Starting phenix.real_space_refine on Thu Aug 6 09:18:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sj5_54938/08_2026/9sj5_54938.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sj5_54938/08_2026/9sj5_54938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sj5_54938/08_2026/9sj5_54938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sj5_54938/08_2026/9sj5_54938.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sj5_54938/08_2026/9sj5_54938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sj5_54938/08_2026/9sj5_54938.map" } resolution = 2.85 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= 0.029 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 294 5.49 5 S 26 5.16 5 C 8184 2.51 5 N 2701 2.21 5 O 3266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14471 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3034 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2990 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 871 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "L" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 633 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "M" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "N" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 380 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 108 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Time building chain proxies: 3.13, per 1000 atoms: 0.22 Number of scatterers: 14471 At special positions: 0 Unit cell: (103.234, 147.581, 119.228, 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 26 16.00 P 294 15.00 O 3266 8.00 N 2701 7.00 C 8184 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: 1.15 Conformation dependent library (CDL) restraints added in 459.2 milliseconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 7 sheets defined 70.5% alpha, 1.5% beta 147 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.990A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.173A 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 removed outlier: 3.547A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.169A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.801A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.537A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.533A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.828A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.783A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.576A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.458A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.522A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.684A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.121A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 61 removed outlier: 3.869A pdb=" N ILE L 58 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU L 59 " --> pdb=" O ASN L 55 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG L 60 " --> pdb=" O ILE L 56 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 68 removed outlier: 3.526A pdb=" N MET L 68 " --> pdb=" O LEU L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 75 Processing helix chain 'M' and resid 7 through 11 removed outlier: 3.962A pdb=" N GLN M 11 " --> pdb=" O PRO M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 4.180A pdb=" N ARG M 18 " --> pdb=" O LEU M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 42 removed outlier: 4.044A pdb=" N MET M 38 " --> pdb=" O THR M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 81 Processing helix chain 'M' and resid 97 through 141 removed outlier: 4.139A pdb=" N MET M 141 " --> pdb=" O GLN M 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 44 Processing helix chain 'O' and resid 9 through 17 Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.178A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.181A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (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: 7.337A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.402A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 543 hydrogen bonds defined for protein. 