Starting phenix.real_space_refine on Fri Jul 3 08:23:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ohb_12899/07_2026/7ohb_12899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ohb_12899/07_2026/7ohb_12899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ohb_12899/07_2026/7ohb_12899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ohb_12899/07_2026/7ohb_12899.map" model { file = "/net/cci-nas-00/data/ceres_data/7ohb_12899/07_2026/7ohb_12899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ohb_12899/07_2026/7ohb_12899.cif" } resolution = 3.4 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= 0.005 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 290 5.49 5 S 18 5.16 5 C 7560 2.51 5 N 2501 2.21 5 O 3055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 13424 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 756 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 171} Time building chain proxies: 2.76, per 1000 atoms: 0.21 Number of scatterers: 13424 At special positions: 0 Unit cell: (92.4, 116.55, 133.35, 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 18 16.00 P 290 15.00 O 3055 8.00 N 2501 7.00 C 7560 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: 0.82 Conformation dependent library (CDL) restraints added in 405.9 milliseconds 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 64.8% alpha, 7.2% beta 144 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.991A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.807A 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 73 removed outlier: 4.318A 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 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.144A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.853A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.563A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.590A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.377A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 81 through 88 removed outlier: 3.649A pdb=" N VAL K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 147 Processing helix chain 'K' and resid 171 through 179 removed outlier: 3.599A pdb=" N LEU K 175 " --> pdb=" O ARG K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 236 removed outlier: 4.087A pdb=" N ILE K 223 " --> pdb=" O GLN K 219 " (cutoff:3.500A) Proline residue: K 232 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.004A 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 96 through 98 removed outlier: 6.471A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.132A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.998A 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: 7.512A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 92 through 93 removed outlier: 3.602A pdb=" N VAL K 102 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR K 124 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS K 120 " --> pdb=" O PHE K 116 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY K 125 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE K 70 " --> pdb=" O GLY K 125 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL K 161 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE K 70 " --> pdb=" O ASN K 159 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN K 159 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA K 72 " --> pdb=" O ILE K 157 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE K 157 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL K 74 " --> pdb=" O PHE K 155 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE K 155 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE K 212 " --> pdb=" O CYS K 164 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL K 213 " --> pdb=" O LEU K 205 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU K 205 " --> pdb=" O VAL K 213 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR K 215 " --> pdb=" O VAL K 203 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL K 203 " --> pdb=" O THR K 215 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2665 1.33 - 1.45: 4528 1.45 - 1.57: 6451 1.57 - 1.69: 578 1.69 - 1.82: 32 Bond restraints: 14254 Sorted by residual: bond pdb=" C3' DT I 60 " pdb=" O3' DT I 60 " ideal model delta sigma weight residual 1.435 1.519 -0.084 1.30e-02 5.92e+03 4.21e+01 bond pdb=" C5' DA I 61 " pdb=" C4' DA I 61 " ideal model delta sigma weight residual 1.512 1.548 -0.036 7.00e-03 2.04e+04 2.62e+01 bond pdb=" C3' DG J -22 " pdb=" C2' DG J -22 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.43e+01 bond pdb=" C3' DC J 30 " pdb=" C2' DC J 30 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 ... (remaining 14249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 19350 2.06 - 4.11: 1054 4.11 - 6.17: 62 6.17 - 8.22: 17 8.22 - 10.28: 3 Bond angle restraints: 20486 Sorted by residual: angle pdb=" O4' DT I 60 " pdb=" C1' DT I 60 " pdb=" N1 DT I 60 " ideal model delta sigma weight residual 108.00 113.45 -5.45 7.00e-01 2.04e+00 6.06e+01 angle pdb=" O5' DA I 61 " pdb=" C5' DA I 61 " pdb=" C4' DA I 61 " ideal model delta sigma weight residual 109.40 114.72 -5.32 8.00e-01 1.56e+00 4.42e+01 angle pdb=" O4' DA I 17 " pdb=" C1' DA I 17 " pdb=" N9 DA I 17 " ideal model delta sigma weight residual 108.00 103.35 4.65 7.00e-01 2.04e+00 4.41e+01 angle pdb=" O5' DA I -45 " pdb=" C5' DA I -45 " pdb=" C4' DA I -45 " ideal model delta sigma weight residual 109.40 113.91 -4.51 8.00e-01 1.56e+00 3.17e+01 angle pdb=" O4' DG I 47 " pdb=" C1' DG I 47 " pdb=" N9 DG I 47 " ideal model delta sigma weight residual 108.00 104.29 3.71 7.00e-01 2.04e+00 2.81e+01 ... (remaining 20481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.96: 5269 20.96 - 41.91: 1340 41.91 - 62.87: 1178 62.87 - 83.83: 66 83.83 - 104.78: 6 Dihedral angle restraints: 7859 sinusoidal: 5121 harmonic: 2738 Sorted by residual: dihedral pdb=" CA GLU K 108 " pdb=" C GLU K 108 " pdb=" N PRO K 109 " pdb=" CA PRO K 109 " ideal model delta harmonic sigma weight residual 0.00 -39.57 39.57 0 5.00e+00 4.00e-02 6.26e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -158.58 -21.42 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA LYS K 199 " pdb=" C LYS K 199 " pdb=" N PRO K 200 " pdb=" CA PRO K 200 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 7856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2001 0.073 - 0.146: 306 0.146 - 0.218: 23 0.218 - 0.291: 4 0.291 - 0.364: 2 Chirality restraints: 2336 Sorted by residual: chirality pdb=" C1' DT I 60 " pdb=" O4' DT I 60 " pdb=" C2' DT I 60 " pdb=" N1 DT I 60 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE K 212 " pdb=" CA ILE K 212 " pdb=" CG1 ILE K 212 " pdb=" CG2 ILE K 212 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB THR K 111 " pdb=" CA THR K 111 " pdb=" OG1 THR K 111 " pdb=" CG2 THR K 111 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2333 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 27 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C VAL G 27 " 0.058 2.00e-02 2.50e+03 pdb=" O VAL G 27 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY G 28 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 60 " 0.006 2.00e-02 2.50e+03 1.84e-02 8.44e+00 pdb=" N1 DT I 60 " -0.037 2.00e-02 2.50e+03 pdb=" C2 DT I 60 " 0.041 2.00e-02 2.50e+03 pdb=" O2 DT I 60 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT I 60 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DT I 60 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT I 60 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 60 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT I 60 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DT I 60 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO G 80 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.039 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2703 2.78 - 3.31: 11633 3.31 - 3.84: 27034 3.84 - 4.37: 31845 4.37 - 4.90: 45229 Nonbonded interactions: 118444 Sorted by model distance: nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 30 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.276 3.040 nonbonded pdb=" O GLY K 174 " pdb=" OG SER K 178 " model vdw 2.278 3.040 nonbonded pdb=" NE2 GLN G 24 " pdb=" OE1 GLN H 44 " model vdw 2.302 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.322 3.120 ... (remaining 118439 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' } ncs_group { reference = (chain 'B' and resid 24 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 27 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 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 : 0.006 0.084 14254 Z= 0.540 Angle : 0.957 10.276 20486 Z= 0.758 Chirality : 0.053 0.364 2336 Planarity : 0.007 0.070 1584 Dihedral : 28.695 104.782 6091 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.89 % Allowed : 4.32 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -2.05 (0.23), residues: 925 helix: -1.01 (0.18), residues: 588 sheet: -0.37 (0.82), residues: 41 loop : -1.97 (0.29), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 96 TYR 0.039 0.002 TYR G 50 PHE 0.025 0.002 PHE K 99 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.54 (14254) covalent geometry : angle 0.95673 / 0.76 (20486) hydrogen bonds : bond 0.12750 / 8.33 ( 840) hydrogen bonds : angle 5.17632 / 3.73 ( 2125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 192 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7946 (t0) cc_final: 0.7506 (t70) REVERT: B 25 ASN cc_start: 0.8125 (m-40) cc_final: 0.7878 (m110) REVERT: C 36 LYS cc_start: 0.8709 (mmtp) cc_final: 0.8461 (mmmm) REVERT: C 74 LYS cc_start: 0.8764 (mppt) cc_final: 0.8531 (mptt) REVERT: E 106 ASP cc_start: 0.7443 (m-30) cc_final: 0.7178 (m-30) REVERT: F 74 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7767 (mt-10) REVERT: G 91 GLU cc_start: 0.8047 (tt0) cc_final: 0.7818 (tt0) REVERT: H 33 SER cc_start: 0.8880 (t) cc_final: 0.8493 (p) REVERT: H 34 TYR cc_start: 0.8858 (m-80) cc_final: 0.8608 (m-80) REVERT: K 69 ASN cc_start: 0.7863 (t0) cc_final: 0.6762 (m110) REVERT: K 121 MET cc_start: 0.7527 (tpt) cc_final: 0.7033 (mtm) outliers start: 7 outliers final: 1 residues processed: 196 average time/residue: 0.1445 time to fit residues: 38.4497 Evaluate side-chains 146 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN E 113 HIS F 93 GLN G 112 GLN H 81 ASN K 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.090933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.055357 restraints weight = 38248.595| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.07 r_work: 0.2663 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14254 Z= 0.163 Angle : 0.687 8.030 20486 Z= 0.395 Chirality : 0.047 0.232 2336 Planarity : 0.005 0.047 1584 Dihedral : 31.755 99.506 4227 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.52 % Allowed : 10.80 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.03 (0.25), residues: 925 helix: 0.85 (0.20), residues: 601 sheet: 0.08 (0.71), residues: 47 loop : -1.79 (0.31), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 40 TYR 0.019 0.002 TYR K 231 PHE 0.012 0.001 PHE K 99 HIS 0.014 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (14254) covalent geometry : angle 0.68688 / 0.39 (20486) hydrogen bonds : bond 0.04687 / 3.15 ( 840) hydrogen bonds : angle 3.67331 / 2.65 ( 2125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8970 (pm20) cc_final: 0.8571 (pm20) REVERT: A 81 ASP cc_start: 0.8708 (t0) cc_final: 0.8345 (t70) REVERT: B 25 ASN cc_start: 0.8201 (m-40) cc_final: 0.7888 (m110) REVERT: C 74 LYS cc_start: 0.8985 (mppt) cc_final: 0.8756 (mptt) REVERT: D 30 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7733 (ttm170) REVERT: F 74 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8472 (mt-10) REVERT: H 30 ARG cc_start: 0.8221 (mtp85) cc_final: 0.7978 (mtp85) REVERT: H 33 SER cc_start: 0.8865 (t) cc_final: 0.8496 (p) REVERT: H 105 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8604 (mmtm) REVERT: K 69 ASN cc_start: 0.7839 (t0) cc_final: 0.6511 (m110) REVERT: K 159 ASN cc_start: 0.9125 (t0) cc_final: 0.8740 (t0) REVERT: K 195 TYR cc_start: 0.8396 (t80) cc_final: 0.8163 (t80) outliers start: 12 outliers final: 9 residues processed: 162 average time/residue: 0.1394 time to fit residues: 31.7549 Evaluate side-chains 151 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain K residue 164 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 84 optimal weight: 40.0000 chunk 45 optimal weight: 0.0870 chunk 43 optimal weight: 4.9990 chunk 104 optimal weight: 50.0000 chunk 87 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.090175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.054063 restraints weight = 38295.543| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.08 r_work: 0.2618 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14254 Z= 0.181 Angle : 0.639 