Starting phenix.real_space_refine on Sat Jul 4 06:52:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k61_22686/07_2026/7k61_22686.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k61_22686/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7k61_22686/07_2026/7k61_22686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k61_22686/07_2026/7k61_22686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k61_22686/07_2026/7k61_22686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k61_22686/07_2026/7k61_22686.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= 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-dev-6108/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: 3.74, per 1000 atoms: 0.21 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: 1.56 Conformation dependent library (CDL) restraints added in 489.2 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: 2.63 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: 3.81 Time building geometry restraints manager: 2.07 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: 24931 1.45 - 2.90: 2109 2.90 - 4.35: 132 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: 2.820 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.890 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.330 ------------------------------------------------------------------------------- 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= 0.635 Angle : 0.803 7.247 27205 Z= 0.660 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 0.80274 / 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 : 0.613 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: H 86 ARG cc_start: 0.8295 (mmt-90) cc_final: 0.7972 (mmt90) 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: 0.9506 time to fit residues: 246.5975 Evaluate side-chains 193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 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: 1.5186 ------------------------------------------------------------------------------- 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 = 0.126484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.078715 restraints weight = 31471.181| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.51 r_work: 0.2916 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 18874 Z= 0.211 Angle : 0.671 8.812 27205 Z= 0.377 Chirality : 0.046 0.272 3064 Planarity : 0.004 0.048 2066 Dihedral : 30.914 178.548 5638 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.02 % Allowed : 10.02 % 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: 1.38 (0.24), residues: 1198 helix: 1.87 (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 0.032 0.002 TYR N 201 PHE 0.011 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 0.00439 / 0.21 (18870) covalent geometry : angle 0.67130 / 0.38 (27197) SS BOND : bond 0.00477 / 0.24 ( 4) SS BOND : angle 1.04304 / 0.49 ( 8) hydrogen bonds : bond 0.04364 / 2.95 ( 1066) hydrogen bonds : angle 3.66599 / 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 230 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.489 Fit side-chains REVERT: A 90 MET cc_start: 0.8939 (mmm) cc_final: 0.8663 (mmp) REVERT: A 94 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8364 (mp0) REVERT: C 56 GLU cc_start: 0.9178 (tt0) cc_final: 0.8968 (tt0) REVERT: C 72 ASP cc_start: 0.8297 (m-30) cc_final: 0.8094 (m-30) REVERT: C 95 LYS cc_start: 0.9293 (ttmm) cc_final: 0.9083 (ttmt) REVERT: D 68 ASP cc_start: 0.8788 (t0) cc_final: 0.8561 (t0) REVERT: E 79 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8245 (ttmt) REVERT: F 77 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8683 (mtpt) REVERT: G 13 LYS cc_start: 0.8717 (tptm) cc_final: 0.8507 (tmtt) REVERT: G 41 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8515 (tt0) REVERT: G 90 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8317 (t0) REVERT: G 110 ASN cc_start: 0.9308 (t0) cc_final: 0.9038 (t0) REVERT: H 86 ARG cc_start: 0.8499 (mmt-90) cc_final: 0.8037 (mmt90) REVERT: M 98 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7474 (mp0) REVERT: M 222 ASP cc_start: 0.8391 (t0) cc_final: 0.8125 (t0) REVERT: M 239 ASP cc_start: 0.7954 (m-30) cc_final: 0.7495 (m-30) REVERT: N 23 MET cc_start: 0.9375 (mmp) cc_final: 0.9042 (mmm) REVERT: N 46 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: N 80 ARG cc_start: 0.8371 (mtm110) cc_final: 0.8110 (mtm110) outliers start: 21 outliers final: 8 residues processed: 215 average time/residue: 0.8388 time to fit residues: 195.8035 Evaluate side-chains 207 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 120 