1599 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 377 hydrogen bonds 754 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3497 1.34 - 1.46: 4284 1.46 - 1.58: 6916 1.58 - 1.70: 585 1.70 - 1.82: 43 Bond restraints: 15325 Sorted by residual: bond pdb=" C3' DC I 143 " pdb=" C2' DC I 143 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DC J 286 " pdb=" C2' DC J 286 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 bond pdb=" C3' DT J 161 " pdb=" C2' DT J 161 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.73e+00 bond pdb=" C3' DC I 33 " pdb=" C2' DC I 33 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.72e+00 bond pdb=" C3' DC I 53 " pdb=" C2' DC I 53 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.66e+00 ... (remaining 15320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 21275 2.15 - 4.30: 621 4.30 - 6.44: 23 6.44 - 8.59: 3 8.59 - 10.74: 2 Bond angle restraints: 21924 Sorted by residual: angle pdb=" O4' DT I 86 " pdb=" C4' DT I 86 " pdb=" C3' DT I 86 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.49e+01 angle pdb=" O4' DC J 289 " pdb=" C4' DC J 289 " pdb=" C3' DC J 289 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.34e+01 angle pdb=" O4' DC J 170 " pdb=" C4' DC J 170 " pdb=" C3' DC J 170 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.17e+01 angle pdb=" O4' DG J 171 " pdb=" C4' DG J 171 " pdb=" C3' DG J 171 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" N3 DT J 178 " pdb=" C4 DT J 178 " pdb=" O4 DT J 178 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 ... (remaining 21919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.08: 5973 21.08 - 42.17: 1400 42.17 - 63.25: 1098 63.25 - 84.34: 53 84.34 - 105.42: 9 Dihedral angle restraints: 8533 sinusoidal: 5469 harmonic: 3064 Sorted by residual: dihedral pdb=" CA MET M 38 " pdb=" C MET M 38 " pdb=" N ALA M 39 " pdb=" CA ALA M 39 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TRP M 25 " pdb=" C TRP M 25 " pdb=" N PRO M 26 " pdb=" CA PRO M 26 " ideal model delta harmonic sigma weight residual -180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA LEU G 116 " pdb=" C LEU G 116 " pdb=" N PRO G 117 " pdb=" CA PRO G 117 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 8530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1740 0.042 - 0.085: 555 0.085 - 0.127: 159 0.127 - 0.169: 15 0.169 - 0.211: 3 Chirality restraints: 2472 Sorted by residual: chirality pdb=" CA GLU N 40 " pdb=" N GLU N 40 " pdb=" C GLU N 40 " pdb=" CB GLU N 40 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE N 37 " pdb=" N ILE N 37 " pdb=" C ILE N 37 " pdb=" CB ILE N 37 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA GLU M 116 " pdb=" N GLU M 116 " pdb=" C GLU M 116 " pdb=" CB GLU M 116 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.37e-01 ... (remaining 2469 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE M 22 " 0.014 2.00e-02 2.50e+03 1.48e-02 3.81e+00 pdb=" CG PHE M 22 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE M 22 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE M 22 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE M 22 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE M 22 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE M 22 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 92 " 0.153 9.50e-02 1.11e+02 6.89e-02 3.42e+00 pdb=" NE ARG F 92 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG F 92 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 92 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 92 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 120 " 0.022 2.00e-02 2.50e+03 9.39e-03 2.42e+00 pdb=" N9 DA I 120 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DA I 120 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 120 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DA I 120 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 120 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 120 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 120 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 120 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 120 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 120 " -0.002 2.00e-02 2.50e+03 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 6701 2.99 - 3.47: 14567 3.47 - 3.95: 27950 3.95 - 4.42: 31297 4.42 - 4.90: 42312 Nonbonded interactions: 122827 Sorted by model distance: nonbonded pdb=" O ASP L 27 " pdb=" CG ARG L 30 " model vdw 2.517 3.440 nonbonded pdb=" O ASN C 110 " pdb=" OD1 ASN C 110 " model vdw 2.550 3.040 nonbonded pdb=" O GLY C 37 " pdb=" OD1 ASN C 38 " model vdw 2.577 3.040 nonbonded pdb=" O LYS M 112 " pdb=" OE1 GLU M 116 " model vdw 2.580 3.040 nonbonded pdb=" O5' DA J 287 " pdb=" O4' DA J 287 " model vdw 2.588 2.432 ... (remaining 122822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 9 through 120) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 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: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.190 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 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 0.036 15325 