044 0.187 1789 Planarity : 0.004 0.037 1195 Dihedral : 30.463 114.116 3267 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.72 % Allowed : 16.84 % Favored : 81.44 % 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: 2.96 (0.31), residues: 692 helix: 2.95 (0.22), residues: 511 sheet: None (None), residues: 0 loop : -1.13 (0.37), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 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 0.00248 / 0.14 (10895) covalent geometry : angle 0.59394 / 0.35 (15675) hydrogen bonds : bond 0.04927 / 3.20 ( 685) hydrogen bonds : angle 2.90946 / 2.07 ( 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 139 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8059 (m-40) cc_final: 0.7739 (m-40) REVERT: B 35 ARG cc_start: 0.8759 (mtp85) cc_final: 0.8482 (mtp180) REVERT: C 75 LYS cc_start: 0.8076 (mttp) cc_final: 0.7385 (tptt) REVERT: C 95 LYS cc_start: 0.8534 (tttt) cc_final: 0.7815 (ttpt) outliers start: 10 outliers final: 3 residues processed: 134 average time/residue: 0.8922 time to fit residues: 124.7143 Evaluate side-chains 127 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 15 LYS 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: 4.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 26 optimal weight: 0.0070 chunk 87 optimal weight: 9.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.147376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112121 restraints weight = 11277.793| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.27 r_work: 0.3183 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1254 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= 0.199 Angle : 0.644 6.284 15675 Z= 0.372 Chirality : 0.046 0.201 1789 Planarity : 0.005 0.040 1195 Dihedral : 30.635 115.521 3267 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.41 % Allowed : 16.49 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.31), residues: 692 helix: 2.74 (0.22), residues: 511 sheet: None (None), residues: 0 loop : -1.31 (0.36), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 72 TYR 0.010 0.002 TYR B 51 PHE 0.008 0.002 PHE B 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (10895) covalent geometry : angle 0.64442 / 0.37 (15675) hydrogen bonds : bond 0.05937 / 3.86 ( 685) hydrogen bonds : angle 2.98715 / 2.13 ( 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 142 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.261 Fit side-chains REVERT: A 133 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: B 35 ARG cc_start: 0.8755 (mtp85) cc_final: 0.8508 (mtp180) REVERT: B 93 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8077 (mm-40) REVERT: C 75 LYS cc_start: 0.8128 (mttp) cc_final: 0.7396 (tptt) REVERT: C 95 LYS cc_start: 0.8605 (tttt) cc_final: 0.7900 (ttpt) REVERT: D 85 LYS cc_start: 0.9171 (mmtp) cc_final: 0.8969 (mptt) REVERT: E 94 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8228 (mm-30) REVERT: G 73 ASN cc_start: 0.7704 (t0) cc_final: 0.7478 (t0) outliers start: 14 outliers final: 7 residues processed: 135 average time/residue: 0.8776 time to fit residues: 123.6945 Evaluate side-chains 134 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 G residue 15 LYS Chi-restraints excluded: chain H residue 108 LYS 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: 0.8980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 40.0000 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 104 GLN D 82 HIS E 76 GLN G 104 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 = 0.3841 r_free = 0.3841 target = 0.146545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111214 restraints weight = 11310.114| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.27 r_work: 0.3192 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10895 Z= 0.161 Angle : 0.628 6.337 15675 Z= 0.364 Chirality : 0.045 0.203 1789 Planarity : 0.004 0.038 1195 Dihedral : 30.641 115.986 3267 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.23 % Allowed : 17.01 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.31), residues: 692 helix: 2.79 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.36 (0.36), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 72 TYR 0.010 0.002 TYR D 83 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 0.00309 / 0.16 (10895) covalent geometry : angle 0.62760 / 0.36 (15675) hydrogen bonds : bond 0.05577 / 3.63 ( 685) hydrogen bonds : angle 2.96235 / 2.11 ( 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 137 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.251 Fit side-chains REVERT: A 133 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8474 (mt-10) REVERT: B 29 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7379 (mm) REVERT: B 35 ARG cc_start: 0.8721 (mtp85) cc_final: 0.8488 (mtp180) REVERT: B 93 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8044 (mm-40) REVERT: C 75 LYS cc_start: 0.8121 (mttp) cc_final: 0.7390 (tptt) REVERT: C 95 LYS cc_start: 0.8599 (tttt) cc_final: 0.7892 (ttpt) REVERT: D 85 LYS cc_start: 0.9167 (mmtp) cc_final: 0.8966 (mptt) REVERT: E 94 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8215 (mm-30) REVERT: E 133 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8366 (mt-10) REVERT: G 73 ASN cc_start: 0.7678 (t0) cc_final: 0.7401 (t0) REVERT: G 75 LYS cc_start: 0.7986 (mmmt) cc_final: 0.7160 (tptt) REVERT: H 71 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7992 (mt-10) outliers start: 13 outliers final: 6 residues processed: 131 average time/residue: 0.8444 time to fit residues: 115.8052 Evaluate side-chains 133 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 15 LYS 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: 10.0000 chunk 22 optimal weight: 0.8980 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: 5.9990 