Starting phenix.real_space_refine on Sat Sep 12 23:06:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k61_22686/09_2026/7k61_22686.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k61_22686/09_2026/7k61_22686.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7k61_22686/09_2026/7k61_22686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k61_22686/09_2026/7k61_22686.map" model { file = "/net/cci-nas-00/data/ceres_data/7k61_22686/09_2026/7k61_22686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k61_22686/09_2026/7k61_22686.cif" } 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2242 atoms to isotropic. 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 394 5.49 5 S 32 5.16 5 C 9904 2.51 5 N 3243 2.21 5 O 4150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 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: 17723 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 4015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4015 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "J" Number of atoms: 4062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4062 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Time building chain proxies: 3.41, per 1000 atoms: 0.19 Number of scatterers: 17723 At special positions: 0 Unit cell: (131.886, 122.314, 195.702, 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 32 16.00 P 394 15.00 O 4150 8.00 N 3243 7.00 C 9904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 42 " - pdb=" SG CYS M 107 " distance=2.03 Simple disulfide: pdb=" SG CYS M 171 " - pdb=" SG CYS M 245 " distance=2.03 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS N 171 " - pdb=" SG CYS N 245 " distance=2.03 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: 1.42 Conformation dependent library (CDL) restraints added in 512.7 milliseconds 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 22 sheets defined 48.4% alpha, 21.7% beta 197 base pairs and 347 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.891A 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 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.593A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.533A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.221A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.709A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.599A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.559A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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 74 removed outlier: 4.251A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain '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 103 through 124 removed outlier: 3.634A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 3.607A pdb=" N THR M 102 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 removed outlier: 3.649A pdb=" N LYS M 214 " --> pdb=" O GLU M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 214' Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 211 through 214 removed outlier: 3.580A pdb=" N LYS N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 214' Processing helix chain 'N' and resid 236 through 240 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.593A 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: 6.415A 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: 7.051A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.502A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.739A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.021A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 removed outlier: 3.702A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.365A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.365A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.089A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.089A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 24 removed outlier: 3.555A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.628A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.483A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 3.800A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER N 249 " --> pdb=" O LEU N 256 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU N 256 " --> pdb=" O SER N 249 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 510 hydrogen bonds 1020 hydrogen bond angles 0 basepair planarities 197 basepair parallelities 347 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 1.95 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: 3737 1.33 - 1.45: 6089 1.45 - 1.57: 8206 1.57 - 1.69: 786 1.69 - 1.82: 52 Bond restraints: 18870 Sorted by residual: bond pdb=" C3' DT J 114 " pdb=" O3' DT J 114 