Z= 0.505 Angle : 0.745 10.741 21924 Z= 0.649 Chirality : 0.044 0.211 2472 Planarity : 0.004 0.069 1762 Dihedral : 27.407 105.424 6541 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.90 % Allowed : 17.60 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.26), residues: 1025 helix: 2.29 (0.19), residues: 700 sheet: -1.42 (2.12), residues: 10 loop : -0.64 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 92 TYR 0.009 0.001 TYR B 51 PHE 0.034 0.002 PHE M 22 TRP 0.017 0.002 TRP M 25 HIS 0.007 0.001 HIS M 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.50 (15325) covalent geometry : angle 0.74510 / 0.65 (21924) hydrogen bonds : bond 0.09822 / 6.63 ( 920) hydrogen bonds : angle 3.83408 / 3.94 ( 2353) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 297 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 GLN cc_start: 0.8988 (tt0) cc_final: 0.8402 (tt0) REVERT: D 68 ASP cc_start: 0.8719 (t0) cc_final: 0.8492 (t0) REVERT: G 73 ASN cc_start: 0.9018 (t0) cc_final: 0.8713 (t0) REVERT: H 68 ASP cc_start: 0.8847 (t0) cc_final: 0.8566 (t0) REVERT: M 22 PHE cc_start: 0.3409 (OUTLIER) cc_final: 0.1531 (t80) REVERT: M 112 LYS cc_start: 0.1220 (pptt) cc_final: 0.0876 (pttp) REVERT: M 141 MET cc_start: 0.7251 (ppp) cc_final: 0.6930 (pmm) outliers start: 8 outliers final: 2 residues processed: 300 average time/residue: 0.7254 time to fit residues: 233.9129 Evaluate side-chains 235 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 232 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain M residue 22 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.0870 chunk 35 optimal weight: 9.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN F 93 GLN H 47 GLN ** M 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.086963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.052818 restraints weight = 43036.949| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.83 r_work: 0.2640 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15325 Z= 0.209 Angle : 0.681 8.753 21924 Z= 0.390 Chirality : 0.045 0.252 2472 Planarity : 0.005 0.069 1762 Dihedral : 30.224 106.291 4376 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.15 % Allowed : 23.54 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.26), residues: 1025 helix: 2.45 (0.19), residues: 708 sheet: -1.38 (2.16), residues: 10 loop : -0.67 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 133 TYR 0.016 0.001 TYR A 41 PHE 0.027 0.002 PHE N 45 TRP 0.007 0.001 TRP N 33 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.21 (15325) covalent geometry : angle 0.68062 / 0.39 (21924) hydrogen bonds : bond 0.04800 / 3.29 ( 920) hydrogen bonds : angle 3.32513 / 3.36 ( 2353) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 242 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.9007 (tt0) cc_final: 0.8803 (pt0) REVERT: E 125 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8475 (mt0) REVERT: A 53 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8800 (ttp-110) REVERT: A 64 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8858 (mmmm) REVERT: B 92 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8803 (mtp85) REVERT: D 34 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8724 (mmmm) REVERT: D 35 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7960 (tp30) REVERT: D 47 GLN cc_start: 0.9183 (tt0) cc_final: 0.8270 (tt0) REVERT: D 68 ASP cc_start: 0.9236 (t0) cc_final: 0.8942 (t0) REVERT: D 105 GLU cc_start: 0.8474 (tt0) cc_final: 0.8154 (tt0) REVERT: F 77 LYS cc_start: 0.9573 (OUTLIER) cc_final: 0.8991 (mmtp) REVERT: G 73 ASN cc_start: 0.9411 (t0) cc_final: 0.8790 (t0) REVERT: G 104 GLN cc_start: 0.9060 (mm110) cc_final: 0.8753 (mm-40) REVERT: H 34 LYS cc_start: 0.9125 (mmmm) cc_final: 0.8813 (mptt) REVERT: H 68 ASP cc_start: 0.9240 (t0) cc_final: 0.8748 (t0) REVERT: H 101 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9132 (mm) REVERT: L 17 ARG cc_start: 0.9399 (mtm-85) cc_final: 0.9046 (mtm-85) REVERT: M 132 ARG cc_start: 0.8855 (tpt170) cc_final: 0.8385 (tpt170) REVERT: M 133 ARG cc_start: 0.9152 (mmm160) cc_final: 0.8892 (mmm160) REVERT: N 45 PHE cc_start: 0.8050 (m-80) cc_final: 0.7533 (m-80) outliers start: 37 outliers final: 15 residues processed: 262 average time/residue: 0.7664 time to fit residues: 215.3199 Evaluate side-chains 244 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 40 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 40 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS L 38 GLN M 77 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.086508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.051933 restraints