MET 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: 9.9990 chunk 30 optimal weight: 0.5980 chunk 116 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3887 r_free = 0.3887 target = 0.127463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.079857 restraints weight = 31721.302| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.53 r_work: 0.2937 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18874 Z= 0.158 Angle : 0.617 6.960 27205 Z= 0.353 Chirality : 0.044 0.262 3064 Planarity : 0.004 0.047 2066 Dihedral : 30.807 179.706 5636 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.79 % Allowed : 10.98 % 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: 1.69 (0.24), residues: 1198 helix: 2.12 (0.21), residues: 552 sheet: 0.43 (0.32), residues: 240 loop : 0.27 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 37 TYR 0.023 0.001 TYR N 201 PHE 0.008 0.001 PHE E 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 0.00316 / 0.16 (18870) covalent geometry : angle 0.61690 / 0.35 (27197) SS BOND : bond 0.00360 / 0.18 ( 4) SS BOND : angle 0.72459 / 0.33 ( 8) hydrogen bonds : bond 0.03889 / 2.65 ( 1066) hydrogen bonds : angle 3.45582 / 2.54 ( 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 247 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 0.502 Fit side-chains REVERT: C 90 ASP cc_start: 0.8967 (t0) cc_final: 0.8749 (t0) REVERT: C 95 LYS cc_start: 0.9319 (ttmm) cc_final: 0.9117 (ttmp) REVERT: D 68 ASP cc_start: 0.8868 (t0) cc_final: 0.8586 (t0) REVERT: G 74 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8739 (mtmm) REVERT: G 90 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8382 (t0) REVERT: G 110 ASN cc_start: 0.9322 (t0) cc_final: 0.9067 (t0) REVERT: H 86 ARG cc_start: 0.8435 (mmt-90) cc_final: 0.7961 (mmt90) REVERT: H 105 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8884 (mm-30) REVERT: M 98 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7386 (mp0) REVERT: M 162 GLU cc_start: 0.8745 (mp0) cc_final: 0.8405 (mp0) REVERT: M 222 ASP cc_start: 0.8376 (t0) cc_final: 0.8099 (t70) REVERT: M 239 ASP cc_start: 0.7991 (m-30) cc_final: 0.7560 (m-30) REVERT: N 30 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8130 (ptm) REVERT: N 46 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7849 (mt0) outliers start: 29 outliers final: 8 residues processed: 222 average time/residue: 0.8761 time to fit residues: 211.2269 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 : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS 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 74 LYS 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 265 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 92 optimal weight: 50.0000 chunk 28 optimal weight: 0.6980 chunk 93 optimal weight: 40.0000 chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN M 110 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.126035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.077953 restraints weight = 31607.062| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.54 r_work: 0.2898 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 18874 Z= 0.236 Angle : 0.646 7.850 27205 Z= 0.361 Chirality : 0.045 0.268 3064 Planarity : 0.004 0.045 2066 Dihedral : 30.922 179.431 5636 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.08 % Allowed : 12.72 % Favored : 84.20 % 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: 1.61 (0.24), residues: 1198 helix: 2.05 (0.21), residues: 552 sheet: 0.40 (0.33), residues: 240 loop : 0.24 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 37 TYR 0.024 0.002 TYR N 201 PHE 0.011 0.001 PHE M 117 TRP 0.008 0.002 TRP N 185 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.24 (18870) covalent geometry : angle 0.64602 / 0.36 (27197) SS BOND : bond 0.00463 / 0.23 ( 4) SS BOND : angle 1.04474 / 0.49 ( 8) hydrogen bonds : bond 0.04404 / 2.98 ( 1066) hydrogen bonds : angle 3.44276 / 2.54 ( 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 232 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.497 Fit side-chains REVERT: B 22 LEU cc_start: 0.8248 (mt) cc_final: 0.7983 (mp) REVERT: B 95 ARG cc_start: 0.8375 (mmt180) cc_final: 0.7939 (mtp-110) REVERT: C 90 ASP cc_start: 0.9096 (t0) cc_final: 0.8827 (t0) REVERT: C 95 LYS cc_start: 0.9285 (ttmm) cc_final: 0.9051 (ttmp) REVERT: D 68 ASP cc_start: 0.8901 (t0) cc_final: 0.8582 (t0) REVERT: D 113 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8805 (tp30) REVERT: F 77 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8658 (mtpt) REVERT: G 73 ASN cc_start: 0.8810 (t160) cc_final: 0.8372 (t0) REVERT: G 90 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8562 (t0) REVERT: G 110 ASN cc_start: 0.9311 (t0) cc_final: 0.9068 (t0) REVERT: H 86 ARG cc_start: 0.8518 (mmt-90) cc_final: 0.8056 (mmt90) REVERT: M 222 ASP cc_start: 0.8368 (t0) cc_final: 0.8085 (t70) REVERT: M 239 ASP cc_start: 0.8098 (m-30) cc_final: 0.7703 (m-30) REVERT: N 23 MET cc_start: 0.9398 (mmp) cc_final: 0.9096 (mmm) REVERT: N 37 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8156 (ttm-80) outliers start: 32 outliers final: 14 residues processed: 208 average time/residue: 0.8751 time to fit residues: 197.8841 Evaluate side-chains 214 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 M residue 228 VAL 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: 0.9990 chunk 53 optimal weight: 6.9990 chunk 90 optimal weight: 50.0000 chunk 57 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN B 75 HIS D 84 ASN ** 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 = 0.3837 r_free = 0.3837 target = 0.125996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077970 restraints weight = 31058.343| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.42 r_work: 0.2860 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18874 Z= 0.173 Angle : 0.620 7.468 27205 Z= 0.349 Chirality : 0.044 0.267 3064 Planarity : 0.004 0.041 2066 Dihedral : 30.916 178.357 5636 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.50 % Allowed : 14.26 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1198 helix: 2.20 (0.21), residues: 552 sheet: 0.39 (0.33), residues: 240 loop : 0.27 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 86 TYR 0.015 0.001 TYR N 201 PHE 0.008 0.001 PHE E 67 TRP 0.006 0.001 TRP M 259 HIS 0.003 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (18870) covalent geometry : angle 0.61986 / 0.35 (27197) SS BOND : bond 0.00401 / 0.20 ( 4) SS BOND : angle 0.85181 / 0.39 ( 8) hydrogen bonds : bond 0.03836 / 2.60 ( 1066) hydrogen bonds : angle 3.35554 / 2.49 ( 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 232 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.518 Fit side-chains REVERT: B 95 ARG cc_start: 0.8478 (mmt180) cc_final: 0.8166 (mtp-110) REVERT: C 95 LYS cc_start: 0.9325 (ttmm) cc_final: 0.9116 (ttmp) REVERT: D 68 ASP cc_start: 0.8865 (t0) cc_final: 0.8626 (t0) REVERT: D 113 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8745 (tp30) REVERT: E 56 LYS cc_start: 0.8989 (ttpp) cc_final: 0.8733 (ttpp) REVERT: F 77 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8738 (mtpt) REVERT: G 73 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8518 (t0) REVERT: H 43 LYS cc_start: 0.9301 (mttt) cc_final: 0.9075 (mtpp) REVERT: H 86 ARG cc_start: 0.8701 (mmt-90) cc_final: 0.8338 (mmt90) REVERT: M 95 ASN cc_start: 0.8971 (m-40) cc_final: 0.8726 (m-40) REVERT: M 239 ASP cc_start: 0.8197 (m-30) cc_final: 0.7822 (m-30) REVERT: N 23 MET cc_start: 0.9377 (mmp) cc_final: 0.9011 (mmm) REVERT: N 37 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.8187 (ttm-80) REVERT: N 222 ASP cc_start: 0.8549 (t0) cc_final: 0.7751 (p0) outliers start: 26 outliers final: 12 residues processed: 210 average time/residue: 0.8725 time to fit residues: 199.1124 Evaluate side-chains 211 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 ASN 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 169 MET 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: 3.9990 chunk 110 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 43 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN ** F 25 ASN ** 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 = 0.3850 r_free = 0.3850 target = 0.126777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.078819 restraints weight = 30934.580| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.43 r_work: 0.2881 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18874 Z= 0.149 Angle : 0.597 7.137 27205 Z= 0.340 Chirality : 0.043 0.259 3064 Planarity : 0.004 0.042 2066 Dihedral : 30.770 178.007 5636 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.31 % Allowed : 15.51 % Favored : 82.18 % 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: 2.34 (0.21), residues: 552 sheet: 0.50 (0.33), residues: 240 loop : 0.28 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 37 TYR 0.014 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.006 0.001 TRP M 60 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (18870) covalent geometry : angle 0.59662 / 0.34 (27197) SS BOND : bond 0.00371 / 0.19 ( 4) SS BOND : angle 0.76249 / 0.35 ( 8) hydrogen bonds : bond 0.03692 / 2.51 ( 1066) hydrogen bonds : angle 