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.39e+01 bond pdb=" C3' DA I 45 " pdb=" O3' DA I 45 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" C3' DG J 107 " pdb=" O3' DG J 107 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.29e+01 bond pdb=" C3' DC J 45 " pdb=" O3' DC J 45 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.19e+01 bond pdb=" C3' DA I 85 " pdb=" O3' DA I 85 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.15e+01 ... (remaining 18865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 24902 1.45 - 2.90: 2137 2.90 - 4.35: 133 4.35 - 5.80: 20 5.80 - 7.25: 5 Bond angle restraints: 27197 Sorted by residual: angle pdb=" O4' DA J 115 " pdb=" C1' DA J 115 " pdb=" N9 DA J 115 " ideal model delta sigma weight residual 108.00 111.32 -3.32 7.00e-01 2.04e+00 2.26e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT I 100 " pdb=" C4 DT I 100 " pdb=" O4 DT I 100 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT I 172 " pdb=" C4 DT I 172 " pdb=" O4 DT I 172 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT J 42 " pdb=" C4 DT J 42 " pdb=" O4 DT J 42 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 ... (remaining 27192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 8344 35.34 - 70.68: 1908 70.68 - 106.02: 20 106.02 - 141.35: 0 141.35 - 176.69: 2 Dihedral angle restraints: 10274 sinusoidal: 6728 harmonic: 3546 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C4' DT J 153 " pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " pdb=" P DC J 154 " ideal model delta sinusoidal sigma weight residual 220.00 43.31 176.69 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 119 " pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " pdb=" P DG J 120 " ideal model delta sinusoidal sigma weight residual 220.00 69.48 150.52 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 10271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1815 0.038 - 0.077: 851 0.077 - 0.115: 321 0.115 - 0.154: 73 0.154 - 0.192: 4 Chirality restraints: 3064 Sorted by residual: chirality pdb=" C3' DT J 153 " pdb=" C4' DT J 153 " pdb=" O3' DT J 153 " pdb=" C2' DT J 153 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CB THR M 177 " pdb=" CA THR M 177 " pdb=" OG1 THR M 177 " pdb=" CG2 THR M 177 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CA SER M 113 " pdb=" N SER M 113 " pdb=" C SER M 113 " pdb=" CB SER M 113 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 3061 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 201 " -0.021 2.00e-02 2.50e+03 2.01e-02 8.06e+00 pdb=" CG TYR N 201 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR N 201 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR N 201 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR N 201 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR N 201 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR N 201 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR N 201 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 73 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C ASN G 73 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN G 73 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS G 74 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO D 103 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.027 5.00e-02 4.00e+02 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 630 2.68 - 3.24: 15654 3.24 - 3.79: 34537 3.79 - 4.35: 44656 4.35 - 4.90: 63674 Nonbonded interactions: 159151 Sorted by model distance: nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.130 3.040 nonbonded pdb=" NH1 ARG H 31 " pdb=" OP1 DG J 150 " model vdw 2.207 3.120 nonbonded pdb=" O THR G 76 " pdb=" OG1 THR H 52 " model vdw 2.217 3.040 nonbonded pdb=" NH2 ARG G 32 " pdb=" OE1 GLU H 35 " model vdw 2.271 3.120 nonbonded pdb=" O THR C 76 " pdb=" OG1 THR D 52 " model vdw 2.280 3.040 ... (remaining 159146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.800 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:8.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 18874 Z= 0.636 Angle : 0.809 7.247 27205 Z= 0.665 Chirality : 0.050 0.192 3064 Planarity : 0.004 0.049 2066 Dihedral : 27.102 176.693 7990 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 1.15 (0.24), residues: 1198 helix: 1.55 (0.21), residues: 550 sheet: 0.29 (0.34), residues: 242 loop : 0.13 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 92 TYR 0.049 0.002 TYR N 201 PHE 0.018 0.002 PHE M 117 TRP 0.019 0.003 TRP M 196 HIS 0.005 0.002 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.64 (18870) covalent geometry : angle 0.80873 / 0.66 (27197) SS BOND : bond 0.00443 / 0.22 ( 4) SS BOND : angle 1.19097 / 0.58 ( 8) hydrogen bonds : bond 0.08451 / 5.78 ( 1066) hydrogen