Starting phenix.real_space_refine on Fri Sep 11 20:14:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t79_10390/09_2026/6t79_10390.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t79_10390/09_2026/6t79_10390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t79_10390/09_2026/6t79_10390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t79_10390/09_2026/6t79_10390.map" model { file = "/net/cci-nas-00/data/ceres_data/6t79_10390/09_2026/6t79_10390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t79_10390/09_2026/6t79_10390.cif" } resolution = 3.2 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= 0.001 sd= 0.010 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 10 5.16 5 C 6732 2.51 5 N 2270 2.21 5 O 2819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12121 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2959 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2986 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Time building chain proxies: 2.67, per 1000 atoms: 0.22 Number of scatterers: 12121 At special positions: 0 Unit cell: (84, 124.95, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 290 15.00 O 2819 8.00 N 2270 7.00 C 6732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 429.9 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 68.9% alpha, 3.1% beta 142 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.601A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.632A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.654A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.859A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.543A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.582A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.562A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.256A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.544A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.686A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 53 through 81 removed outlier: 3.521A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.831A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.600A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.540A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.600A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.976A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.732A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.582A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.563A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.254A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.546A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 3.687A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 53 through 81 removed outlier: 3.522A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.830A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.497A 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: 6.526A 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: 7.021A 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: 7.267A 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: 6.927A 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 'G' and resid 77 through 78 364 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.41 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: 2040 1.33 - 1.45: 4244 1.45 - 1.56: 6042 1.56 - 1.68: 580 1.68 - 1.80: 20 Bond restraints: 12926 Sorted by residual: bond pdb=" C1' DT I 100 " pdb=" N1 DT I 100 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" C1' DT I 60 " pdb=" N1 DT I 60 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" C3' DC I 13 " pdb=" O3' DC I 13 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.46e+01 bond pdb=" C3' DC J 48 " pdb=" C2' DC J 48 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.44e+01 bond pdb=" C1' DC J 104 " pdb=" N1 DC J 104 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.35e+01 ... (remaining 12921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 16896 1.73 - 3.46: 1680 3.46 - 5.19: 89 5.19 - 6.91: 13 6.91 - 8.64: 9 Bond angle restraints: 18687 Sorted by residual: angle pdb=" O4' DG J 57 " pdb=" C4' DG J 57 " pdb=" C3' DG J 57 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.86e+01 angle pdb=" N3 DT I 60 " pdb=" C4 DT I 60 " pdb=" O4 DT I 60 " ideal model delta sigma weight residual 119.90 122.73 -2.83 6.00e-01 2.78e+00 2.22e+01 angle pdb=" N3 DT I 122 " pdb=" C4 DT I 122 " pdb=" O4 DT I 122 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" N3 DT I 61 " pdb=" C4 DT I 61 " pdb=" O4 DT I 61 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" N3 DT I 100 " pdb=" C4 DT I 100 " pdb=" O4 DT I 100 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.14e+01 ... (remaining 18682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.80: 5224 28.80 - 57.60: 1786 57.60 - 86.40: 123 86.40 - 115.20: 0 115.20 - 144.00: 5 Dihedral angle restraints: 7138 sinusoidal: 4890 harmonic: 2248 Sorted by residual: dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C4' DT I 92 " pdb=" C3' DT I 92 " pdb=" O3' DT I 92 " pdb=" P DT I 93 " ideal model delta sinusoidal sigma weight residual 220.00 76.00 144.00 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DC I 13 " pdb=" C3' DC I 13 " pdb=" O3' DC I 13 " pdb=" P DT I 14 " ideal model delta sinusoidal sigma weight residual 220.00 76.90 143.10 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 7135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1561 0.055 - 0.110: 483 0.110 - 0.165: 70 0.165 - 0.220: 5 0.220 - 0.275: 2 Chirality restraints: 2121 Sorted by residual: chirality pdb=" C3' DT I 87 " pdb=" C4' DT I 87 " pdb=" O3' DT I 87 " pdb=" C2' DT I 87 " both_signs ideal model delta sigma weight residual False -2.73 -2.46 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C3' DC I 13 " pdb=" C4' DC I 13 " pdb=" O3' DC I 13 " pdb=" C2' DC I 13 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" P DT I 93 " pdb=" OP1 DT I 93 " pdb=" OP2 DT I 93 " pdb=" O5' DT I 93 " both_signs ideal model delta sigma weight residual True 2.34 -2.54 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2118 not shown) Planarity restraints: 1359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.046 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO C 80 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO A 121 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO G 80 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.038 5.00e-02 4.00e+02 ... (remaining 1356 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 799 2.72 - 3.27: 10004 3.27 - 3.81: 23673 3.81 - 4.36: 29233 4.36 - 4.90: 41366 Nonbonded interactions: 105075 Sorted by model distance: nonbonded pdb=" OE1 GLU C 61 " pdb=" CD2 LEU D 103 " model vdw 2.178 3.460 nonbonded pdb=" O ASP B 68 " pdb=" OG1 THR B 71 " model vdw 2.198 3.040 nonbonded pdb=" OE2 GLU C 61 " pdb=" CD2 LEU D 103 " model vdw 2.253 3.460 nonbonded pdb=" CE1 TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.293 3.340 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.309 3.040 ... (remaining 105070 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 18 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.710 Find NCS groups from input model: 0.130 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 : 0.007 0.060 12926 Z= 0.603 Angle : 0.994 8.642 18687 Z= 0.835 Chirality : 0.051 0.275 2121 Planarity : 0.007 0.069 1359 Dihedral : 28.192 144.003 5688 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.23 (0.22), residues: 760 helix: -2.03 (0.16), residues: 535 sheet: None (None), residues: 0 loop : -1.90 (0.34), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 89 TYR 0.012 0.002 TYR G 57 PHE 0.017 0.002 PHE H 62 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.60 (12926) covalent geometry : angle 0.99411 / 0.84 (18687) hydrogen bonds : bond 0.12056 / 8.12 ( 704) hydrogen bonds : angle 4.27089 / 3.06 ( 1766) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.328 Fit side-chains REVERT: E 122 LYS cc_start: 0.7991 (ptmt) cc_final: 0.7660 (ptpp) REVERT: F 45 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7882 (mtp85) REVERT: H 76 ARG cc_start: 0.8101 (ptp90) cc_final: 0.7813 (ptp90) REVERT: H 112 THR cc_start: 0.8775 (p) cc_final: 0.8550 (p) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1982 time to fit residues: 45.0246 Evaluate side-chains 113 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 50.0000 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 108 ASN A 113 HIS A 125 GLN D 46 HIS D 60 ASN D 81 ASN E 68 GLN E 108 ASN F 25 ASN F 75 HIS G 73 ASN H 46 HIS H 92 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.157573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116668 restraints weight = 18784.039| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.27 r_work: 0.3305 