weight = 43370.603| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.88 r_work: 0.2632 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15325 Z= 0.214 Angle : 0.662 8.792 21924 Z= 0.376 Chirality : 0.044 0.239 2472 Planarity : 0.005 0.065 1762 Dihedral : 30.452 108.013 4373 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.71 % Allowed : 23.09 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.26), residues: 1025 helix: 2.50 (0.19), residues: 708 sheet: -1.37 (2.16), residues: 10 loop : -0.66 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 108 TYR 0.015 0.001 TYR B 51 PHE 0.017 0.002 PHE N 45 TRP 0.010 0.001 TRP N 33 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 (15325) covalent geometry : angle 0.66227 / 0.38 (21924) hydrogen bonds : bond 0.04589 / 3.14 ( 920) hydrogen bonds : angle 3.21773 / 3.28 ( 2353) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.9041 (tt0) cc_final: 0.8833 (pt0) REVERT: E 105 GLU cc_start: 0.9281 (tt0) cc_final: 0.9076 (tt0) REVERT: E 125 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8551 (mt0) REVERT: E 129 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8647 (tpt90) REVERT: A 53 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8802 (ttm170) REVERT: A 64 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8904 (mmmm) REVERT: A 106 ASP cc_start: 0.9062 (m-30) cc_final: 0.8844 (m-30) REVERT: B 92 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8834 (mtp85) REVERT: D 47 GLN cc_start: 0.9151 (tt0) cc_final: 0.8230 (tt0) REVERT: D 52 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.8793 (t) REVERT: D 68 ASP cc_start: 0.9266 (t0) cc_final: 0.8985 (t0) REVERT: D 105 GLU cc_start: 0.8559 (tt0) cc_final: 0.8142 (tt0) REVERT: F 77 LYS cc_start: 0.9570 (OUTLIER) cc_final: 0.8994 (mmtp) REVERT: G 73 ASN cc_start: 0.9363 (t0) cc_final: 0.8891 (t0) REVERT: G 104 GLN cc_start: 0.9101 (mm110) cc_final: 0.8889 (mm-40) REVERT: H 33 ARG cc_start: 0.8314 (mtt-85) cc_final: 0.8094 (mtt-85) REVERT: H 68 ASP cc_start: 0.9252 (t0) cc_final: 0.8775 (t0) REVERT: H 101 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9142 (mm) REVERT: H 105 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8910 (mt-10) REVERT: L 35 ARG cc_start: 0.7359 (ptp-110) cc_final: 0.7033 (ptp-110) REVERT: L 38 GLN cc_start: 0.7815 (mt0) cc_final: 0.7498 (pp30) REVERT: N 35 GLU cc_start: 0.8780 (mp0) cc_final: 0.8572 (mp0) REVERT: N 45 PHE cc_start: 0.8014 (m-80) cc_final: 0.7758 (m-80) outliers start: 42 outliers final: 15 residues processed: 252 average time/residue: 0.6990 time to fit residues: 188.3606 Evaluate side-chains 242 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 40 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 50.0000 chunk 122 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 109 optimal weight: 40.0000 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.084959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.050356 restraints weight = 43432.827| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.80 r_work: 0.2590 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15325 Z= 0.280 Angle : 0.709 8.288 21924 Z= 0.392 Chirality : 0.046 0.242 2472 Planarity : 0.005 0.050 1762 Dihedral : 30.762 111.458 4373 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.61 % Allowed : 23.43 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.26), residues: 1025 helix: 2.39 (0.18), residues: 709 sheet: -1.47 (2.09), residues: 10 loop : -0.80 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 17 TYR 0.014 0.002 TYR B 51 PHE 0.018 0.002 PHE M 22 TRP 0.008 0.001 TRP N 33 HIS 0.009 0.001 HIS M 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.28 (15325) covalent geometry : angle 0.70891 / 0.39 (21924) hydrogen bonds : bond 0.05189 / 3.54 ( 920) hydrogen bonds : angle 3.24157 / 3.23 ( 2353) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8874 (pt0) REVERT: E 125 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8610 (mt0) REVERT: E 129 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8677 (tpt90) REVERT: A 53 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8857 (ttp-110) REVERT: A 64 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8917 (mmmm) REVERT: A 81 ASP cc_start: 0.8663 (t0) cc_final: 0.8371 (t0) REVERT: B 91 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.9222 (ttpp) REVERT: B 92 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8931 (mtp85) REVERT: C 38 ASN cc_start: 0.8788 (p0) cc_final: 0.8500 (p0) REVERT: D 52 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.8781 (t) REVERT: D 68 ASP cc_start: 0.9334 (t0) cc_final: 0.9035 (t0) REVERT: D 105 GLU cc_start: 0.8616 (tt0) cc_final: 0.8241 (tt0) REVERT: F 24 ASP cc_start: 0.8336 (p0) cc_final: 0.8052 (p0) REVERT: F 77 LYS cc_start: 0.9578 (OUTLIER) cc_final: 0.8996 (mmtp) REVERT: G 73 ASN cc_start: 0.9299 (t0) cc_final: 0.8829 (t0) REVERT: G 90 ASP cc_start: 0.8845 (t70) cc_final: 0.8448 (t0) REVERT: H 34 LYS cc_start: 0.9063 (mmmm) cc_final: 0.8718 (mptt) REVERT: H 68 ASP cc_start: 0.9287 (t0) cc_final: 0.8808 (t0) REVERT: H 101 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9090 (mm) REVERT: L 25 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9364 (tm) REVERT: L 34 ILE cc_start: 0.8526 (pt) cc_final: 0.8146 (pp) REVERT: L 38 GLN cc_start: 0.7819 (mt0) cc_final: 0.7587 (pp30) REVERT: M 132 ARG cc_start: 0.9173 (ttt180) cc_final: 0.8970 (tpt170) REVERT: N 35 GLU cc_start: 0.8855 (mp0) cc_final: 0.8646 (mp0) outliers start: 50 outliers final: 20 residues processed: 249 average time/residue: 0.7409 time to fit residues: 197.5124 Evaluate side-chains 241 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain N residue 23 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 123 optimal weight: 30.0000 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 20.0000 chunk 73 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.086780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.052261 restraints weight = 43267.796| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.85 r_work: 0.2642 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15325 Z= 0.147 Angle : 0.642 8.034 21924 Z= 0.366 Chirality : 0.042 0.229 2472 Planarity : 0.004 0.041 1762 Dihedral : 30.643 112.624 4373 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.14 % Allowed : 26.12 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.26), residues: 1025 helix: 2.43 (0.19), residues: 708 sheet: -1.47 (2.15), residues: 10 loop : -0.72 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 33 TYR 0.013 0.001 TYR D 40 PHE 0.017 0.002 PHE M 124 TRP 0.014 0.001 TRP N 33 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (15325) covalent geometry : angle 0.64178 / 0.37 (21924) hydrogen bonds : bond 0.03983 / 2.76 ( 920) hydrogen bonds : angle 3.12350 / 3.13 ( 2353) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.9067 (tt0) cc_final: 0.8858 (pt0) REVERT: E 129 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8704 (tpt90) REVERT: A 53 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8825 (ttm170) REVERT: A 59 GLU cc_start: 0.8209 (pm20) cc_final: 0.7675 (pm20) REVERT: A 81 ASP cc_start: 0.8564 (t0) cc_final: 0.8305 (t0) REVERT: A 120 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8349 (mtm) REVERT: C 38 ASN cc_start: 0.8724 (p0) cc_final: 0.8476 (p0) REVERT: D 47 GLN cc_start: 0.9141 (tt0) cc_final: 0.8241 (tt0) REVERT: D 52 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.8750 (t) REVERT: D 68 ASP cc_start: 0.9271 (t0) cc_final: 0.9017 (t0) REVERT: D 105 GLU cc_start: 0.8606 (tt0) cc_final: 0.8217 (tt0) REVERT: F 84 MET cc_start: 0.9004 (mmm) cc_final: 0.8479 (mmm) REVERT: G 73 ASN cc_start: 0.9275 (t0) cc_final: 0.8784 (t0) REVERT: G 90 ASP cc_start: 0.8837 (t70) cc_final: 0.8457 (t0) REVERT: G 104 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8888 (mm-40) REVERT: H 33 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8195 (mtt-85) REVERT: H 68 ASP cc_start: 0.9250 (t0) cc_final: 0.8781 (t0) REVERT: H 101 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9124 (mm) REVERT: L 35 ARG cc_start: 0.7013 (ptp-110) cc_final: 0.6693 (ptp-110) REVERT: L 38 GLN cc_start: 0.7855 (mt0) cc_final: 0.7627 (pp30) REVERT: M 141 MET cc_start: 0.8156 (ppp) cc_final: 0.7626 (pmm) outliers start: 28 outliers final: 9 residues processed: 245 average time/residue: 0.8213 time to fit residues: 215.0372 Evaluate side-chains 232 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain N residue 23 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.085595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.051116 restraints weight = 43625.562| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.81 r_work: 0.2617 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15325 Z= 0.216 Angle : 0.680 9.842 21924 Z= 0.378 Chirality : 0.043 0.233 2472 Planarity : 0.004 0.046 1762 Dihedral : 30.708 114.223 4373 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.60 % Allowed : 25.90 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.26), residues: 1025 helix: 2.41 (0.19), residues: 711 sheet: -1.72 (2.02), residues: 10 loop : -0.76 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 33 TYR 0.011 0.001 TYR F 51 PHE 0.016 0.002 PHE M 124 