3.25685 / 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 237 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.481 Fit side-chains REVERT: B 22 LEU cc_start: 0.8426 (mt) cc_final: 0.8202 (mp) REVERT: B 95 ARG cc_start: 0.8460 (mmt180) cc_final: 0.8195 (mtp-110) REVERT: C 73 ASN cc_start: 0.8813 (t0) cc_final: 0.8598 (t160) REVERT: D 68 ASP cc_start: 0.8860 (t0) cc_final: 0.8620 (t0) REVERT: E 56 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8715 (ttpp) REVERT: E 94 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: G 73 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8505 (t0) REVERT: G 74 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8712 (mtmm) REVERT: H 43 LYS cc_start: 0.9329 (mttt) cc_final: 0.9078 (mtpp) REVERT: H 86 ARG cc_start: 0.8684 (mmt-90) cc_final: 0.8313 (mmt90) REVERT: M 239 ASP cc_start: 0.8105 (m-30) cc_final: 0.7894 (m-30) REVERT: N 23 MET cc_start: 0.9384 (mmp) cc_final: 0.9024 (mmm) REVERT: N 37 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8304 (ttm-80) outliers start: 24 outliers final: 13 residues processed: 219 average time/residue: 0.8974 time to fit residues: 212.9818 Evaluate side-chains 217 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 87 SER 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 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: 1.9990 chunk 58 optimal weight: 0.7980 chunk 137 optimal weight: 0.0270 overall best weight: 1.3644 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.126210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.078117 restraints weight = 31044.304| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.43 r_work: 0.2867 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18874 Z= 0.186 Angle : 0.613 7.971 27205 Z= 0.345 Chirality : 0.043 0.264 3064 Planarity : 0.004 0.042 2066 Dihedral : 30.825 177.622 5636 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.12 % Allowed : 16.47 % Favored : 81.41 % 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: 1.81 (0.24), residues: 1198 helix: 2.29 (0.21), residues: 552 sheet: 0.61 (0.34), residues: 230 loop : 0.14 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 49 TYR 0.016 0.002 TYR D 40 PHE 0.008 0.001 PHE C 25 TRP 0.007 0.001 TRP N 259 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (18870) covalent geometry : angle 0.61251 / 0.35 (27197) SS BOND : bond 0.00411 / 0.21 ( 4) SS BOND : angle 0.90014 / 0.41 ( 8) hydrogen bonds : bond 0.03885 / 2.63 ( 1066) hydrogen bonds : angle 3.26469 / 2.42 ( 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 224 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.504 Fit side-chains REVERT: B 22 LEU cc_start: 0.8438 (mt) cc_final: 0.8218 (mp) REVERT: B 95 ARG cc_start: 0.8522 (mmt180) cc_final: 0.8275 (mtp-110) REVERT: C 73 ASN cc_start: 0.8843 (t0) cc_final: 0.8628 (t160) REVERT: D 68 ASP cc_start: 0.8885 (t0) cc_final: 0.8632 (t0) REVERT: E 56 LYS cc_start: 0.8988 (ttpp) cc_final: 0.8736 (ttpp) REVERT: G 73 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8468 (t0) REVERT: G 74 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8717 (mtmm) REVERT: G 91 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: H 86 ARG cc_start: 0.8680 (mmt-90) cc_final: 0.8315 (mmt90) REVERT: M 23 MET cc_start: 0.9178 (tpp) cc_final: 0.8646 (tpt) REVERT: M 30 MET cc_start: 0.8457 (ptp) cc_final: 0.8213 (ptm) REVERT: M 37 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.8472 (ttm-80) REVERT: M 239 ASP cc_start: 0.8195 (m-30) cc_final: 0.7813 (m-30) REVERT: N 23 MET cc_start: 0.9368 (mmp) cc_final: 0.9041 (mmm) REVERT: N 37 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8199 (ttm-80) REVERT: N 222 ASP cc_start: 0.8401 (t70) cc_final: 0.7719 (p0) outliers start: 22 outliers final: 14 residues processed: 207 average time/residue: 0.8826 time to fit residues: 198.1426 Evaluate side-chains 216 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 91 GLU 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 169 MET Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 140 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 10.9990 chunk 143 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3836 r_free = 0.3836 target = 0.125805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077359 restraints weight = 31009.293| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.48 r_work: 0.2859 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18874 Z= 0.199 Angle : 0.621 6.876 27205 Z= 0.348 Chirality : 0.043 0.268 3064 Planarity : 0.004 0.041 2066 Dihedral : 30.864 177.031 5636 