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12926 Z= 0.151 Angle : 0.709 8.523 18687 Z= 0.413 Chirality : 0.049 0.424 2121 Planarity : 0.006 0.063 1359 Dihedral : 31.679 152.300 4132 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.24 % Allowed : 8.37 % Favored : 90.39 % 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: -1.04 (0.27), residues: 760 helix: -0.25 (0.20), residues: 541 sheet: None (None), residues: 0 loop : -1.53 (0.35), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 72 TYR 0.012 0.001 TYR F 88 PHE 0.009 0.001 PHE H 62 HIS 0.008 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (12926) covalent geometry : angle 0.70890 / 0.41 (18687) hydrogen bonds : bond 0.05034 / 3.28 ( 704) hydrogen bonds : angle 3.17928 / 2.29 ( 1766) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.321 Fit side-chains REVERT: B 68 ASP cc_start: 0.7994 (m-30) cc_final: 0.7708 (m-30) REVERT: C 73 ASN cc_start: 0.8445 (t0) cc_final: 0.7675 (t0) REVERT: C 75 LYS cc_start: 0.8324 (mmtm) cc_final: 0.7948 (mptt) REVERT: E 41 TYR cc_start: 0.7408 (m-10) cc_final: 0.7199 (m-80) REVERT: E 122 LYS cc_start: 0.7975 (ptmt) cc_final: 0.7685 (ptpp) REVERT: H 76 ARG cc_start: 0.8319 (ptp90) cc_final: 0.7919 (ptp-170) outliers start: 8 outliers final: 2 residues processed: 127 average time/residue: 0.1404 time to fit residues: 24.4634 Evaluate side-chains 114 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 82 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 50.0000 chunk 79 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 50.0000 chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 92 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.154046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112258 restraints weight = 18928.990| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.27 r_work: 0.3235 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12926 Z= 0.245 Angle : 0.761 9.272 18687 Z= 0.429 Chirality : 0.052 0.356 2121 Planarity : 0.006 0.048 1359 Dihedral : 31.843 147.279 4132 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.40 % Allowed : 12.25 % Favored : 86.36 % 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: -0.56 (0.28), residues: 760 helix: 0.12 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.38 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 11 TYR 0.014 0.002 TYR C 57 PHE 0.019 0.003 PHE A 84 HIS 0.005 0.002 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.24 (12926) covalent geometry : angle 0.76102 / 0.43 (18687) hydrogen bonds : bond 0.06009 / 4.00 ( 704) hydrogen bonds : angle 3.18931 / 2.28 ( 1766) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.342 Fit side-chains REVERT: B 68 ASP cc_start: 0.7991 (m-30) cc_final: 0.7614 (m-30) REVERT: B 79 LYS cc_start: 0.8533 (mmtt) cc_final: 0.8084 (mptt) REVERT: E 122 LYS cc_start: 0.7989 (ptmt) cc_final: 0.7710 (ptpp) outliers start: 9 outliers final: 6 residues processed: 120 average time/residue: 0.1543 time to fit residues: 24.8121 Evaluate side-chains 110 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 79 optimal weight: 50.0000 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 78 optimal weight: 50.0000 chunk 100 optimal weight: 50.0000 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.155198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113678 restraints weight = 18685.702| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.25 r_work: 0.3258 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12926 Z= 0.174 Angle : 0.695 9.220 18687 Z= 0.397 Chirality : 0.048 0.368 2121 Planarity : 0.005 0.044 1359 Dihedral : 31.811 148.332 4132 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.55 % Allowed : 12.87 % Favored : 85.58 % 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: 0.02 (0.29), residues: 760 helix: 0.56 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.20 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 35 TYR 0.024 0.002 TYR F 88 PHE 0.011 0.001 PHE A 84 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (12926) covalent geometry : angle 0.69531 / 0.40 (18687) hydrogen bonds : bond 0.04825 / 3.18 ( 704) hydrogen bonds : angle 3.02518 / 2.17 ( 1766) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.313 Fit side-chains REVERT: B 68 ASP cc_start: 0.7963 (m-30) cc_final: 0.7606 (m-30) REVERT: B 79 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8092 (mppt) REVERT: C 73 ASN