bonds : angle 4.32086 / 3.20 ( 2604) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.477 Fit side-chains REVERT: A 56 LYS cc_start: 0.8783 (tttp) cc_final: 0.8570 (ttmt) REVERT: A 105 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7334 (mt-10) REVERT: C 56 GLU cc_start: 0.8491 (tt0) cc_final: 0.8246 (tt0) REVERT: C 61 GLU cc_start: 0.8342 (tp30) cc_final: 0.7984 (mm-30) REVERT: D 116 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8616 (ttpp) REVERT: G 110 ASN cc_start: 0.8905 (t0) cc_final: 0.8673 (t0) REVERT: M 98 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7668 (mp0) outliers start: 0 outliers final: 2 residues processed: 240 average time/residue: 0.9093 time to fit residues: 235.8535 Evaluate side-chains 195 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 51 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN B 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS G 73 ASN N 192 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.126569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.078795 restraints weight = 31502.401| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.51 r_work: 0.2914 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18874 Z= 0.202 Angle : 0.686 8.865 27205 Z= 0.382 Chirality : 0.047 0.288 3064 Planarity : 0.004 0.048 2066 Dihedral : 30.815 177.916 5638 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.22 % Allowed : 9.83 % Favored : 87.96 % 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: 1.39 (0.24), residues: 1198 helix: 1.88 (0.22), residues: 552 sheet: 0.28 (0.33), residues: 240 loop : 0.12 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 33 TYR 0.031 0.002 TYR N 201 PHE 0.010 0.002 PHE M 117 TRP 0.012 0.002 TRP N 185 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (18870) covalent geometry : angle 0.68601 / 0.38 (27197) SS BOND : bond 0.00485 / 0.24 ( 4) SS BOND : angle 1.09567 / 0.52 ( 8) hydrogen bonds : bond 0.04361 / 2.95 ( 1066) hydrogen bonds : angle 3.67019 / 2.69 ( 2604) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.523 Fit side-chains REVERT: A 90 MET cc_start: 0.8942 (mmm) cc_final: 0.8668 (mmp) REVERT: A 94 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8371 (mp0) REVERT: C 95 LYS cc_start: 0.9293 (ttmm) cc_final: 0.9086 (ttmt) REVERT: D 68 ASP cc_start: 0.8777 (t0) cc_final: 0.8557 (t0) REVERT: E 79 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8249 (ttmt) REVERT: F 77 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8698 (mtpt) REVERT: G 41 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: G 90 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8298 (t0) REVERT: G 110 ASN cc_start: 0.9337 (t0) cc_final: 0.9075 (t0) REVERT: M 98 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7514 (mp0) REVERT: M 222 ASP cc_start: 0.8377 (t0) cc_final: 0.8128 (t0) REVERT: N 46 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: N 80 ARG cc_start: 0.8381 (mtm110) cc_final: 0.8110 (mtm110) outliers start: 23 outliers final: 9 residues processed: 215 average time/residue: 0.8436 time to fit residues: 197.0155 Evaluate side-chains 209 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 104 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.127080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.079400 restraints weight = 31723.866| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.52 r_work: 0.2927 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18874 Z= 0.164 Angle : 0.635 6.726 27205 Z= 0.358 Chirality : 0.045 0.283 3064 Planarity : 0.004 0.046 2066 Dihedral : 30.738 178.830 5636 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.99 % Allowed : 10.79 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.24), residues: 1198 helix: 2.12 (0.21), residues: 552 sheet: 0.41 (0.32), residues: 240 loop : 0.26 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 37 TYR 0.023 0.001 TYR N 201 PHE 0.008 0.001 PHE A 67 TRP 0.006 0.001 TRP M 60 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (18870) covalent geometry : angle 0.63508 / 0.36 (27197) SS BOND : bond 0.00374 / 0.19 ( 4) SS BOND : angle 0.76082 / 0.35 ( 8) hydrogen bonds : bond 0.03945 / 2.68 ( 1066) hydrogen bonds : angle 3.47412 / 2.56 ( 2604) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.523 Fit side-chains REVERT: C 90 ASP cc_start: 0.8991 (t0) cc_final: 0.8763 (t0) REVERT: C 95 LYS cc_start: 0.9314 (ttmm) cc_final: 0.9109 (ttmp) REVERT: D 68 ASP cc_start: 0.8869 (t0) cc_final: 0.8586 (t0) REVERT: G 90 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8297 (t0) REVERT: G 110 ASN cc_start: 0.9318 (t0) cc_final: 0.9061 (t0) REVERT: H 105 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8886 (mm-30) REVERT: M 162 GLU cc_start: 0.8737 (mp0) cc_final: 0.8380 (mp0) REVERT: M 222 ASP cc_start: 0.8365 (t0) cc_final: 0.8019 (t0) REVERT: M 239 ASP cc_start: 0.7880 (m-30) cc_final: 0.7585 (m-30) REVERT: N 23 MET cc_start: 0.9392 (mmp) cc_final: 0.9026 (mmm) REVERT: N 30 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8143 (ptm) REVERT: N 46 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8108 (mt0) outliers start: 31 outliers final: 10 residues processed: 221 average time/residue: 0.8540 time to fit residues: 204.9717 Evaluate side-chains 213 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 30 MET Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 111 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 92 optimal weight: 50.0000 chunk 28 optimal weight: 0.7980 chunk 93 optimal weight: 40.0000 chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN B 75 HIS D 84 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.123485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.074782 restraints weight = 31061.826| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.42 r_work: 0.2797 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 18874 Z= 0.363 Angle : 0.739 8.729 27205 Z= 0.397 Chirality : 0.050 0.303 3064 Planarity : 0.005 0.051 2066 Dihedral : 31.030 179.580 5636 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.28 % Allowed : 12.81 % Favored : 83.91 % 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: 1.29 (0.24), residues: 1198 helix: 1.73 (0.21), residues: 552 sheet: 0.36 (0.33), residues: 240 loop : 0.08 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 49 TYR 0.028 0.002 TYR N 201 PHE 0.016 0.002 PHE M 117 TRP 0.011 0.002 TRP N 259 HIS 0.005 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00796 / 0.36 (18870) covalent geometry : angle 0.73835 / 0.40 (27197) SS BOND : bond 0.00572 / 0.29 ( 4) SS BOND : angle 1.31316 / 0.62 ( 8) hydrogen bonds : bond 0.05365 / 3.63 ( 1066) hydrogen bonds : angle 3.57948 / 2.64 ( 2604) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 0.502 Fit side-chains REVERT: A 105 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8176 (mt-10) REVERT: B 22 LEU cc_start: 0.8577 (mt) cc_final: 0.8355 (mp) REVERT: B 95 ARG cc_start: 0.8622 (mmt180) cc_final: 0.8278 (mtp-110) REVERT: C 90 ASP cc_start: 0.9137 (t0) cc_final: 0.8903 (t0) REVERT: D 68 ASP cc_start: 0.8941 (t0) cc_final: 0.8683 (t0) REVERT: E 56 LYS cc_start: 0.8983 (ttpp) cc_final: 0.8746 (ttpp) REVERT: E 94 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: F 77 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8770 (mtpt) REVERT: G 73 ASN cc_start: 0.8885 (t160) cc_final: 0.8522 (t160) REVERT: G 91 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: G 110 ASN cc_start: 0.9341 (t0) cc_final: 0.9122 (t0) REVERT: H 92 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8571 (ttp80) REVERT: H 93 GLU cc_start: 0.8913 (mp0) cc_final: 0.8634 (mp0) REVERT: M 31 HIS cc_start: 0.8278 (m90) cc_final: 0.8039 (m-70) REVERT: M 37 ARG cc_start: 0.8698 (ttm-80) cc_final: 0.8333 (ttm-80) REVERT: M 95 ASN cc_start: 0.9050 (m-40) cc_final: 0.8738 (m-40) REVERT: M 222 ASP cc_start: 0.8420 (t0) cc_final: 0.8140 (t0) REVERT: M 239 ASP cc_start: 0.8276 (m-30) cc_final: 0.7942 (m-30) REVERT: N 30 MET cc_start: 0.8729 (mtp) cc_final: 0.8434 (ptm) REVERT: N 37 ARG cc_start: 0.8688 (mmm-85) cc_final: 0.8189 (ttm-80) outliers start: 34 outliers final: 14 residues processed: 218 average time/residue: 0.8864 time to fit residues: 209.2156 Evaluate side-chains 211 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 3 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 90 optimal weight: 50.0000 chunk 57 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.125610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.077385 restraints weight = 31009.451| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.44 r_work: 0.2848 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18874 Z= 0.167 Angle : 0.652 7.405 27205 Z= 0.359 Chirality : 0.045 0.291 3064 Planarity : 0.004 0.043 2066 Dihedral : 30.969 179.447 5636 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.50 % Allowed : 14.93 % Favored : 82.56 % 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: 1.48 (0.24), residues: 1198 helix: 1.91 (0.21), residues: 564 sheet: 0.44 (0.33), residues: 232 loop : 0.08 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 37 TYR 0.016 0.001 TYR H 42 PHE 0.008 0.001 PHE E 67 TRP 0.006 0.001 TRP M 60 HIS 0.005 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (18870) covalent geometry : angle 0.65147 / 0.36 (27197) SS BOND : bond 0.00400 / 0.20 ( 4) SS BOND : angle 0.79675 / 0.36 ( 8) hydrogen bonds : bond 0.03897 / 2.65 ( 1066) hydrogen bonds : angle 3.42824 / 2.54 ( 2604) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.585 Fit side-chains REVERT: B 95 ARG cc_start: 0.8480 (mmt180) cc_final: 0.8207 (mtp-110) REVERT: C 73 ASN cc_start: 0.8828 (t0) cc_final: 0.8613 (t160) REVERT: D 68 ASP cc_start: 0.8882 (t0) cc_final: 0.8643 (t0) REVERT: E 56 LYS cc_start: 0.8991 (ttpp) cc_final: 0.8741 (ttpp) REVERT: F 77 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8781 (mtpt) REVERT: G 73 ASN cc_start: 0.8914 (t160) cc_final: 0.8514 (t0) REVERT: G 90 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8553 (t0) REVERT: H 93 GLU cc_start: 0.8910 (mp0) cc_final: 0.8668 (mp0) REVERT: M 23 MET cc_start: 0.9141 (tpp) cc_final: 0.8655 (tpt) REVERT: M 239 ASP cc_start: 0.8292 (m-30) cc_final: 0.7942 (m-30) REVERT: N 23 MET cc_start: 0.9384 (mmp) cc_final: 0.9024 (mmm) REVERT: N 37 ARG cc_start: 0.8697 (mmm-85) cc_final: 0.8186 (ttm-80) outliers start: 26 outliers final: 11 residues processed: 217 average time/residue: 0.8047 time to fit residues: 190.1348 Evaluate side-chains 213 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 40 optimal weight: 0.9980 chunk 110 optimal weight: 0.0030 chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 0.0670 overall best weight: 0.3528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.127902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.080292 restraints weight = 31029.207| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.44 r_work: 0.2908 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 18874 Z= 0.126 Angle : 0.604 7.646 27205 Z= 0.344 Chirality : 0.043 0.273 3064 Planarity : 0.004 0.045 2066 Dihedral : 30.637 179.779 5636 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.60 % Allowed : 16.09 % Favored : 81.31 % 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: 1.88 (0.24), residues: 1198 helix: 2.39 (0.21), residues: 552 sheet: 0.44 (0.33), residues: 240 loop : 0.25 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 37 TYR 0.014 0.001 TYR H 42 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP M 60 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.13 (18870) covalent geometry : angle 0.60377 / 0.34 (27197) SS BOND : bond 0.00331 / 0.17 ( 4) SS BOND : angle 0.53762 / 0.25 ( 8) hydrogen bonds : bond 0.03647 / 2.49 ( 1066) hydrogen bonds : angle 3.25088 / 2.41 ( 2604) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.484 Fit side-chains REVERT: B 95 ARG cc_start: 0.8393 (mmt180) cc_final: 0.8162 (mtp-110) REVERT: C 73 ASN cc_start: 0.8774 (t0) cc_final: 0.8569 (t160) REVERT: C 110 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8572 (p0) REVERT: D 68 ASP cc_start: 0.8800 (t0) cc_final: 0.8569 (t0) REVERT: E 56 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8741 (ttpp) REVERT: G 73 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8538 (t0) REVERT: G 74 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8710 (mtmm) REVERT: M 30 MET cc_start: 0.8463 (ptp) cc_final: 0.8165 (ptm) REVERT: M 239 ASP cc_start: 0.8092 (m-30) cc_final: 0.7684 (m-30) REVERT: N 23 MET cc_start: 0.9320 (mmp) cc_final: 0.8957 (mmm) REVERT: N 37 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.8376 (ttm-80) REVERT: N 222 ASP cc_start: 0.8500 (t0) cc_final: 0.7965 (p0) outliers start: 27 outliers final: 10 residues processed: 223 average time/residue: 0.8544 time to fit residues: 206.8305 Evaluate side-chains 214 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 50.0000 chunk 77 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 137 optimal weight: 0.0040 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN ** G 73 ASN ** 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 = 0.3850 r_free = 0.3850 target = 0.126600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.078623 restraints weight = 31125.861| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.45 r_work: 0.2877 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18874 Z= 0.168 Angle : 0.616 7.032 27205 Z= 0.346 Chirality : 0.043 0.275 3064 Planarity : 0.004 0.043 2066 Dihedral : 30.670 179.290 5636 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.02 % Allowed : 16.96 % Favored : 81.02 % 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: 1.89 (0.24), residues: 1198 helix: 2.39 (0.21), residues: 552 sheet: 0.46 (0.33), residues: 240 loop : 0.25 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 49 TYR 0.017 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP M 259 HIS 0.003 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (18870) covalent geometry : angle 0.61584 / 0.35 (27197) SS BOND : bond 0.00371 / 0.19 ( 4) SS BOND : angle 0.79957 / 0.37 ( 8) hydrogen bonds : bond 