TRP 0.010 0.001 TRP N 33 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.22 (15325) covalent geometry : angle 0.67991 / 0.38 (21924) hydrogen bonds : bond 0.04621 / 3.18 ( 920) hydrogen bonds : angle 3.18405 / 3.17 ( 2353) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8862 (pt0) REVERT: E 129 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8681 (tpt90) REVERT: A 53 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8854 (ttp-110) REVERT: A 59 GLU cc_start: 0.8430 (pm20) cc_final: 0.8118 (pm20) REVERT: A 64 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8903 (mmmm) REVERT: A 81 ASP cc_start: 0.8596 (t0) cc_final: 0.8345 (t0) REVERT: D 52 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.8780 (t) REVERT: D 68 ASP cc_start: 0.9305 (t0) cc_final: 0.9039 (t0) REVERT: D 92 ARG cc_start: 0.9013 (ttp80) cc_final: 0.8402 (ttp80) REVERT: D 105 GLU cc_start: 0.8639 (tt0) cc_final: 0.8229 (tt0) REVERT: G 13 LYS cc_start: 0.9428 (tppp) cc_final: 0.9166 (tppp) REVERT: G 73 ASN cc_start: 0.9254 (t0) cc_final: 0.8775 (t0) REVERT: G 90 ASP cc_start: 0.8816 (t70) cc_final: 0.8399 (t0) REVERT: G 104 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8960 (mm-40) REVERT: H 33 ARG cc_start: 0.8588 (mtt90) cc_final: 0.8211 (mtt-85) REVERT: H 68 ASP cc_start: 0.9282 (t0) cc_final: 0.8800 (t0) REVERT: H 101 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9104 (mm) REVERT: M 141 MET cc_start: 0.8195 (ppp) cc_final: 0.7769 (pmm) outliers start: 41 outliers final: 16 residues processed: 240 average time/residue: 0.7070 time to fit residues: 181.4335 Evaluate side-chains 232 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain M residue 78 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 83 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.086528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.052201 restraints weight = 43255.943| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.87 r_work: 0.2644 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15325 Z= 0.159 Angle : 0.658 10.529 21924 Z= 0.370 Chirality : 0.042 0.244 2472 Planarity : 0.005 0.058 1762 Dihedral : 30.671 115.714 4373 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.03 % Allowed : 27.24 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.26), residues: 1025 helix: 2.44 (0.19), residues: 711 sheet: -1.81 (1.98), residues: 10 loop : -0.72 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG M 133 TYR 0.012 0.001 TYR D 40 PHE 0.035 0.002 PHE N 22 TRP 0.007 0.001 TRP N 33 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 (15325) covalent geometry : angle 0.65752 / 0.37 (21924) hydrogen bonds : bond 0.04034 / 2.80 ( 920) hydrogen bonds : angle 3.11990 / 3.10 ( 2353) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8871 (pt0) REVERT: E 125 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: E 129 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8676 (tpt90) REVERT: A 53 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8780 (ttp80) REVERT: A 59 GLU cc_start: 0.8457 (pm20) cc_final: 0.8202 (pm20) REVERT: A 64 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8902 (mmmm) REVERT: A 81 ASP cc_start: 0.8613 (t0) cc_final: 0.8340 (t0) REVERT: A 120 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8352 (mtm) REVERT: D 34 LYS cc_start: 0.8992 (mmmm) cc_final: 0.8619 (mptp) REVERT: D 52 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.8773 (t) REVERT: D 68 ASP cc_start: 0.9280 (t0) cc_final: 0.9035 (t0) REVERT: D 105 GLU cc_start: 0.8615 (tt0) cc_final: 0.8255 (tt0) REVERT: G 73 ASN cc_start: 0.9236 (t0) cc_final: 0.8770 (t0) REVERT: G 90 ASP cc_start: 0.8757 (t70) cc_final: 0.8270 (t0) REVERT: G 104 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8944 (mm-40) REVERT: H 33 ARG cc_start: 0.8580 (mtt90) cc_final: 0.8218 (mtt-85) REVERT: H 68 ASP cc_start: 0.9258 (t0) cc_final: 0.8792 (t0) REVERT: H 101 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9113 (mm) REVERT: H 108 LYS cc_start: 0.9042 (mtpm) cc_final: 0.8756 (tttp) REVERT: M 141 MET cc_start: 0.8192 (ppp) cc_final: 0.7763 (pmm) outliers start: 27 outliers final: 13 residues processed: 236 average time/residue: 0.7635 time to fit residues: 192.8912 Evaluate side-chains 236 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain M residue 78 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 100 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.086321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.051955 restraints weight = 43397.718| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.83 r_work: 0.2639 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15325 