cc_start: 0.8590 (t0) cc_final: 0.8077 (t0) REVERT: C 75 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8119 (mptt) REVERT: D 105 LYS cc_start: 0.8593 (ptpp) cc_final: 0.8350 (ptmm) REVERT: E 122 LYS cc_start: 0.7978 (ptmt) cc_final: 0.7708 (ptpp) REVERT: F 92 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7526 (ttt90) outliers start: 10 outliers final: 8 residues processed: 118 average time/residue: 0.1524 time to fit residues: 24.1828 Evaluate side-chains 120 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 50.0000 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 50.0000 chunk 30 optimal weight: 9.9990 chunk 88 optimal weight: 50.0000 chunk 9 optimal weight: 5.9990 chunk 96 optimal weight: 50.0000 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.155190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.113590 restraints weight = 18909.693| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.26 r_work: 0.3257 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12926 Z= 0.174 Angle : 0.689 9.418 18687 Z= 0.393 Chirality : 0.048 0.379 2121 Planarity : 0.004 0.043 1359 Dihedral : 31.773 148.359 4132 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.55 % Allowed : 13.18 % Favored : 85.27 % 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: 0.27 (0.29), residues: 760 helix: 0.74 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.08 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 35 TYR 0.015 0.002 TYR F 88 PHE 0.013 0.001 PHE A 84 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (12926) covalent geometry : angle 0.68895 / 0.39 (18687) hydrogen bonds : bond 0.04790 / 3.16 ( 704) hydrogen bonds : angle 2.97278 / 2.13 ( 1766) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.327 Fit side-chains REVERT: B 68 ASP cc_start: 0.8079 (m-30) cc_final: 0.7730 (m-30) REVERT: B 79 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8113 (mppt) REVERT: C 73 ASN cc_start: 0.8571 (t0) cc_final: 0.7941 (t0) REVERT: C 75 LYS cc_start: 0.8428 (mmtm) cc_final: 0.8022 (mptt) REVERT: D 105 LYS cc_start: 0.8610 (ptpp) cc_final: 0.8333 (ptmm) REVERT: E 122 LYS cc_start: 0.8002 (ptmt) cc_final: 0.7737 (ptpp) REVERT: F 92 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7530 (ttt90) outliers start: 10 outliers final: 7 residues processed: 124 average time/residue: 0.1504 time to fit residues: 25.0938 Evaluate side-chains 120 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 50.0000 chunk 31 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 95 optimal weight: 40.0000 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 50.0000 chunk 75 optimal weight: 50.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.156980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115746 restraints weight = 18704.841| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.25 r_work: 0.3291 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12926 Z= 0.130 Angle : 0.648 9.382 18687 Z= 0.375 Chirality : 0.046 0.397 2121 Planarity : 0.004 0.041 1359 Dihedral : 31.653 149.944 4132 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.55 % Allowed : 13.64 % Favored : 84.81 % 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: 0.76 (0.29), residues: 760 helix: 1.12 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.97 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 35 TYR 0.009 0.001 TYR F 51 PHE 0.007 0.001 PHE A 84 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.13 (12926) covalent geometry : angle 0.64790 / 0.38 (18687) hydrogen bonds : bond 0.04279 / 2.80 ( 704) hydrogen bonds : angle 2.84848 / 2.05 ( 1766) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.315 Fit side-chains REVERT: B 53 GLU cc_start: 0.7703 (tt0) cc_final: 0.7261 (mt-10) REVERT: B 68 ASP cc_start: 0.8036 (m-30) cc_final: 0.7698 (m-30) REVERT: B 79 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8053 (mppt) REVERT: C 73 ASN cc_start: 0.8542 (t0) cc_final: 0.8161 (t0) REVERT: C 75 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8187 (mmtt) REVERT: D 105 LYS cc_start: 0.8564 (ptpp) cc_final: 0.8305 (ptmm) REVERT: E 122 LYS cc_start: 0.7996 (ptmt) cc_final: 0.7729 (ptpp) REVERT: G 75 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8298 (mmtp) outliers start: 10 outliers final: 6 residues processed: 123 average time/residue: 0.1470 time to fit residues: 24.4239 Evaluate side-chains 121 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 