0.03780 / 2.56 ( 1066) hydrogen bonds : angle 3.23422 / 2.40 ( 2604) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.463 Fit side-chains REVERT: B 95 ARG cc_start: 0.8480 (mmt180) cc_final: 0.8243 (mtp-110) REVERT: C 73 ASN cc_start: 0.8813 (t0) cc_final: 0.8612 (t160) REVERT: C 110 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8583 (p0) REVERT: D 68 ASP cc_start: 0.8882 (t0) cc_final: 0.8638 (t0) REVERT: E 56 LYS cc_start: 0.9002 (ttpp) cc_final: 0.8742 (ttpp) REVERT: G 73 ASN cc_start: 0.8979 (OUTLIER) cc_final: 0.8558 (t0) REVERT: G 74 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8715 (mtmm) REVERT: H 43 LYS cc_start: 0.9219 (mttm) cc_final: 0.9009 (mttt) REVERT: H 76 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: M 37 ARG cc_start: 0.8790 (ttm-80) cc_final: 0.8587 (ttm-80) REVERT: M 239 ASP cc_start: 0.8172 (m-30) cc_final: 0.7809 (m-30) REVERT: N 23 MET cc_start: 0.9312 (mmp) cc_final: 0.8979 (mmm) REVERT: N 37 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8372 (ttm-80) outliers start: 21 outliers final: 9 residues processed: 204 average time/residue: 0.8462 time to fit residues: 187.3753 Evaluate side-chains 209 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 140 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.126498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.078571 restraints weight = 31058.482| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.43 r_work: 0.2872 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18874 Z= 0.166 Angle : 0.615 6.934 27205 Z= 0.345 Chirality : 0.043 0.282 3064 Planarity : 0.004 0.042 2066 Dihedral : 30.678 178.206 5634 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.02 % Allowed : 17.15 % Favored : 80.83 % 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: 1.91 (0.24), residues: 1198 helix: 2.38 (0.21), residues: 552 sheet: 0.54 (0.33), residues: 240 loop : 0.26 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 33 TYR 0.016 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.009 0.001 TRP M 185 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (18870) covalent geometry : angle 0.61510 / 0.35 (27197) SS BOND : bond 0.00403 / 0.20 ( 4) SS BOND : angle 0.78490 / 0.35 ( 8) hydrogen bonds : bond 0.03749 / 2.54 ( 1066) hydrogen bonds : angle 3.23728 / 2.41 ( 2604) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.502 Fit side-chains REVERT: B 95 ARG cc_start: 0.8494 (mmt180) cc_final: 0.8275 (mtp-110) REVERT: C 110 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8581 (p0) REVERT: D 68 ASP cc_start: 0.8885 (t0) cc_final: 0.8633 (t0) REVERT: E 56 LYS cc_start: 0.9007 (ttpp) cc_final: 0.8763 (ttpp) REVERT: E 94 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8633 (mm-30) REVERT: E 123 ASP cc_start: 0.9165 (OUTLIER) cc_final: 0.8774 (m-30) REVERT: G 73 ASN cc_start: 0.8972 (OUTLIER) cc_final: 0.8563 (t0) REVERT: H 43 LYS cc_start: 0.9228 (mttm) cc_final: 0.9001 (mttt) REVERT: M 37 ARG cc_start: 0.8818 (ttm-80) cc_final: 0.8175 (ttm-80) REVERT: M 239 ASP cc_start: 0.8085 (m-30) cc_final: 0.7748 (m-30) REVERT: N 23 MET cc_start: 0.9313 (mmp) cc_final: 0.8986 (mmm) REVERT: N 37 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8366 (ttm-80) outliers start: 21 outliers final: 11 residues processed: 203 average time/residue: 0.8198 time to fit residues: 180.8214 Evaluate side-chains 211 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 121 optimal weight: 6.9990 chunk 92 optimal weight: 50.0000 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 88 optimal weight: 10.9990 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.126503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078073 restraints weight = 31060.519| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.49 r_work: 0.2874 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18874 Z= 0.166 Angle : 0.617 7.885 27205 Z= 0.345 Chirality : 0.043 0.281 3064 Planarity : 0.004 0.042 2066 Dihedral : 30.676 177.875 5634 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.02 % Allowed : 17.34 % Favored : 80.64 % 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: 1.91 (0.24), residues: 1198 helix: 2.39 (0.21), residues: 552 sheet: 0.52 (0.33), residues: 240 loop : 0.26 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 33 TYR 0.016 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP M 60 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (18870) covalent geometry : angle 0.61710 / 0.35 (27197) SS BOND : bond 0.00386 / 0.20 ( 4) SS BOND : angle 0.82269 / 0.37 ( 8) hydrogen bonds : bond 0.03748 / 2.54 ( 1066) hydrogen bonds : angle 3.23712 / 2.41 ( 2604) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.327 Fit side-chains