Starting phenix.real_space_refine on Thu Mar 5 04:12:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k61_22686/03_2026/7k61_22686.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k61_22686/03_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_22686/03_2026/7k61_22686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k61_22686/03_2026/7k61_22686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k61_22686/03_2026/7k61_22686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k61_22686/03_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-5986/lib/python3.9/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: 4.13, per 1000 atoms: 0.23 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: 1.48 Conformation dependent library (CDL) restraints added in 504.0 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: 3.07 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: 3.72 Time building geometry restraints manager: 2.05 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=" CA ASN G 89 " pdb=" C ASN G 89 " ideal model delta sigma weight residual 1.523 1.492 0.031 1.80e-02 3.09e+03 3.03e+00 bond pdb=" CB THR H 52 " pdb=" CG2 THR H 52 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CG1 ILE C 62 " pdb=" CD1 ILE C 62 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.36e+00 bond pdb=" CG1 ILE D 61 " pdb=" CD1 ILE D 61 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.14e+00 bond pdb=" CB PRO E 66 " pdb=" CG PRO E 66 " ideal model delta sigma weight residual 1.492 1.424 0.068 5.00e-02 4.00e+02 1.86e+00 ... (remaining 18865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 25919 1.45 - 2.90: 1166 2.90 - 4.35: 87 4.35 - 5.80: 20 5.80 - 7.25: 5 Bond angle restraints: 27197 Sorted by residual: angle pdb=" CA ASN G 73 " pdb=" CB ASN G 73 " pdb=" CG ASN G 73 " ideal model delta sigma weight residual 112.60 115.50 -2.90 1.00e+00 1.00e+00 8.42e+00 angle pdb=" N GLN N 88 " pdb=" CA GLN N 88 " pdb=" C GLN N 88 " ideal model delta sigma weight residual 114.31 110.82 3.49 1.29e+00 6.01e-01 7.34e+00 angle pdb=" C TYR N 69 " pdb=" N ALA N 70 " pdb=" CA ALA N 70 " ideal model delta sigma weight residual 121.54 126.44 -4.90 1.91e+00 2.74e-01 6.59e+00 angle pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta sigma weight residual 122.15 114.90 7.25 2.83e+00 1.25e-01 6.56e+00 angle pdb=" N ASN G 73 " pdb=" CA ASN G 73 " pdb=" C ASN G 73 " ideal model delta sigma weight residual 113.28 110.18 3.10 1.22e+00 6.72e-01 6.48e+00 ... (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 - 0.035: 1923 0.035 - 0.069: 879 0.069 - 0.104: 198 0.104 - 0.138: 58 0.138 - 0.173: 6 Chirality restraints: 3064 Sorted by residual: 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 chirality pdb=" CB THR M 102 " pdb=" CA THR M 102 " pdb=" OG1 THR M 102 " pdb=" CG2 THR M 102 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.26e-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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.650 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 18874 Z= 0.324 Angle : 0.669 7.247 27205 Z= 0.401 Chirality : 0.041 0.173 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 covalent geometry : bond 0.00739 (18870) covalent geometry : angle 0.66913 (27197) SS BOND : bond 0.00443 ( 4) SS BOND : angle 1.19097 ( 8) hydrogen bonds : bond 0.08451 ( 1066) hydrogen bonds : angle 4.32086 ( 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 : 0.459 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: 0.9920 time to fit residues: 255.5681 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 : 0.482 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 4.9990 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: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN B 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN E 68 GLN E 113 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.126282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.078264 restraints weight = 31504.848| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.56 r_work: 0.2914 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18874 Z= 0.238 Angle : 0.598 7.055 27205 Z= 0.350 Chirality : 0.037 0.147 3064 Planarity : 0.004 0.049 2066 