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.60 % Allowed : 16.57 % 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: 1.76 (0.24), residues: 1198 helix: 2.25 (0.21), residues: 552 sheet: 0.56 (0.34), residues: 230 loop : 0.13 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 49 TYR 0.016 0.002 TYR H 42 PHE 0.009 0.001 PHE C 25 TRP 0.007 0.001 TRP N 259 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (18870) covalent geometry : angle 0.62119 / 0.35 (27197) SS BOND : bond 0.00417 / 0.21 ( 4) SS BOND : angle 0.95452 / 0.44 ( 8) hydrogen bonds : bond 0.03958 / 2.67 ( 1066) hydrogen bonds : angle 3.29242 / 2.45 ( 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 234 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.533 Fit side-chains REVERT: B 22 LEU cc_start: 0.8430 (mt) cc_final: 0.8183 (mp) REVERT: B 95 ARG cc_start: 0.8516 (mmt180) cc_final: 0.8286 (mtp-110) REVERT: C 73 ASN cc_start: 0.8840 (t0) cc_final: 0.8637 (t160) REVERT: D 68 ASP cc_start: 0.8912 (t0) cc_final: 0.8698 (t0) REVERT: E 56 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8746 (ttpp) REVERT: E 94 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: E 97 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: G 73 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8515 (t0) REVERT: G 91 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: H 86 ARG cc_start: 0.8696 (mmt-90) cc_final: 0.8327 (mmt90) REVERT: H 92 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8434 (mtp85) REVERT: M 23 MET cc_start: 0.9112 (tpp) cc_final: 0.8680 (tpt) REVERT: M 30 MET cc_start: 0.8613 (ptp) cc_final: 0.8365 (ptm) REVERT: M 37 ARG cc_start: 0.8788 (ttm-80) cc_final: 0.8075 (ttm-80) REVERT: M 239 ASP cc_start: 0.8133 (m-30) cc_final: 0.7704 (m-30) REVERT: N 23 MET cc_start: 0.9371 (mmp) cc_final: 0.9058 (mmm) REVERT: N 37 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8256 (ttm-80) outliers start: 27 outliers final: 15 residues processed: 216 average time/residue: 0.9276 time to fit residues: 216.6623 Evaluate side-chains 216 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 D residue 51 ASP Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 51 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 121 optimal weight: 5.9990 chunk 92 optimal weight: 50.0000 chunk 46 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3851 r_free = 0.3851 target = 0.126819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.078679 restraints weight = 31016.159| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.48 r_work: 0.2885 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1653 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= 0.140 Angle : 0.605 8.028 27205 Z= 0.342 Chirality : 0.043 0.260 3064 Planarity : 0.004 0.041 2066 Dihedral : 30.838 176.682 5636 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.02 % Allowed : 16.86 % 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: 1.89 (0.24), residues: 1198 helix: 2.36 (0.21), residues: 552 sheet: 0.60 (0.34), residues: 230 loop : 0.21 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 33 TYR 0.015 0.001 TYR D 40 PHE 0.008 0.001 PHE A 67 TRP 0.007 0.001 TRP M 60 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (18870) covalent geometry : angle 0.60491 / 0.34 (27197) SS BOND : bond 0.00374 / 0.19 ( 4) SS BOND : angle 0.75960 / 0.35 ( 8) hydrogen bonds : bond 0.03685 / 2.50 ( 1066) hydrogen bonds : angle 3.25794 / 2.42 ( 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 223 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.498 Fit side-chains REVERT: B 22 LEU cc_start: 0.8424 (mt) cc_final: 0.8178 (mp) REVERT: B 95 ARG cc_start: 0.8479 (mmt180) cc_final: 0.8262 (mtp-110) REVERT: D 68 ASP cc_start: 0.8873 (t0) cc_final: 0.8623 (t0) REVERT: E 56 LYS cc_start: 0.8991 (ttpp) cc_final: 0.8736 (ttpp) REVERT: E 94 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: E 97 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: G 73 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8581 (t0) REVERT: G 74 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8714 (mtmm) REVERT: H 86 ARG cc_start: 0.8658 (mmt-90) cc_final: 0.8287 (mmt90) REVERT: H 92 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7379 (ttp80) REVERT: M 23 MET cc_start: 0.9069 (tpp) cc_final: 0.8666 (tpt) REVERT: M 37 ARG cc_start: 0.8831 (ttm-80) cc_final: 0.8163 (ttm-80) REVERT: M 239 ASP cc_start: 0.8099 (m-30) cc_final: 0.7712 (m-30) REVERT: N 23 MET cc_start: 0.9300 (mmp) cc_final: 0.8993 (mmm) REVERT: N 37 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.8352 (ttm-80) outliers start: 21 outliers final: 