REVERT: B 95 ARG cc_start: 0.8472 (mmt180) cc_final: 0.8259 (mtp-110) REVERT: C 110 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8570 (p0) REVERT: D 68 ASP cc_start: 0.8898 (t0) cc_final: 0.8631 (t0) REVERT: E 56 LYS cc_start: 0.9003 (ttpp) cc_final: 0.8749 (ttpp) REVERT: E 94 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8639 (mm-30) REVERT: E 123 ASP cc_start: 0.9178 (OUTLIER) cc_final: 0.8785 (m-30) REVERT: G 73 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8547 (t0) REVERT: G 74 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8708 (mtmm) REVERT: M 37 ARG cc_start: 0.8852 (ttm-80) cc_final: 0.8217 (ttm-80) REVERT: M 239 ASP cc_start: 0.8033 (m-30) cc_final: 0.7656 (m-30) REVERT: N 23 MET cc_start: 0.9323 (mmp) cc_final: 0.8987 (mmm) REVERT: N 37 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8356 (ttm-80) REVERT: N 222 ASP cc_start: 0.8442 (t0) cc_final: 0.7965 (p0) outliers start: 21 outliers final: 10 residues processed: 201 average time/residue: 0.8533 time to fit residues: 186.1317 Evaluate side-chains 209 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 94 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.126929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.079262 restraints weight = 30946.433| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.47 r_work: 0.2892 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18874 Z= 0.146 Angle : 0.609 6.918 27205 Z= 0.342 Chirality : 0.043 0.279 3064 Planarity : 0.004 0.069 2066 Dihedral : 30.654 177.548 5634 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.54 % Allowed : 17.53 % Favored : 80.92 % 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: 1.94 (0.24), residues: 1198 helix: 2.43 (0.21), residues: 552 sheet: 0.50 (0.33), residues: 240 loop : 0.27 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 49 TYR 0.016 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.008 0.001 TRP M 60 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (18870) covalent geometry : angle 0.60934 / 0.34 (27197) SS BOND : bond 0.00370 / 0.19 ( 4) SS BOND : angle 0.75945 / 0.34 ( 8) hydrogen bonds : bond 0.03646 / 2.47 ( 1066) hydrogen bonds : angle 3.22334 / 2.40 ( 2604) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.416 Fit side-chains REVERT: B 95 ARG cc_start: 0.8468 (mmt180) cc_final: 0.8267 (mtp-110) REVERT: C 110 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8572 (p0) REVERT: D 68 ASP cc_start: 0.8871 (t0) cc_final: 0.8668 (t0) REVERT: E 56 LYS cc_start: 0.9013 (ttpp) cc_final: 0.8770 (ttpp) REVERT: E 94 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8638 (mm-30) REVERT: E 123 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8781 (m-30) REVERT: G 73 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8649 (t0) REVERT: G 74 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8906 (mtmm) REVERT: M 37 ARG cc_start: 0.8764 (ttm-80) cc_final: 0.8149 (ttm-80) REVERT: M 239 ASP cc_start: 0.8119 (m-30) cc_final: 0.7748 (m-30) REVERT: N 23 MET cc_start: 0.9320 (mmp) cc_final: 0.8967 (mmm) REVERT: N 37 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8351 (ttm-80) REVERT: N 222 ASP cc_start: 0.8436 (t0) cc_final: 0.7865 (p0) outliers start: 16 outliers final: 9 residues processed: 199 average time/residue: 0.7993 time to fit residues: 172.7713 Evaluate side-chains 208 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 116 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 74 optimal weight: 50.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.126939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.078779 restraints weight = 31203.597| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.49 r_work: 0.2881 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18874 Z= 0.152 Angle : 0.605 6.887 27205 Z= 0.340 Chirality : 0.043 0.279 3064 Planarity : 0.004 0.042 2066 Dihedral : 30.639 177.317 5634 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.64 % Allowed : 17.24 % Favored : 81.12 % 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: 1.97 (0.24), residues: 1198 helix: 2.42 (0.21), residues: 552 sheet: 0.55 (0.33), residues: 240 loop : 0.29 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 49 TYR 0.020 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.008 0.001 TRP M 60 HIS 0.003 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (18870) covalent geometry : angle 0.60485 / 0.34 (27197) SS BOND : bond 0.00373 / 0.19 ( 4) SS BOND : angle 0.78030 / 0.35 ( 8) hydrogen bonds : bond 0.03660 / 2.48 ( 1066) hydrogen bonds : angle 3.22224 / 2.39 ( 2604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8762.46 seconds wall clock time: 149 minutes 14.47 seconds (8954.47 seconds total)