Z= 0.174 Angle : 0.672 12.087 21924 Z= 0.375 Chirality : 0.042 0.269 2472 Planarity : 0.005 0.072 1762 Dihedral : 30.662 116.688 4373 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.36 % Allowed : 27.47 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.26), residues: 1025 helix: 2.44 (0.19), residues: 711 sheet: -1.85 (1.95), residues: 10 loop : -0.68 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 33 TYR 0.012 0.001 TYR F 88 PHE 0.021 0.002 PHE N 22 TRP 0.007 0.001 TRP N 33 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (15325) covalent geometry : angle 0.67163 / 0.37 (21924) hydrogen bonds : bond 0.04153 / 2.86 ( 920) hydrogen bonds : angle 3.14903 / 3.21 ( 2353) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8849 (pt0) REVERT: E 125 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: E 129 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8689 (tpt90) REVERT: A 53 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8779 (ttm170) REVERT: A 59 GLU cc_start: 0.8464 (pm20) cc_final: 0.8191 (pm20) REVERT: A 64 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8895 (mmmm) REVERT: A 81 ASP cc_start: 0.8669 (t0) cc_final: 0.8391 (t0) REVERT: A 120 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8373 (mtm) REVERT: D 47 GLN cc_start: 0.9220 (tt0) cc_final: 0.8242 (tt0) REVERT: D 52 THR cc_start: 0.9389 (OUTLIER) cc_final: 0.8765 (t) REVERT: D 68 ASP cc_start: 0.9291 (t0) cc_final: 0.9035 (t0) REVERT: D 105 GLU cc_start: 0.8601 (tt0) cc_final: 0.7635 (tt0) REVERT: D 108 LYS cc_start: 0.9058 (mtpm) cc_final: 0.8599 (ttpp) REVERT: G 13 LYS cc_start: 0.9373 (tppp) cc_final: 0.9076 (tppp) REVERT: G 73 ASN cc_start: 0.9222 (t0) cc_final: 0.8750 (t0) REVERT: G 90 ASP cc_start: 0.8735 (t70) cc_final: 0.8269 (t0) REVERT: G 92 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8870 (mt-10) REVERT: G 104 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8937 (mm-40) REVERT: H 33 ARG cc_start: 0.8587 (mtt90) cc_final: 0.8231 (mtt-85) REVERT: H 68 ASP cc_start: 0.9261 (t0) cc_final: 0.8795 (t0) REVERT: H 101 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9062 (mm) REVERT: H 108 LYS cc_start: 0.9026 (mtpm) cc_final: 0.8742 (tttp) REVERT: M 141 MET cc_start: 0.8189 (ppp) cc_final: 0.7767 (pmm) outliers start: 30 outliers final: 15 residues processed: 232 average time/residue: 0.8047 time to fit residues: 199.4475 Evaluate side-chains 237 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain M residue 78 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 81 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** 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 = 0.3632 r_free = 0.3632 target = 0.086330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.051949 restraints weight = 43396.197| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.80 r_work: 0.2638 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15325 Z= 0.170 Angle : 0.677 11.382 21924 Z= 0.378 Chirality : 0.043 0.237 2472 Planarity : 0.005 0.077 1762 Dihedral : 30.675 118.060 4373 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.25 % Allowed : 27.35 % Favored : 69.39 % 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: 2.26 (0.26), residues: 1025 helix: 2.43 (0.19), residues: 711 sheet: -1.86 (1.96), residues: 10 loop : -0.70 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 33 TYR 0.012 0.001 TYR D 40 PHE 0.014 0.002 PHE M 22 TRP 0.007 0.001 TRP N 33 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (15325) covalent geometry : angle 0.67693 / 0.38 (21924) hydrogen bonds : bond 0.04110 / 2.85 ( 920) hydrogen bonds : angle 3.18209 / 3.25 ( 2353) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8855 (pt0) REVERT: E 125 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: E 129 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8696 (tpt90) REVERT: A 53 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8833 (ttp-110) REVERT: A 59 GLU cc_start: 0.8474 (pm20) cc_final: 0.8184 (pm20) REVERT: A 64 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8912 (mmmm) REVERT: A 81 ASP cc_start: 0.8685 (t0) cc_final: 0.8418 (t0) REVERT: B 77 LYS cc_start: 0.9513 (mmmm) cc_final: 0.9001 (mmtt) REVERT: D 34 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8617 (mptt) REVERT: D 47 GLN cc_start: 0.9218 (tt0) cc_final: 0.8270 (tt0) REVERT: D 52 THR cc_start: 0.9389 (OUTLIER) cc_final: 0.8717 (t) REVERT: D 68 ASP cc_start: 0.9286 (t0) cc_final: 0.9061 (t0) REVERT: D 105 GLU cc_start: 0.8620 (tt0) cc_final: 0.7601 (tt0) REVERT: D 108 LYS cc_start: 0.9057 (mtpm) cc_final: 0.8627 (ttpp) REVERT: G 73 ASN