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 104 GLN D 82 HIS E 76 GLN G 104 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 = 0.3807 r_free = 0.3807 target = 0.143735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108290 restraints weight = 11410.490| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.27 r_work: 0.3145 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10895 Z= 0.302 Angle : 0.731 7.144 15675 Z= 0.407 Chirality : 0.052 0.226 1789 Planarity : 0.006 0.053 1195 Dihedral : 30.883 118.405 3267 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.09 % Allowed : 16.67 % Favored : 80.24 % 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: 2.12 (0.30), residues: 692 helix: 2.37 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.013 0.003 TYR D 83 PHE 0.009 0.003 PHE B 100 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.30 (10895) covalent geometry : angle 0.73084 / 0.41 (15675) hydrogen bonds : bond 0.07494 / 4.87 ( 685) hydrogen bonds : angle 3.13180 / 2.23 ( 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 140 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.279 Fit side-chains REVERT: A 133 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8543 (mt-10) REVERT: B 35 ARG cc_start: 0.8800 (mtp85) cc_final: 0.8523 (mtp180) REVERT: B 93 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: C 75 LYS cc_start: 0.8201 (mttp) cc_final: 0.7453 (tptt) REVERT: C 95 LYS cc_start: 0.8639 (tttt) cc_final: 0.7924 (ttpt) REVERT: D 85 LYS cc_start: 0.9167 (mmtp) cc_final: 0.8967 (mptt) REVERT: E 131 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.7095 (mtp180) REVERT: E 133 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: G 75 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7114 (tptt) outliers start: 18 outliers final: 7 residues processed: 132 average time/residue: 0.9283 time to fit residues: 128.0238 Evaluate side-chains 131 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 G residue 15 LYS 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: 0.5980 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 104 GLN D 82 HIS E 76 GLN G 84 GLN G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.146006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110737 restraints weight = 11243.510| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.26 r_work: 0.3185 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10895 Z= 0.142 Angle : 0.661 6.373 15675 Z= 0.377 Chirality : 0.047 0.225 1789 Planarity : 0.004 0.039 1195 Dihedral : 30.867 121.175 3267 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.55 % Allowed : 18.38 % 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: 2.51 (0.31), residues: 692 helix: 2.69 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.63 (0.35), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 72 TYR 0.012 0.002 TYR F 51 PHE 0.009 0.001 PHE D 65 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (10895) covalent geometry : angle 0.66112 / 0.38 (15675) hydrogen bonds : bond 0.05608 / 3.64 ( 685) hydrogen bonds : angle 3.09192 / 2.23 ( 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 132 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.208 Fit side-chains REVERT: A 73 GLU cc_start: 0.8398 (tt0) cc_final: 0.8162 (tt0) REVERT: A 133 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8493 (mt-10) REVERT: B 25 ASN cc_start: 0.8183 (m-40) cc_final: 0.7983 (m110) REVERT: B 93 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8148 (mm-40) REVERT: C 75 LYS cc_start: 0.8108 (mttp) cc_final: 0.7359 (tptt) REVERT: C 95 LYS cc_start: 0.8583 (tttt) cc_final: 0.7874 (ttpt) REVERT: D 85 LYS cc_start: 0.9138 (mmtp) cc_final: 0.8935 (mptt) REVERT: D 108 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7852 (mmtp) REVERT: G 75 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7251 (tmtt) outliers start: 9 outliers final: 7 residues processed: 129 average time/residue: 0.8338 time to fit residues: 112.3600 Evaluate side-chains 128 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 31 LYS 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 G residue 15 LYS 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: 0.6980 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 34 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.146309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111007 restraints weight = 11302.773| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.27 r_work: 0.3171 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10895 Z= 0.150 Angle : 0.654 7.260 15675 Z= 0.371 Chirality : 0.046 0.222 1789 Planarity : 0.004 0.038 1195 Dihedral : 30.812 122.143 3267 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 2.67 (0.31), residues: 692 helix: 2.79 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.53 (0.36), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 35 TYR 0.010 0.001 TYR F 51 PHE 0.008 0.001 PHE B 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (10895) covalent geometry : angle 0.65360 / 0.37 (15675) hydrogen bonds : bond 0.05400 / 3.52 ( 685) hydrogen bonds : angle 2.98891 / 2.14 ( 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: 9 poor density : 121 time to evaluate : 0.239 Fit side-chains REVERT: A 73 GLU cc_start: 0.8407 (tt0) cc_final: 0.7933 (tt0) REVERT: A 133 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8517 (mt-10) REVERT: B 25 ASN cc_start: 0.8228 (m-40) cc_final: 0.7771 (m110) REVERT: B 93 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8148 (mm-40) REVERT: C 75 LYS cc_start: 0.8120 (mttp) cc_final: 0.7363 (tptt) REVERT: C 95 LYS cc_start: 0.8595 (tttt) cc_final: 0.7878 (ttpt) REVERT: D 85 LYS cc_start: 0.9146 (mmtp) cc_final: 0.8944 (mptt) REVERT: E 94 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8154 (mm-30) REVERT: G 75 