Starting phenix.real_space_refine on Fri Aug 22 19:50:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gse_34233/08_2025/8gse_34233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gse_34233/08_2025/8gse_34233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gse_34233/08_2025/8gse_34233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gse_34233/08_2025/8gse_34233.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gse_34233/08_2025/8gse_34233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gse_34233/08_2025/8gse_34233.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 4751 2.51 5 N 1252 2.21 5 O 1424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7474 Number of models: 1 Model: "" Number of chains: 5 Chain: "1" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1900 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 17, 'TRANS': 219} Chain: "2" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1964 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 238} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1816 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 18, 'TRANS': 215} Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 907 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 887 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 1.76, per 1000 atoms: 0.24 Number of scatterers: 7474 At special positions: 0 Unit cell: (110.7, 86.4, 132.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1424 8.00 N 1252 7.00 C 4751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " 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: 0.54 Conformation dependent library (CDL) restraints added in 301.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 15 sheets defined 10.9% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain '1' and resid 59 through 62 Processing helix chain '1' and resid 63 through 69 Processing helix chain '1' and resid 100 through 109 Processing helix chain '1' and resid 159 through 164 Processing helix chain '2' and resid 152 through 156 Processing helix chain '2' and resid 158 through 168 removed outlier: 3.767A pdb=" N GLY 2 162 " --> pdb=" O MET 2 158 " (cutoff:3.500A) Processing helix chain '2' and resid 211 through 216 removed outlier: 3.937A pdb=" N LEU 2 215 " --> pdb=" O VAL 2 211 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER 2 216 " --> pdb=" O ALA 2 212 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 211 through 216' Processing helix chain '2' and resid 238 through 242 Processing helix chain '2' and resid 247 through 254 removed outlier: 3.816A pdb=" N LEU 2 251 " --> pdb=" O VAL 2 248 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR 2 252 " --> pdb=" O GLY 2 249 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE 2 253 " --> pdb=" O ASN 2 250 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 11 removed outlier: 3.572A pdb=" N ASN 3 11 " --> pdb=" O PRO 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 48 removed outlier: 3.574A pdb=" N ALA 3 47 " --> pdb=" O LEU 3 43 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU 3 48 " --> pdb=" O MET 3 44 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 43 through 48' Processing helix chain '3' and resid 64 through 69 removed outlier: 3.646A pdb=" N ALA 3 67 " --> pdb=" O SER 3 64 " (cutoff:3.500A) Processing helix chain '3' and resid 98 through 105 Processing helix chain '3' and resid 144 through 150 Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.829A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain '1' and resid 72 through 79 removed outlier: 6.690A pdb=" N VAL 1 238 " --> pdb=" O VAL 1 74 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE 1 76 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU 1 236 " --> pdb=" O ILE 1 76 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR 1 78 " --> pdb=" O SER 1 234 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER 1 234 " --> pdb=" O THR 1 78 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS 1 243 " --> pdb=" O ASP 1 116 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL 1 245 " --> pdb=" O ARG 1 114 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG 1 114 " --> pdb=" O VAL 1 245 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA 1 247 " --> pdb=" O TYR 1 112 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR 1 112 " --> pdb=" O ALA 1 247 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL 1 249 " --> pdb=" O PHE 1 110 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE 1 110 " --> pdb=" O VAL 1 249 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA 1 179 " --> pdb=" O PHE 1 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 72 through 79 removed outlier: 6.690A pdb=" N VAL 1 238 " --> pdb=" O VAL 1 74 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE 1 76 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU 1 236 " --> pdb=" O ILE 1 76 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR 1 78 " --> pdb=" O SER 1 234 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER 1 234 " --> pdb=" O THR 1 78 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS 1 243 " --> pdb=" O ASP 1 116 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL 1 245 " --> pdb=" O ARG 1 114 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG 1 114 " --> pdb=" O VAL 1 245 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA 1 247 " --> pdb=" O TYR 1 112 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR 1 112 " --> pdb=" O ALA 1 247 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL 1 249 " --> pdb=" O PHE 1 110 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE 1 110 " --> pdb=" O VAL 1 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 90 through 94 Processing sheet with id=AA4, first strand: chain '2' and resid 83 through 84 Processing sheet with id=AA5, first strand: chain '2' and resid 133 through 140 removed outlier: 5.298A