cc_start: 0.9211 (t0) cc_final: 0.8747 (t0) REVERT: G 90 ASP cc_start: 0.8738 (t70) cc_final: 0.8250 (t0) REVERT: G 104 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8945 (mm-40) REVERT: H 33 ARG cc_start: 0.8580 (mtt90) cc_final: 0.8219 (mtt-85) REVERT: H 68 ASP cc_start: 0.9260 (t0) cc_final: 0.8796 (t0) REVERT: H 101 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9091 (mm) REVERT: H 108 LYS cc_start: 0.9024 (mtpm) cc_final: 0.8747 (tttp) REVERT: M 141 MET cc_start: 0.8183 (ppp) cc_final: 0.7808 (pmm) outliers start: 29 outliers final: 12 residues processed: 232 average time/residue: 0.8366 time to fit residues: 207.1831 Evaluate side-chains 234 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 78 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 2 optimal weight: 0.0770 chunk 28 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.086025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.051643 restraints weight = 43576.729| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.84 r_work: 0.2631 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15325 Z= 0.193 Angle : 0.710 15.402 21924 Z= 0.388 Chirality : 0.043 0.269 2472 Planarity : 0.005 0.060 1762 Dihedral : 30.722 119.499 4372 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.91 % Allowed : 28.25 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.26), residues: 1025 helix: 2.37 (0.19), residues: 710 sheet: -1.83 (1.97), residues: 10 loop : -0.70 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 33 TYR 0.013 0.001 TYR F 88 PHE 0.023 0.002 PHE N 22 TRP 0.007 0.001 TRP N 33 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (15325) covalent geometry : angle 0.70979 / 0.39 (21924) hydrogen bonds : bond 0.04324 / 2.97 ( 920) hydrogen bonds : angle 3.21163 / 3.26 ( 2353) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8858 (pt0) REVERT: E 125 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8375 (mt0) REVERT: E 129 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8696 (tpt90) REVERT: A 53 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8842 (ttp-110) REVERT: A 81 ASP cc_start: 0.8758 (t0) cc_final: 0.8498 (t0) REVERT: D 47 GLN cc_start: 0.9226 (tt0) cc_final: 0.8315 (tt0) REVERT: D 52 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.8746 (t) REVERT: D 68 ASP cc_start: 0.9312 (t0) cc_final: 0.9069 (t0) REVERT: D 105 GLU cc_start: 0.8624 (tt0) cc_final: 0.7905 (tt0) REVERT: D 108 LYS cc_start: 0.9073 (mtpm) cc_final: 0.8673 (ttpp) REVERT: F 84 MET cc_start: 0.8939 (mmm) cc_final: 0.8457 (mmm) REVERT: G 13 LYS cc_start: 0.9340 (tppp) cc_final: 0.9019 (tppt) REVERT: G 90 ASP cc_start: 0.8733 (t70) cc_final: 0.8290 (t0) REVERT: G 104 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8946 (mm-40) REVERT: H 33 ARG cc_start: 0.8596 (mtt90) cc_final: 0.8232 (mtt-85) REVERT: H 68 ASP cc_start: 0.9280 (t0) cc_final: 0.8811 (t0) REVERT: H 101 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9069 (mm) REVERT: H 108 LYS cc_start: 0.9035 (mtpm) cc_final: 0.8758 (tttp) REVERT: M 141 MET cc_start: 0.8208 (ppp) cc_final: 0.7850 (pmm) outliers start: 26 outliers final: 12 residues processed: 228 average time/residue: 0.7171 time to fit residues: 175.2334 Evaluate side-chains 226 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain M residue 78 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 114 optimal weight: 30.0000 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 HIS ** M 77 HIS ** 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 = 0.3631 r_free = 0.3631 target = 0.086294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.051900 restraints weight = 43301.794| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.81 r_work: 0.2636 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15325 Z= 0.176 Angle : 0.709 12.747 21924 Z= 0.393 Chirality : 0.043 0.251 2472 Planarity : 0.005 0.084 1762 Dihedral : 30.709 120.484 4372 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.91 % Allowed : 29.48 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.26), residues: 1025 helix: 2.31 (0.19), residues: 711 sheet: -1.89 (1.96), residues: 10 loop : -0.71 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 33 TYR 0.012 0.001 TYR D 40 PHE 0.018 0.002 PHE N 22 TRP 0.004 0.001 TRP N 33 HIS 0.010 0.001 HIS M 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (15325) covalent geometry : angle 0.70924 / 0.39 (21924) hydrogen bonds : bond 0.04158 / 2.89 ( 920) hydrogen bonds : angle 3.23974 / 3.33 ( 2353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6017.12 seconds wall clock time: 102 minutes 43.48 seconds (6163.48 seconds total)