Dihedral : 30.410 176.546 5638 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.12 % Allowed : 9.83 % Favored : 88.05 % 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: 1.51 (0.24), residues: 1198 helix: 1.94 (0.21), residues: 552 sheet: 0.39 (0.33), residues: 240 loop : 0.18 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 33 TYR 0.033 0.002 TYR N 201 PHE 0.009 0.001 PHE A 67 TRP 0.009 0.002 TRP M 196 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00542 (18870) covalent geometry : angle 0.59779 (27197) SS BOND : bond 0.00482 ( 4) SS BOND : angle 0.94227 ( 8) hydrogen bonds : bond 0.03816 ( 1066) hydrogen bonds : angle 3.49297 ( 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 236 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.501 Fit side-chains REVERT: D 68 ASP cc_start: 0.8831 (t0) cc_final: 0.8603 (t0) REVERT: G 41 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: G 73 ASN cc_start: 0.8813 (t0) cc_final: 0.8509 (t0) REVERT: G 90 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8586 (t70) REVERT: G 110 ASN cc_start: 0.9324 (t0) cc_final: 0.9064 (t0) REVERT: H 86 ARG cc_start: 0.8515 (mmt-90) cc_final: 0.8020 (mmt90) REVERT: H 93 GLU cc_start: 0.8878 (mp0) cc_final: 0.8627 (mp0) REVERT: M 222 ASP cc_start: 0.8425 (t0) cc_final: 0.8162 (t0) REVERT: M 239 ASP cc_start: 0.8125 (m-30) cc_final: 0.7832 (m-30) REVERT: N 20 ASP cc_start: 0.8702 (m-30) cc_final: 0.8260 (m-30) REVERT: N 23 MET cc_start: 0.9350 (mmp) cc_final: 0.9063 (mmm) REVERT: N 30 MET cc_start: 0.8687 (mtp) cc_final: 0.8412 (ptm) REVERT: N 122 LYS cc_start: 0.8556 (mppt) cc_final: 0.8340 (mmmt) outliers start: 22 outliers final: 6 residues processed: 219 average time/residue: 0.8268 time to fit residues: 195.9173 Evaluate side-chains 202 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain N residue 169 MET 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: 2.9990 chunk 30 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 75 HIS D 84 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 = 0.3865 r_free = 0.3865 target = 0.126077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.078410 restraints weight = 31718.542| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.53 r_work: 0.2907 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18874 Z= 0.241 Angle : 0.580 6.622 27205 Z= 0.340 Chirality : 0.037 0.146 3064 Planarity : 0.004 0.045 2066 Dihedral : 30.371 178.314 5636 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.70 % Allowed : 11.85 % Favored : 85.45 % 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: 2.09 (0.21), residues: 552 sheet: 0.49 (0.33), residues: 240 loop : 0.27 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.024 0.002 TYR N 201 PHE 0.010 0.001 PHE M 117 TRP 0.008 0.002 TRP N 259 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00549 (18870) covalent geometry : angle 0.58019 (27197) SS BOND : bond 0.00447 ( 4) SS BOND : angle 1.00889 ( 8) hydrogen bonds : bond 0.03713 ( 1066) hydrogen bonds : angle 3.38031 ( 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 245 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.322 Fit side-chains REVERT: A 105 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8032 (mt-10) REVERT: B 22 LEU cc_start: 0.8070 (mt) cc_final: 0.7819 (mp) REVERT: B 95 ARG cc_start: 0.8384 (mmt180) cc_final: 0.8011 (mtp-110) REVERT: C 90 ASP cc_start: 0.9012 (t0) cc_final: 0.8776 (t0) REVERT: D 68 ASP cc_start: 0.8895 (t0) cc_final: 0.8583 (t0) REVERT: E 56 LYS cc_start: 0.8886 (ttpp) cc_final: 0.8572 (ttpp) REVERT: E 94 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: F 77 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8649 (mtpt) REVERT: G 73 ASN cc_start: 0.8911 (t0) cc_final: 0.8513 (t0) REVERT: G 74 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8682 (mtmm) REVERT: G 110 ASN cc_start: 0.9320 (t0) cc_final: 0.9074 (t0) REVERT: H 86 ARG cc_start: 0.8528 (mmt-90) cc_final: 0.8036 (mmt90) REVERT: H 93 GLU cc_start: 0.8921 (mp0) cc_final: 0.8586 (mp0) REVERT: M 31 HIS cc_start: 0.8259 (m90) cc_final: 0.7923 (m-70) REVERT: M 37 ARG cc_start: 0.8860 (mtm110) cc_final: 0.8550 (ttm-80) REVERT: M 95 ASN cc_start: 0.8989 (m-40) cc_final: 0.8635 (m-40) REVERT: M 222 ASP cc_start: 0.8415 (t0) cc_final: 0.8129 (t0) REVERT: M 239 ASP cc_start: 0.7964 (m-30) cc_final: 0.7649 (m-30) REVERT: N 23 MET cc_start: 0.9323 (mmp) cc_final: 0.9012 (mmm) outliers start: 28 outliers final: 13 residues processed: 223 average time/residue: 0.8453 time to fit residues: 203.5239 Evaluate side-chains 216 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 74 LYS Chi-restraints excluded: chain H residue 35 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 111 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 92 optimal weight: 30.0000 chunk 28 optimal weight: 0.3980 chunk 93 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 0.0470 overall best weight: 1.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.126727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.079068 restraints weight = 31610.312| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.53 r_work: 0.2922 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18874 Z= 0.212 Angle : 0.565 6.869 27205 Z= 0.332 Chirality : 0.036 0.139 3064 Planarity : 0.004 0.043 2066 Dihedral : 30.289 178.810 5636 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.89 % Allowed : 13.97 % Favored : 83.14 % 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: 1.80 (0.24), residues: 1198 helix: 2.21 (0.21), residues: 552 sheet: 0.51 (0.33), residues: 240 loop : 0.31 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 33 TYR 0.017 0.002 TYR N 201 PHE 0.009 0.001 PHE A 67 TRP 0.007 0.001 TRP N 259 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00482 (18870) covalent geometry : angle 0.56537 (27197) SS BOND : bond 0.00395 ( 4) SS BOND : angle 0.84312 ( 8) hydrogen bonds : bond 0.03486 ( 1066) hydrogen bonds : angle 3.29586 ( 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 238 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.478 Fit side-chains REVERT: B 95 ARG cc_start: 0.8339 (mmt180) cc_final: 0.8018 (mtp-110) REVERT: C 90 ASP cc_start: 0.9097 (t0) cc_final: 0.8870 (t0) REVERT: D 68 ASP cc_start: 0.8890 (t0) cc_final: 0.8573 (t0) REVERT: E 56 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8562 (ttpp) REVERT: E 94 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: E 97 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: G 73 ASN cc_start: 0.8899 (t0) cc_final: 0.8496 (t0) REVERT: G 74 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8689 (mtmm) REVERT: G 90 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8513 (t0) REVERT: G 91 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: G 110 ASN cc_start: 0.9330 (t0) cc_final: 0.9095 (t0) REVERT: H 43 LYS cc_start: 0.9168 (mttt) cc_final: 0.8967 (mttm) REVERT: H 86 ARG cc_start: 0.8518 (mmt-90) cc_final: 0.8030 (mmt90) REVERT: H 93 GLU cc_start: 0.8903 (mp0) cc_final: 0.8474 (mp0) REVERT: M 222 ASP cc_start: 0.8306 (t0) cc_final: 0.8012 (t70) REVERT: M 239 ASP cc_start: 0.7851 (m-30) cc_final: 0.7576 (m-30) REVERT: N 23 MET cc_start: 0.9343 (mmp) cc_final: 0.9014 (mmm) outliers start: 30 outliers final: 7 residues processed: 216 average time/residue: 0.8376 time to fit residues: 195.9614 Evaluate side-chains 208 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 97 GLU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 228 VAL 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: 0.8980 chunk 53 optimal weight: 0.0570 chunk 90 optimal weight: 20.0000 chunk 57 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.127363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079503 restraints weight = 31589.076| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.54 r_work: 0.2956 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18874 Z= 0.174 Angle : 0.557 7.071 27205 Z= 0.328 Chirality : 0.035 0.138 3064 Planarity : 0.004 0.057 2066 Dihedral : 30.251 179.085 5634 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.31 % Allowed : 15.22 % Favored : 82.47 % 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: 1.90 (0.24), residues: 1198 helix: 2.33 (0.21), residues: 552 sheet: 0.52 (0.33), residues: 240 loop : 0.34 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 37 TYR 0.014 0.001 TYR H 42 PHE 0.009 0.001 PHE A 67 TRP 0.006 0.001 TRP M 60 HIS 0.004 0.001 