12 residues processed: 206 average time/residue: 0.9023 time to fit residues: 201.3113 Evaluate side-chains 215 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 87 SER 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 E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 74 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 94 optimal weight: 10.0000 chunk 110 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.127194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.079027 restraints weight = 30989.268| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.49 r_work: 0.2894 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18874 Z= 0.137 Angle : 0.597 6.677 27205 Z= 0.340 Chirality : 0.042 0.257 3064 Planarity : 0.004 0.040 2066 Dihedral : 30.770 176.506 5636 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.64 % Allowed : 17.53 % 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: 1.93 (0.24), residues: 1198 helix: 2.39 (0.21), residues: 552 sheet: 0.61 (0.34), residues: 230 loop : 0.23 (0.31), residues: 416 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 A 67 TRP 0.008 0.001 TRP M 60 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (18870) covalent geometry : angle 0.59687 / 0.34 (27197) SS BOND : bond 0.00371 / 0.19 ( 4) SS BOND : angle 0.71297 / 0.33 ( 8) hydrogen bonds : bond 0.03616 / 2.45 ( 1066) hydrogen bonds : angle 3.22216 / 2.39 ( 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 217 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.499 Fit side-chains REVERT: A 64 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8750 (mttm) REVERT: B 22 LEU cc_start: 0.8422 (mt) cc_final: 0.8171 (mp) REVERT: B 95 ARG cc_start: 0.8445 (mmt180) cc_final: 0.8235 (mtp-110) REVERT: C 110 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8577 (p0) REVERT: D 68 ASP cc_start: 0.8870 (t0) cc_final: 0.8626 (t0) REVERT: E 56 LYS cc_start: 0.9011 (ttpp) cc_final: 0.8762 (ttpp) REVERT: E 94 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: E 97 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: G 73 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8588 (t0) REVERT: G 74 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8713 (mtmm) REVERT: H 86 ARG cc_start: 0.8656 (mmt-90) cc_final: 0.8280 (mmt90) REVERT: H 92 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7383 (ttp80) REVERT: M 23 MET cc_start: 0.9045 (tpp) cc_final: 0.8658 (tpt) REVERT: M 37 ARG cc_start: 0.8726 (ttm-80) cc_final: 0.8086 (ttm-80) REVERT: M 239 ASP cc_start: 0.8084 (m-30) cc_final: 0.7735 (m-30) REVERT: N 23 MET cc_start: 0.9309 (mmp) cc_final: 0.8986 (mmm) REVERT: N 37 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8370 (ttm-80) outliers start: 17 outliers final: 8 residues processed: 204 average time/residue: 0.9176 time to fit residues: 202.4112 Evaluate side-chains 211 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 87 SER 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 E residue 97 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 92 ARG Chi-restraints excluded: chain M residue 177 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 116 optimal weight: 8.9990 chunk 53 optimal weight: 0.0670 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 50.0000 overall best weight: 0.6320 ------------------------------------------------------------------------------- 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.127962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.080315 restraints weight = 31320.819| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.45 r_work: 0.2913 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18874 Z= 0.134 Angle : 0.580 7.274 27205 Z= 0.334 Chirality : 0.041 0.255 3064 Planarity : 0.004 0.043 2066 Dihedral : 30.635 175.844 5636 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.83 % Allowed : 17.63 % Favored : 80.54 % 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: 2.03 (0.24), residues: 1198 helix: 2.47 (0.21), residues: 552 sheet: 0.74 (0.34), residues: 228 loop : 0.23 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 49 TYR 0.015 0.001 TYR D 40 PHE 0.009 0.001 PHE A 67 TRP 0.010 0.001 TRP M 60 HIS 0.003 0.001 HIS N 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (18870) covalent geometry : angle 0.58018 / 0.33 (27197) SS BOND : bond 0.00359 / 0.18 ( 4) SS BOND : angle 0.71770 / 0.33 ( 8) hydrogen bonds : bond 0.03562 / 2.42 ( 1066) hydrogen bonds : angle 3.14498 / 2.33 ( 2604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9023.18 seconds wall clock time: 154 minutes 0.20 seconds (9240.20 seconds total)