7.867 20486 Z= 0.372 Chirality : 0.045 0.222 2336 Planarity : 0.004 0.047 1584 Dihedral : 31.493 94.272 4226 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.91 % Allowed : 12.96 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.88 (0.27), residues: 925 helix: 1.57 (0.21), residues: 599 sheet: 0.19 (0.72), residues: 47 loop : -1.55 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 40 TYR 0.014 0.002 TYR K 139 PHE 0.009 0.001 PHE A 67 HIS 0.007 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (14254) covalent geometry : angle 0.63940 / 0.37 (20486) hydrogen bonds : bond 0.04446 / 2.98 ( 840) hydrogen bonds : angle 3.40003 / 2.46 ( 2125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9066 (pm20) cc_final: 0.8591 (pm20) REVERT: A 81 ASP cc_start: 0.8707 (t0) cc_final: 0.8370 (t70) REVERT: C 74 LYS cc_start: 0.9099 (mppt) cc_final: 0.8839 (mptt) REVERT: D 30 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7679 (ttm170) REVERT: E 115 LYS cc_start: 0.9211 (mmtp) cc_final: 0.8983 (mmtp) REVERT: F 74 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8496 (mt-10) REVERT: H 30 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7968 (mtp85) REVERT: H 33 SER cc_start: 0.8938 (t) cc_final: 0.8627 (p) REVERT: K 69 ASN cc_start: 0.7922 (t0) cc_final: 0.6427 (m110) REVERT: K 159 ASN cc_start: 0.9103 (t0) cc_final: 0.8847 (t0) REVERT: K 195 TYR cc_start: 0.8381 (t80) cc_final: 0.8034 (t80) outliers start: 15 outliers final: 12 residues processed: 157 average time/residue: 0.1472 time to fit residues: 31.9159 Evaluate side-chains 150 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 11 optimal weight: 0.5980 chunk 111 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 112 optimal weight: 0.0050 chunk 98 optimal weight: 30.0000 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 99 optimal weight: 50.0000 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.090199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.054050 restraints weight = 38383.787| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.98 r_work: 0.2629 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14254 Z= 0.161 Angle : 0.622 8.618 20486 Z= 0.363 Chirality : 0.044 0.227 2336 Planarity : 0.004 0.044 1584 Dihedral : 31.282 94.853 4226 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.78 % Allowed : 14.99 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.29 (0.27), residues: 925 helix: 1.93 (0.21), residues: 599 sheet: 0.06 (0.70), residues: 47 loop : -1.45 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 29 TYR 0.013 0.002 TYR H 37 PHE 0.010 0.001 PHE E 67 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (14254) covalent geometry : angle 0.62218 / 0.36 (20486) hydrogen bonds : bond 0.04116 / 2.77 ( 840) hydrogen bonds : angle 3.25054 / 2.35 ( 2125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9074 (pm20) cc_final: 0.8572 (pm20) REVERT: A 76 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8481 (mm-40) REVERT: A 81 ASP cc_start: 0.8686 (t0) cc_final: 0.8374 (t70) REVERT: D 30 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7700 (ttm170) REVERT: E 115 LYS cc_start: 0.9201 (mmtp) cc_final: 0.8988 (mmtp) REVERT: F 74 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8508 (mt-10) REVERT: H 33 SER cc_start: 0.8963 (t) cc_final: 0.8717 (p) REVERT: K 69 ASN cc_start: 0.8147 (t0) cc_final: 0.6462 (m110) REVERT: K 159 ASN cc_start: 0.8964 (t0) cc_final: 0.8763 (t0) REVERT: K 195 TYR cc_start: 0.8418 (t80) cc_final: 0.8068 (t80) outliers start: 14 outliers final: 10 residues processed: 157 average time/residue: 0.1453 time to fit residues: 31.7390 Evaluate side-chains 146 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 106 optimal weight: 30.0000 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.090472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.054162 restraints weight = 38590.177| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.03 r_work: 0.2628 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14254 Z= 0.150 Angle : 0.608 8.350 20486 Z= 0.357 Chirality : 0.044 0.222 2336 Planarity : 0.004 0.043 1584 Dihedral : 31.143 95.619 4226 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.03 % Allowed : 16.26 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.53 (0.27), residues: 925 helix: 2.13 (0.21), residues: 599 sheet: 0.04 (0.70), residues: 47 loop : -1.38 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.019 0.001 TYR K 139 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (14254) covalent geometry : angle 0.60810 / 0.36 (20486) hydrogen bonds : bond 0.04020 / 2.70 ( 840) hydrogen bonds : angle 3.15892 / 2.28 ( 2125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9088 (pm20) cc_final: 0.8583 (pm20) REVERT: A 76 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8476 (mm-40) REVERT: A 81 ASP cc_start: 0.8672 (t0) cc_final: 0.8379 (t70) REVERT: E 115 LYS cc_start: 0.9190 (mmtp) cc_final: 0.8979 (mmtp) REVERT: F 24 ASP cc_start: 0.7375 (p0) cc_final: 0.7062 (p0) REVERT: F 27 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8707 (mp10) REVERT: F 74 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8462 (mt-10) REVERT: H 30 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7903 (mtp85) REVERT: H 33 SER cc_start: 0.8962 (t) cc_final: 0.8740 (p) REVERT: H 42 LEU cc_start: 0.9437 (tp) cc_final: 0.9220 (tp) REVERT: K 69 ASN cc_start: 0.8161 (t0) cc_final: 0.6372 (m110) REVERT: K 195 TYR cc_start: 0.8390 (t80) cc_final: 0.8032 (t80) outliers start: 16 outliers final: 14 residues processed: 158 average time/residue: 0.1435 time to fit residues: 31.6469 Evaluate side-chains 153 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 205 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 104 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 86 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.090558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.054299 restraints weight = 38252.878| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.00 r_work: 0.2634 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14254 Z= 0.152 Angle : 0.607 9.154 20486 Z= 0.354 Chirality : 0.043 0.215 2336 Planarity : 0.004 0.043 1584 Dihedral : 31.029 95.975 4226 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.03 % Allowed : 16.52 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.64 (0.27), residues: 925 helix: 2.24 (0.21), residues: 599 sheet: -0.05 (0.69), residues: 47 loop : -1.37 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.023 0.001 TYR K 139 PHE 0.009 0.001 PHE E 67 HIS 0.002 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (14254) covalent geometry : angle 0.60653 / 0.35 (20486) hydrogen bonds : bond 0.03957 / 2.66 ( 840) hydrogen bonds : angle 3.08453 / 2.23 ( 2125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9061 (pm20) cc_final: 0.8592 (pm20) REVERT: A 76 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8501 (mm-40) REVERT: A 81 ASP cc_start: 0.8677 (t0) cc_final: 0.8398 (t70) REVERT: D 30 ARG cc_start: 0.8124 (mtm110) cc_final: 0.7841 (mtm180) REVERT: E 90 MET cc_start: 0.8883 (mmm) cc_final: 0.8664 (mmp) REVERT: E 115 LYS cc_start: 0.9196 (mmtp) cc_final: 0.8993 (mmtp) REVERT: F 24 ASP cc_start: 0.7654 (p0) cc_final: 0.7398 (p0) REVERT: F 27 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8671 (mp10) REVERT: F 74 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8455 (mt-10) REVERT: H 30 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7876 (mtp85) REVERT: H 42 LEU cc_start: 0.9405 (tp) cc_final: 0.9177 (tp) REVERT: H 102 GLU cc_start: 0.7372 (tp30) cc_final: 0.7165 (tp30) REVERT: K 69 ASN cc_start: 0.8113 (t0) cc_final: 0.6505 (m110) REVERT: K 121 MET cc_start: 0.8246 (tpt) cc_final: 0.7358 (mpp) REVERT: K 159 ASN cc_start: 0.8490 (t0) cc_final: 0.8264 (t0) REVERT: K 195 TYR cc_start: 0.8335 (t80) cc_final: 0.7926 (t80) outliers start: 16 outliers final: 14 residues processed: 157 average time/residue: 0.1363 time to fit residues: 29.9040 Evaluate side-chains 157 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 205 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 85 optimal weight: 50.0000 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.088881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.052188 restraints weight = 38182.912| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.99 r_work: 0.2572 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 14254 Z= 0.254 Angle : 0.678 9.384 20486 Z= 0.382 Chirality : 0.045 0.235 2336 Planarity : 0.005 0.045 1584 Dihedral : 31.235 94.760 4226 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.92 % Allowed : 17.15 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.31 (0.27), residues: 925 helix: 1.98 (0.21), residues: 599 sheet: -0.02 (0.69), residues: 47 loop : -1.51 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 83 TYR 0.017 0.002 TYR K 139 PHE 0.014 0.002 PHE E 104 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.25 (14254) covalent geometry : angle 0.67780 / 0.38 (20486) hydrogen bonds : bond 0.04643 / 3.11 ( 840) hydrogen bonds : angle 3.29229 / 2.39 ( 2125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9083 (pm20) cc_final: 0.8601 (pm20) REVERT: A 76 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8550 (mm-40) REVERT: A 81 ASP cc_start: 0.8745 (t0) cc_final: 0.8420 (t70) REVERT: C 91 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7857 (tp30) REVERT: D 30 ARG cc_start: 0.8252 (mtm110) cc_final: 0.7895 (ttm170) REVERT: D 31 LYS cc_start: 0.8838 (ptmt) cc_final: 0.8618 (ptmm) REVERT: F 74 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8533 (mt-10) REVERT: H 48 ASP cc_start: 0.8186 (p0) cc_final: 0.7971 (p0) REVERT: K 69 ASN cc_start: 0.8090 (t0) cc_final: 0.6246 (m-40) REVERT: K 121 MET cc_start: 0.8440 (tpt) cc_final: 0.7510 (mpp) REVERT: K 159 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8220 (t0) REVERT: K 195 TYR cc_start: 0.8382 (t80) cc_final: 0.7970 (t80) outliers start: 23 outliers final: 19 residues processed: 152 average time/residue: 0.1423 time to fit residues: 30.4100 Evaluate side-chains 155 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 205 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.089543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.053140 restraints weight = 37842.991| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.96 r_work: 0.2603 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14254 Z= 0.173 Angle : 0.633 9.648 20486 Z= 0.363 Chirality : 0.044 0.227 2336 Planarity : 0.004 0.038 1584 Dihedral : 31.106 95.316 4226 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.41 % Allowed : 17.66 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.47 (0.27), residues: 925 helix: 2.12 (0.21), residues: 599 sheet: -0.06 (0.68), residues: 47 loop : -1.45 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.015 0.001 TYR K 139 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (14254) covalent geometry : angle 0.63261 / 0.36 (20486) hydrogen bonds : bond 0.04054 / 2.72 ( 840) hydrogen bonds : angle 3.18661 / 2.31 ( 2125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9031 (pm20) cc_final: 0.8612 (pm20) REVERT: A 76 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8577 (mm-40) REVERT: A 81 ASP cc_start: 0.8693 (t0) cc_final: 0.8401 (t70) REVERT: C 91 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7788 (tp30) REVERT: D 30 ARG cc_start: 0.8270 (mtm110) cc_final: 0.7931 (ttm170) REVERT: E 90 MET cc_start: 0.8925 (mmm) cc_final: 0.8560 (mmp) REVERT: F 53 GLU cc_start: 0.7728 (tt0) cc_final: 0.7500 (tt0) REVERT: F 74 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8505 (mt-10) REVERT: H 42 LEU cc_start: 0.9456 (tp) cc_final: 0.9246 (tp) REVERT: H 48 ASP cc_start: 0.8140 (p0) cc_final: 0.7918 (p0) REVERT: K 69 ASN cc_start: 0.8032 (t0) cc_final: 0.6178 (m-40) REVERT: K 121 MET cc_start: 0.8372 (tpt) cc_final: 0.7416 (mpp) REVERT: K 195 TYR cc_start: 0.8342 (t80) cc_final: 0.8051 (t80) outliers start: 19 outliers final: 15 residues processed: 154 average time/residue: 0.1355 time to fit residues: 28.9137 Evaluate side-chains 153 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 205 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 89 optimal weight: 20.0000 chunk 48 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.090511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.054394 restraints weight = 38377.889| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.99 r_work: 0.2636 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14254 Z= 0.141 Angle : 0.615 9.270 20486 Z= 0.357 Chirality : 0.042 0.215 2336 Planarity : 0.004 0.043 1584 Dihedral : 30.877 96.240 4226 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.65 % Allowed : 18.04 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.68 (0.27), residues: 925 helix: 2.30 (0.21), residues: 599 sheet: -0.06 (0.68), residues: 47 loop : -1.41 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 30 TYR 0.029 0.001 TYR K 231 PHE 0.011 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (14254) covalent geometry : angle 0.61484 / 0.36 (20486) hydrogen bonds : bond 0.03810 / 2.56 ( 840) hydrogen bonds : angle 3.06623 / 2.22 ( 2125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9008 (pm20) cc_final: 0.8702 (pm20) REVERT: A 76 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8577 (mm-40) REVERT: A 81 ASP cc_start: 0.8583 (t0) cc_final: 0.8264 (t0) REVERT: C 91 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7728 (tp30) REVERT: D 30 ARG cc_start: 0.8224 (mtm110) cc_final: 0.7915 (ttm170) REVERT: E 90 MET cc_start: 0.8867 (mmm) cc_final: 0.8512 (mmp) REVERT: F 74 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8451 (mt-10) REVERT: H 30 ARG cc_start: 0.8275 (mtp85) cc_final: 0.8062 (mtp85) REVERT: K 69 ASN cc_start: 0.8021 (t0) cc_final: 0.6372 (m110) REVERT: K 121 MET cc_start: 0.8367 (tpt) cc_final: 0.7448 (mpp) REVERT: K 159 ASN cc_start: 0.8487 (t0) cc_final: 0.8089 (t0) REVERT: K 195 TYR cc_start: 0.8346 (t80) cc_final: 0.8002 (t80) outliers start: 13 outliers final: 11 residues processed: 155 average time/residue: 0.1350 time to fit residues: 29.3744 Evaluate side-chains 151 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 77 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.088216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.051309 restraints weight = 38516.708| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.01 r_work: 0.2548 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 14254 Z= 0.328 Angle : 0.740 10.864 20486 Z= 0.406 Chirality : 0.047 0.244 2336 Planarity : 0.005 0.039 1584 Dihedral : 31.243 94.070 4226 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.65 % Allowed : 18.81 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.16 (0.27), residues: 925 helix: 1.87 (0.21), residues: 599 sheet: 0.01 (0.67), residues: 47 loop : -1.59 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 29 TYR 0.016 0.002 TYR G 39 PHE 0.017 0.002 PHE E 104 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.33 (14254) covalent geometry : angle 0.73999 / 0.41 (20486) hydrogen bonds : bond 0.04935 / 3.30 ( 840) hydrogen bonds : angle 3.37759 / 2.45 ( 2125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9049 (pm20) cc_final: 0.8633 (pm20) REVERT: A 76 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8647 (mm-40) REVERT: A 81 ASP cc_start: 0.8715 (t0) cc_final: 0.8459 (t70) REVERT: D 30 ARG cc_start: 0.8337 (mtm110) cc_final: 0.8005 (ttm170) REVERT: F 74 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8560 (mt-10) REVERT: H 39 TYR cc_start: 0.8527 (t80) cc_final: 0.8178 (t80) REVERT: K 121 MET cc_start: 0.8550 (tpt) cc_final: 0.7562 (mpp) REVERT: K 195 TYR cc_start: 0.8401 (t80) cc_final: 0.8149 (t80) outliers start: 13 outliers final: 10 residues processed: 144 average time/residue: 0.1318 time to fit residues: 26.2332 Evaluate side-chains 139 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 89 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 chunk 75 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.089949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.053427 restraints weight = 38276.626| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.98 r_work: 0.2612 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14254 Z= 0.152 Angle : 0.641 9.616 20486 Z= 0.366 Chirality : 0.043 0.223 2336 Planarity : 0.004 0.037 1584 Dihedral : 31.005 95.148 4226 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.52 % Allowed : 19.06 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.48 (0.27), residues: 925 helix: 2.09 (0.21), residues: 605 sheet: 0.01 (0.68), residues: 47 loop : -1.46 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.013 0.001 TYR G 57 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (14254) covalent geometry : angle 0.64074 / 0.37 (20486) hydrogen bonds : bond 0.03895 / 2.60 ( 840) hydrogen bonds : angle 3.15417 / 2.28 ( 2125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3190.91 seconds wall clock time: 55 minutes 23.99 seconds (3323.99 seconds total)