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00391 (18870) covalent geometry : angle 0.55681 (27197) SS BOND : bond 0.00360 ( 4) SS BOND : angle 0.84518 ( 8) hydrogen bonds : bond 0.03317 ( 1066) hydrogen bonds : angle 3.24714 ( 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 227 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.485 Fit side-chains REVERT: B 95 ARG cc_start: 0.8305 (mmt180) cc_final: 0.8005 (mtp-110) REVERT: C 90 ASP cc_start: 0.9111 (t0) cc_final: 0.8887 (t0) REVERT: D 68 ASP cc_start: 0.8896 (t0) cc_final: 0.8569 (t0) REVERT: E 56 LYS cc_start: 0.8870 (ttpp) cc_final: 0.8557 (ttpp) REVERT: E 94 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: E 97 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: G 73 ASN cc_start: 0.8903 (t0) cc_final: 0.8483 (t0) REVERT: G 74 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8683 (mtmm) REVERT: G 90 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8502 (t0) REVERT: G 110 ASN cc_start: 0.9331 (t0) cc_final: 0.9103 (t0) REVERT: H 43 LYS cc_start: 0.9174 (mttt) cc_final: 0.8860 (mtpp) REVERT: H 86 ARG cc_start: 0.8487 (mmt-90) cc_final: 0.7993 (mmt90) REVERT: H 93 GLU cc_start: 0.8897 (mp0) cc_final: 0.8550 (mp0) REVERT: M 30 MET cc_start: 0.8575 (ptp) cc_final: 0.8333 (ptm) REVERT: M 222 ASP cc_start: 0.8295 (t0) cc_final: 0.7987 (t70) REVERT: M 239 ASP cc_start: 0.7942 (m-30) cc_final: 0.7656 (m-30) REVERT: N 23 MET cc_start: 0.9281 (mmp) cc_final: 0.8975 (mmm) outliers start: 24 outliers final: 13 residues processed: 210 average time/residue: 0.8749 time to fit residues: 198.9105 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 : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 110 ASN 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 74 LYS Chi-restraints excluded: chain G residue 87 ILE 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 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: 0.8980 chunk 110 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 0.0570 chunk 29 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.129356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.082208 restraints weight = 31479.109| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.53 r_work: 0.3006 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18874 Z= 0.147 Angle : 0.531 6.524 27205 Z= 0.316 Chirality : 0.034 0.127 3064 Planarity : 0.003 0.046 2066 Dihedral : 29.904 179.254 5634 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.73 % Allowed : 15.80 % Favored : 82.47 % 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: 2.10 (0.24), residues: 1198 helix: 2.56 (0.21), residues: 552 sheet: 0.58 (0.33), residues: 240 loop : 0.36 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 37 TYR 0.012 0.001 TYR D 40 PHE 0.009 0.001 PHE A 67 TRP 0.008 0.001 TRP N 60 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00322 (18870) covalent geometry : angle 0.53075 (27197) SS BOND : bond 0.00338 ( 4) SS BOND : angle 0.62632 ( 8) hydrogen bonds : bond 0.03055 ( 1066) hydrogen bonds : angle 3.10560 ( 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 228 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.465 Fit side-chains REVERT: A 64 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8446 (mttm) REVERT: B 22 LEU cc_start: 0.7966 (mt) cc_final: 0.7706 (mp) REVERT: B 79 LYS cc_start: 0.8885 (mttm) cc_final: 0.8466 (mttp) REVERT: B 95 ARG cc_start: 0.8337 (mmt180) cc_final: 0.8078 (mtp-110) REVERT: C 110 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8534 (p0) REVERT: D 68 ASP cc_start: 0.8806 (t0) cc_final: 0.8489 (t0) REVERT: E 56 LYS cc_start: 0.8945 (ttpp) cc_final: 0.8638 (ttpp) REVERT: E 94 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: E 97 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: F 77 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8646 (mtpt) REVERT: G 73 ASN cc_start: 0.8984 (t0) cc_final: 0.8557 (t0) REVERT: G 90 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8491 (t0) REVERT: H 43 LYS cc_start: 0.9205 (mttt) cc_final: 0.8903 (mtpp) REVERT: H 86 ARG cc_start: 0.8448 (mmt-90) cc_final: 0.7965 (mmt90) REVERT: H 93 GLU cc_start: 0.8839 (mp0) cc_final: 0.8582 (mp0) REVERT: M 37 ARG cc_start: 0.8796 (ttm110) cc_final: 0.8511 (ttm-80) REVERT: M 222 ASP cc_start: 0.8240 (t0) cc_final: 0.7976 (t70) REVERT: M 239 ASP cc_start: 0.7828 (m-30) cc_final: 0.7595 (m-30) REVERT: N 23 MET cc_start: 0.9244 (mmp) cc_final: 0.8973 (mmm) outliers start: 18 outliers final: 5 residues processed: 215 average time/residue: 0.8436 time to fit residues: 196.4397 Evaluate side-chains 206 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN 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 77 LYS Chi-restraints excluded: chain G residue 90 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 47 optimal weight: 0.3980 chunk 63 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN M 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.126737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.078949 restraints weight = 31003.018| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.45 r_work: 0.2882 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18874 Z= 0.199 Angle : 0.548 6.567 27205 Z= 0.323 Chirality : 0.035 0.136 3064 Planarity : 0.003 0.042 2066 Dihedral : 30.052 178.602 5634 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.60 % Allowed : 15.80 % Favored : 81.60 % 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: 2.00 (0.24), residues: 1198 helix: 2.42 (0.21), residues: 552 sheet: 0.60 (0.33), residues: 240 loop : 0.34 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 37 TYR 0.016 0.001 TYR D 40 PHE 0.009 0.001 PHE C 25 TRP 0.007 0.001 TRP M 60 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00449 (18870) covalent geometry : angle 0.54839 (27197) SS BOND : bond 0.00379 ( 4) SS BOND : angle 0.82354 ( 8) hydrogen bonds : bond 0.03375 ( 1066) hydrogen bonds : angle 3.13107 ( 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: 27 poor density : 197 time to evaluate : 0.507 Fit side-chains REVERT: B 22 LEU cc_start: 0.8386 (mt) cc_final: 0.8152 (mp) REVERT: C 110 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8607 (p0) REVERT: E 56 LYS cc_start: 0.9029 (ttpp) cc_final: 0.8772 (ttpp) REVERT: E 94 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: E 97 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: F 77 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8710 (mtpt) REVERT: G 73 ASN cc_start: 0.8965 (t0) cc_final: 0.8567 (t0) REVERT: G 74 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8906 (mtmm) REVERT: H 43 LYS cc_start: 0.9354 (mttt) cc_final: 0.9145 (mtpp) REVERT: H 86 ARG cc_start: 0.8707 (mmt-90) cc_final: 0.8313 (mmt90) REVERT: H 92 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.7396 (ttp80) REVERT: H 93 GLU cc_start: 0.8937 (mp0) cc_final: 0.8607 (mp0) REVERT: M 21 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9169 (mp) REVERT: M 30 MET cc_start: 0.8549 (ptp) cc_final: 0.8257 (ptm) REVERT: N 222 ASP cc_start: 0.8255 (t70) cc_final: 0.7758 (p0) outliers start: 27 outliers final: 7 residues processed: 206 average time/residue: 0.8782 time to fit residues: 194.9563 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 : 0.394 ------------------------------------------------------------------------------- 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 110 ASN 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 77 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 177 THR 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: 3.9990 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS H 84 ASN M 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.124927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.076619 restraints weight = 30939.198| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.46 r_work: 0.2834 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 18874 Z= 0.277 Angle : 0.589 6.651 27205 Z= 0.342 Chirality : 0.038 0.143 3064 Planarity : 0.004 0.043 2066 Dihedral : 30.351 178.396 5634 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.41 % Allowed : 16.57 % 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: 1.77 (0.24), residues: 1198 helix: 2.17 (0.21), residues: 552 sheet: 0.57 (0.33), residues: 240 loop : 0.26 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 37 TYR 0.017 0.002 TYR D 40 PHE 0.010 0.001 PHE C 25 TRP 0.008 0.002 TRP M 60 HIS 0.003 