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7232 (tmtt) outliers start: 9 outliers final: 5 residues processed: 125 average time/residue: 0.8233 time to fit residues: 107.5177 Evaluate side-chains 126 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 G residue 15 LYS Chi-restraints excluded: chain H residue 108 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 46 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 67 optimal weight: 40.0000 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 88 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 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 = 0.3845 r_free = 0.3845 target = 0.146961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111757 restraints weight = 11277.506| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.26 r_work: 0.3201 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10895 Z= 0.139 Angle : 0.636 8.714 15675 Z= 0.364 Chirality : 0.045 0.219 1789 Planarity : 0.004 0.039 1195 Dihedral : 30.784 123.252 3267 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.37 % Allowed : 18.90 % 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: 2.73 (0.31), residues: 692 helix: 2.83 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.49 (0.36), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 79 TYR 0.010 0.001 TYR F 51 PHE 0.009 0.001 PHE D 65 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (10895) covalent geometry : angle 0.63553 / 0.36 (15675) hydrogen bonds : bond 0.05186 / 3.38 ( 685) hydrogen bonds : angle 2.97781 / 2.14 ( 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 126 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.214 Fit side-chains REVERT: A 133 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: B 25 ASN cc_start: 0.8222 (m-40) cc_final: 0.7998 (m-40) REVERT: B 93 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8122 (mm-40) REVERT: C 75 LYS cc_start: 0.8111 (mttp) cc_final: 0.7357 (tptt) REVERT: C 95 LYS cc_start: 0.8599 (tttt) cc_final: 0.7889 (ttpt) REVERT: D 108 LYS cc_start: 0.8325 (mtpp) cc_final: 0.7829 (mmtm) REVERT: E 94 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8169 (mm-30) REVERT: G 75 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7315 (tmtt) REVERT: H 71 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7956 (mt-10) outliers start: 8 outliers final: 5 residues processed: 122 average time/residue: 0.9175 time to fit residues: 117.0174 Evaluate side-chains 126 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 G residue 15 LYS 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 15 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.0570 chunk 24 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.147191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112056 restraints weight = 11214.866| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.26 r_work: 0.3206 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1382 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= 0.136 Angle : 0.628 6.415 15675 Z= 0.361 Chirality : 0.045 0.219 1789 Planarity : 0.004 0.038 1195 Dihedral : 30.746 124.130 3267 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.20 % Allowed : 19.76 % Favored : 79.04 % 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: 2.75 (0.31), residues: 692 helix: 2.84 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.46 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 72 TYR 0.009 0.001 TYR G 50 PHE 0.009 0.001 PHE D 65 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (10895) covalent geometry : angle 0.62764 / 0.36 (15675) hydrogen bonds : bond 0.05117 / 3.33 ( 685) hydrogen bonds : angle 2.95381 / 2.12 ( 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 126 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.181 Fit side-chains REVERT: A 133 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8497 (mt-10) REVERT: B 93 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8111 (mm-40) REVERT: C 75 LYS cc_start: 0.8112 (mttp) cc_final: 0.7356 (tptt) REVERT: C 95 LYS cc_start: 0.8597 (tttt) cc_final: 0.7886 (ttpt) REVERT: E 94 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8172 (mm-30) REVERT: G 75 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7311 (tmtt) REVERT: H 71 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7949 (mt-10) outliers start: 7 outliers final: 4 residues processed: 123 average time/residue: 0.8068 time to fit residues: 103.8155 Evaluate side-chains 123 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU 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 G residue 15 LYS 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: 3.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 104 GLN D 82 HIS E 76 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.147367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112171 restraints weight = 11316.081| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.27 r_work: 0.3210 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10895 Z= 0.138 Angle : 0.620 6.519 15675 Z= 0.359 Chirality : 0.045 0.213 1789 Planarity : 0.004 0.038 1195 Dihedral : 30.705 125.471 3267 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.37 % Allowed : 19.76 % Favored : 78.87 % 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: 2.87 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.42 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 72 TYR 0.009 0.001 TYR F 51 PHE 0.010 0.001 PHE D 65 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (10895) covalent geometry : angle 0.61996 / 0.36 (15675) hydrogen bonds : bond 0.05031 / 3.28 ( 685) hydrogen bonds : angle 2.92530 / 2.10 ( 1744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3843.85 seconds wall clock time: 65 minutes 50.93 seconds (3950.93 seconds total)