84 optimal weight: 40.0000 chunk 13 optimal weight: 0.9990 chunk 80 optimal weight: 30.0000 chunk 5 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 90 optimal weight: 50.0000 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.157690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116581 restraints weight = 18739.664| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.24 r_work: 0.3306 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 12926 Z= 0.130 Angle : 0.649 9.445 18687 Z= 0.372 Chirality : 0.045 0.400 2121 Planarity : 0.004 0.041 1359 Dihedral : 31.540 150.967 4132 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.09 % Allowed : 14.26 % Favored : 84.65 % 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: 1.14 (0.29), residues: 760 helix: 1.43 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.91 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 35 TYR 0.011 0.001 TYR H 80 PHE 0.008 0.001 PHE A 84 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (12926) covalent geometry : angle 0.64862 / 0.37 (18687) hydrogen bonds : bond 0.04175 / 2.75 ( 704) hydrogen bonds : angle 2.76667 / 1.99 ( 1766) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.332 Fit side-chains REVERT: B 53 GLU cc_start: 0.7611 (tt0) cc_final: 0.7301 (mt-10) REVERT: B 68 ASP cc_start: 0.8035 (m-30) cc_final: 0.7692 (m-30) REVERT: B 79 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8032 (mppt) REVERT: C 73 ASN cc_start: 0.8547 (t0) cc_final: 0.8116 (t0) REVERT: C 75 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8161 (mmtt) REVERT: D 105 LYS cc_start: 0.8571 (ptpp) cc_final: 0.8325 (mtmm) REVERT: E 122 LYS cc_start: 0.8013 (ptmt) cc_final: 0.7656 (pttt) outliers start: 7 outliers final: 4 residues processed: 121 average time/residue: 0.1470 time to fit residues: 24.1352 Evaluate side-chains 117 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 50.0000 chunk 46 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 60 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 0.0970 chunk 12 optimal weight: 5.9990 chunk 85 optimal weight: 50.0000 chunk 27 optimal weight: 0.9980 chunk 87 optimal weight: 50.0000 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.158241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116889 restraints weight = 18715.573| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.26 r_work: 0.3310 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12926 Z= 0.131 Angle : 0.629 9.518 18687 Z= 0.365 Chirality : 0.044 0.395 2121 Planarity : 0.004 0.041 1359 Dihedral : 31.400 151.066 4132 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.78 % Allowed : 15.19 % Favored : 84.03 % 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: 1.33 (0.29), residues: 760 helix: 1.58 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.86 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 35 TYR 0.012 0.001 TYR H 80 PHE 0.010 0.001 PHE A 84 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (12926) covalent geometry : angle 0.62930 / 0.36 (18687) hydrogen bonds : bond 0.04126 / 2.73 ( 704) hydrogen bonds : angle 2.71132 / 1.94 ( 1766) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.256 Fit side-chains REVERT: B 68 ASP cc_start: 0.8059 (m-30) cc_final: 0.7709 (m-30) REVERT: B 79 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8025 (mppt) REVERT: C 73 ASN cc_start: 0.8540 (t0) cc_final: 0.8117 (t0) REVERT: D 105 LYS cc_start: 0.8529 (ptpp) cc_final: 0.8316 (mtmm) REVERT: E 122 LYS cc_start: 0.7982 (ptmt) cc_final: 0.7726 (ptpp) REVERT: F 35 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7952 (mtm180) outliers start: 5 outliers final: 5 residues processed: 115 average time/residue: 0.1412 time to fit residues: 21.8479 Evaluate side-chains 115 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 8.9990 chunk 86 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 82 optimal weight: 50.0000 chunk 65 optimal weight: 0.5980 chunk 97 optimal weight: 50.0000 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 92 GLN F 25 ASN H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.157125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115516 restraints weight = 18656.191| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.26 r_work: 0.3287 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12926 Z= 0.155 Angle : 0.649 9.702 18687 Z= 0.372 Chirality : 0.045 0.390 2121 Planarity : 0.004 0.041 1359 Dihedral : 31.391 150.292 4132 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.09 % Allowed : 14.57 % Favored : 84.34 % 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: 1.26 (0.29), residues: 760 helix: 1.52 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.87 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 42 TYR 0.015 0.001 TYR A 54 PHE 0.015 0.001 PHE A 84 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (12926) covalent geometry : angle 0.64873 / 0.37 (18687) hydrogen bonds : bond 0.04458 / 2.97 ( 704) hydrogen bonds : angle 2.80573 / 2.01 ( 1766) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.324 Fit side-chains REVERT: B 53 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6895 (mt-10) REVERT: B 68 ASP cc_start: 0.8065 (m-30) cc_final: 0.7716 (m-30) REVERT: C 73 ASN cc_start: 0.8343 (t0) cc_final: 0.8099 (t0) REVERT: D 105 LYS cc_start: 0.8540 (ptpp) cc_final: 0.8309 (mtmm) REVERT: E 122 LYS cc_start: 0.8008 (ptmt) cc_final: 0.7770 (ptpp) REVERT: F 35 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7970 (mtm180) REVERT: H 73 GLU cc_start: 0.8331 (tp30) cc_final: 0.8054 (tp30) outliers start: 7 outliers final: 4 residues processed: 115 average time/residue: 0.1523 time to fit residues: 23.3869 Evaluate side-chains 114 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 63 optimal weight: 0.3980 chunk 20 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 50.0000 chunk 74 optimal weight: 50.0000 chunk 91 optimal weight: 40.0000 chunk 50 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.158017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116613 restraints weight = 18780.075| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.27 r_work: 0.3305 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12926 Z= 0.130 Angle : 0.631 9.560 18687 Z= 0.366 Chirality : 0.044 0.392 2121 Planarity : 0.004 0.045 1359 Dihedral : 31.375 150.587 4132 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.93 % Allowed : 15.50 % Favored : 83.57 % 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: 1.42 (0.29), residues: 760 helix: 1.63 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.78 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 35 TYR 0.035 0.002 TYR F 88 PHE 0.007 0.001 PHE A 84 HIS 0.002 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (12926) covalent geometry : angle 0.63144 / 0.37 (18687) hydrogen bonds : bond 0.04151 / 2.76 ( 704) hydrogen bonds : angle 2.78526 / 2.00 ( 1766) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.337 Fit side-chains REVERT: B 53 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6926 (mt-10) REVERT: B 68 ASP cc_start: 0.8050 (m-30) cc_final: 0.7720 (m-30) REVERT: B 79 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8004 (mppt) REVERT: C 73 ASN cc_start: 0.8339 (t0) cc_final: 0.8091 (t0) REVERT: D 105 LYS cc_start: 0.8534 (ptpp) cc_final: 0.8307 (mtmm) REVERT: E 122 LYS cc_start: 0.8038 (ptmt) cc_final: 0.7777 (ptpp) REVERT: F 35 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7960 (mtm180) outliers start: 6 outliers final: 6 residues processed: 111 average time/residue: 0.1463 time to fit residues: 22.1141 Evaluate side-chains 114 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 50.0000 chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.158303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.117988 restraints weight = 18664.255| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.16 r_work: 0.3328 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12926 Z= 0.129 Angle : 0.623 9.619 18687 Z= 0.362 Chirality : 0.044 0.391 2121 Planarity : 0.004 0.041 1359 Dihedral : 31.359 150.776 4132 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.78 % Allowed : 15.50 % Favored : 83.72 % 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: 1.53 (0.29), residues: 760 helix: 1.72 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.76 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 35 TYR 0.019 0.001 TYR F 88 PHE 0.009 0.001 PHE A 84 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.13 (12926) covalent geometry : angle 0.62300 / 0.36 (18687) hydrogen bonds : bond 0.04101 / 2.72 ( 704) hydrogen bonds : angle 2.73260 / 1.96 ( 1766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3188.88 seconds wall clock time: 55 minutes 15.62 seconds (3315.62 seconds total)