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00633 (18870) covalent geometry : angle 0.58836 (27197) SS BOND : bond 0.00482 ( 4) SS BOND : angle 1.13555 ( 8) hydrogen bonds : bond 0.03874 ( 1066) hydrogen bonds : angle 3.28066 ( 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 222 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.495 Fit side-chains REVERT: A 105 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 22 LEU cc_start: 0.8422 (mt) cc_final: 0.8182 (mp) REVERT: D 116 LYS cc_start: 0.9161 (ttpt) cc_final: 0.8954 (ttpp) REVERT: E 56 LYS cc_start: 0.9032 (ttpp) cc_final: 0.8790 (ttpp) REVERT: E 94 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: E 97 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: F 77 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8729 (mtpt) REVERT: G 73 ASN cc_start: 0.8969 (t0) cc_final: 0.8588 (t0) REVERT: G 74 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8889 (mtmm) REVERT: G 91 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8083 (tp30) REVERT: H 52 THR cc_start: 0.9260 (m) cc_final: 0.8843 (t) REVERT: H 86 ARG cc_start: 0.8749 (mmt-90) cc_final: 0.8367 (mmt90) REVERT: H 92 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8366 (mtp85) REVERT: H 93 GLU cc_start: 0.8942 (mp0) cc_final: 0.8607 (mp0) REVERT: M 21 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9162 (mp) REVERT: M 30 MET cc_start: 0.8633 (ptp) cc_final: 0.8368 (ptm) REVERT: N 23 MET cc_start: 0.9287 (mmp) cc_final: 0.8843 (mmm) REVERT: N 222 ASP cc_start: 0.8359 (t70) cc_final: 0.7814 (p0) outliers start: 25 outliers final: 9 residues processed: 205 average time/residue: 0.8890 time to fit residues: 196.4664 Evaluate side-chains 208 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 13 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 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 257 ASP 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: 30.0000 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.126071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.078030 restraints weight = 30854.288| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.49 r_work: 0.2876 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18874 Z= 0.169 Angle : 0.566 6.736 27205 Z= 0.333 Chirality : 0.035 0.145 3064 Planarity : 0.004 0.037 2066 Dihedral : 30.372 178.541 5634 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.64 % Allowed : 17.63 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.24), residues: 1198 helix: 2.25 (0.21), residues: 552 sheet: 0.59 (0.33), residues: 240 loop : 0.30 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 37 TYR 0.017 0.002 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP M 60 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00378 (18870) covalent geometry : angle 0.56626 (27197) SS BOND : bond 0.00374 ( 4) SS BOND : angle 0.88817 ( 8) hydrogen bonds : bond 0.03650 ( 1066) hydrogen bonds : angle 3.28380 ( 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: 17 poor density : 200 time to evaluate : 0.461 Fit side-chains REVERT: A 105 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8114 (mt-10) REVERT: E 56 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8794 (ttpp) REVERT: E 94 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: E 97 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: F 77 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8718 (mtpt) REVERT: G 73 ASN cc_start: 0.8959 (t0) cc_final: 0.8542 (t0) REVERT: G 74 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8885 (mtmm) REVERT: H 86 ARG cc_start: 0.8707 (mmt-90) cc_final: 0.8321 (mmt90) REVERT: H 92 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7391 (ttp80) REVERT: H 93 GLU cc_start: 0.8933 (mp0) cc_final: 0.8594 (mp0) REVERT: M 21 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9142 (mp) REVERT: N 222 ASP cc_start: 0.8328 (t70) cc_final: 0.7795 (p0) outliers start: 17 outliers final: 7 residues processed: 206 average time/residue: 0.9034 time to fit residues: 200.5671 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 : 0.481 ------------------------------------------------------------------------------- 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 13 LYS Chi-restraints excluded: chain C residue 110 ASN 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 77 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain M residue 21 ILE 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: 4.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN M 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.126271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.078025 restraints weight = 30797.219| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.43 r_work: 0.2870 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18874 Z= 0.180 Angle : 0.561 6.419 27205 Z= 0.329 Chirality : 0.035 0.140 3064 Planarity : 0.004 0.062 2066 Dihedral : 30.298 178.380 5634 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.64 % Allowed : 17.92 % Favored : 80.44 % 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: 2.29 (0.21), residues: 552 sheet: 0.59 (0.33), residues: 240 loop : 0.32 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG M 37 TYR 0.019 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP N 60 HIS 0.005 0.001 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00404 (18870) covalent geometry : angle 0.56130 (27197) SS BOND : bond 0.00406 ( 4) SS BOND : angle 0.83454 ( 8) hydrogen bonds : bond 0.03397 ( 1066) hydrogen bonds : angle 3.23739 ( 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 215 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.469 Fit side-chains REVERT: A 105 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8079 (mt-10) REVERT: E 56 LYS cc_start: 0.9029 (ttpp) cc_final: 0.8786 (ttpp) REVERT: E 94 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: E 97 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: F 77 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8722 (mtpt) REVERT: G 73 ASN cc_start: 0.8961 (t0) cc_final: 0.8530 (t0) REVERT: G 74 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8888 (mtmm) REVERT: H 52 THR cc_start: 0.9268 (m) cc_final: 0.8879 (t) REVERT: H 86 ARG cc_start: 0.8704 (mmt-90) cc_final: 0.8320 (mmt90) REVERT: H 92 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7388 (ttp80) REVERT: H 93 GLU cc_start: 0.8926 (mp0) cc_final: 0.8585 (mp0) REVERT: M 21 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9132 (mp) REVERT: M 30 MET cc_start: 0.8635 (ptp) cc_final: 0.8362 (ptm) REVERT: N 23 MET cc_start: 0.9305 (mmp) cc_final: 0.8939 (mmm) REVERT: N 222 ASP cc_start: 0.8342 (t70) cc_final: 0.7805 (p0) outliers start: 17 outliers final: 7 residues processed: 204 average time/residue: 0.9183 time to fit residues: 202.0678 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 : 0.462 ------------------------------------------------------------------------------- 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 13 LYS Chi-restraints excluded: chain C residue 110 ASN 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 77 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain M residue 21 ILE 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: 7.9990 chunk 53 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.126353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.078202 restraints weight = 31084.600| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.45 r_work: 0.2876 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18874 Z= 0.201 Angle : 0.558 8.081 27205 Z= 0.327 Chirality : 0.035 0.132 3064 Planarity : 0.004 0.053 2066 Dihedral : 30.118 177.779 5634 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.93 % Allowed : 18.11 % Favored : 79.96 % 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: 1.91 (0.24), residues: 1198 helix: 2.29 (0.22), residues: 552 sheet: 0.65 (0.34), residues: 240 loop : 0.32 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 37 TYR 0.019 0.001 TYR D 40 PHE 0.008 0.001 PHE E 67 TRP 0.009 0.001 TRP N 60 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00456 (18870) covalent geometry : angle 0.55824 (27197) SS BOND : bond 0.00420 ( 4) SS BOND : angle 0.92312 ( 8) hydrogen bonds : bond 0.03395 ( 1066) hydrogen bonds : angle 3.19577 ( 2604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8747.63 seconds wall clock time: 148 minutes 52.01 seconds (8932.01 seconds total)