pdb=" N THR 2 134 " --> pdb=" O VAL 2 314 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL 2 314 " --> pdb=" O THR 2 134 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASP 2 136 " --> pdb=" O VAL 2 312 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL 2 312 " --> pdb=" O ASP 2 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 133 through 140 removed outlier: 5.298A pdb=" N THR 2 134 " --> pdb=" O VAL 2 314 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL 2 314 " --> pdb=" O THR 2 134 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASP 2 136 " --> pdb=" O VAL 2 312 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL 2 312 " --> pdb=" O ASP 2 136 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG 2 172 " --> pdb=" O ALA 2 319 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA 2 319 " --> pdb=" O ARG 2 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 222 through 223 removed outlier: 3.685A pdb=" N LYS 2 222 " --> pdb=" O TRP 2 148 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS 2 190 " --> pdb=" O PHE 2 295 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LYS 2 297 " --> pdb=" O GLN 2 188 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLN 2 188 " --> pdb=" O LYS 2 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 51 through 52 removed outlier: 3.600A pdb=" N SER 3 51 " --> pdb=" O ALA 3 214 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL 3 72 " --> pdb=" O CYS 3 208 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 51 through 52 removed outlier: 3.600A pdb=" N SER 3 51 " --> pdb=" O ALA 3 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 81 through 86 removed outlier: 7.149A pdb=" N GLN 3 81 " --> pdb=" O TYR 3 194 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR 3 194 " --> pdb=" O GLN 3 81 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE 3 83 " --> pdb=" O CYS 3 192 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR 3 189 " --> pdb=" O SER 3 135 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR 3 152 " --> pdb=" O TYR 3 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 177 through 178 removed outlier: 3.507A pdb=" N ARG 3 177 " --> pdb=" O TRP 3 110 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR 3 107 " --> pdb=" O LEU 3 225 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU 3 225 " --> pdb=" O TYR 3 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.845A pdb=" N ASP H 57 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR H 52 " --> pdb=" O ASP H 57 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 68 through 71 removed outlier: 3.542A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB6, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.683A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.76 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2395 1.34 - 1.46: 1887 1.46 - 1.58: 3326 1.58 - 1.70: 0 1.70 - 1.81: 73 Bond restraints: 7681 Sorted by residual: bond pdb=" CB PHE 3 220 " pdb=" CG PHE 3 220 " ideal model delta sigma weight residual 1.502 1.473 0.029 2.30e-02 1.89e+03 1.61e+00 bond pdb=" CA ILE 3 168 " pdb=" CB ILE 3 168 " ideal model delta sigma weight residual 1.533 1.521 0.013 1.05e-02 9.07e+03 1.45e+00 bond pdb=" C PHE 2 254 " pdb=" N PRO 2 255 " ideal model delta sigma weight residual 1.332 1.345 -0.013 1.12e-02 7.97e+03 1.37e+00 bond pdb=" N ILE 2 293 " pdb=" CA ILE 2 293 " ideal model delta sigma weight residual 1.454 1.463 -0.009 7.70e-03 1.69e+04 1.34e+00 bond pdb=" C THR 3 196 " pdb=" N GLY 3 197 " ideal model delta sigma weight residual 1.334 1.322 0.012 1.12e-02 7.97e+03 1.24e+00 ... (remaining 7676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 10273 2.07 - 4.14: 189 4.14 - 6.21: 8 6.21 - 8.28: 0 8.28 - 10.35: 1 Bond angle restraints: 10471 Sorted by residual: angle pdb=" N VAL 2 102 " pdb=" CA VAL 2 102 " pdb=" C VAL 2 102 " ideal model delta sigma weight residual 111.91 108.18 3.73 8.90e-01 1.26e+00 1.75e+01 angle pdb=" C TYR H 32 " pdb=" N GLY H 33 " pdb=" CA GLY H 33 " ideal model delta sigma weight residual 121.61 118.58 3.03 7.70e-01 1.69e+00 1.55e+01 angle pdb=" N VAL 2 248 " pdb=" CA VAL 2 248 " pdb=" C VAL 2 248 " ideal model delta sigma weight residual 113.00 108.89 4.11 1.30e+00 5.92e-01 9.99e+00 angle pdb=" N ASP 1 136 " pdb=" CA ASP 1 136 " pdb=" C ASP 1 136 " ideal model delta sigma weight residual 110.06 114.41 -4.35 1.43e+00 4.89e-01 9.25e+00 angle pdb=" N PHE 3 220 " pdb=" CA PHE 3 220 " pdb=" C PHE 3 220 " ideal model delta sigma weight residual 110.35 114.20 -3.85 1.36e+00 5.41e-01 8.01e+00 ... (remaining 10466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 4083 17.51 - 35.01: 351 35.01 - 52.52: 62 52.52 - 70.03: 10 70.03 - 87.53: 10 Dihedral angle restraints: 4516 sinusoidal: 1742 harmonic: 2774 Sorted by residual: dihedral pdb=" CA PHE 3 220 " pdb=" C PHE 3 220 " pdb=" N SER 3 221 " pdb=" CA SER 3 221 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 57.81 35.19 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CA GLU 3 102 " pdb=" C GLU 3 102 " pdb=" N ILE 3 103 " pdb=" CA ILE 3 103 " ideal model delta harmonic sigma weight residual 180.00 163.36 16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 4513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 939 0.058 - 0.117: 181 0.117 - 0.175: 17 0.175 - 0.233: 0 0.233 - 0.292: 2 Chirality restraints: 1139 Sorted by residual: chirality pdb=" CB ILE 3 231 " pdb=" CA ILE 3 231 " pdb=" CG1 ILE 3 231 " pdb=" CG2 ILE 3 231 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE 1 186 " pdb=" CA ILE 1 186 " pdb=" CG1 ILE 1 186 " pdb=" CG2 ILE 1 186 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ASN 1 211 " pdb=" N ASN 1 211 " pdb=" C ASN 1 211 " pdb=" CB ASN 1 211 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1136 not shown) Planarity restraints: 1351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE 3 220 " 0.029 2.00e-02 2.50e+03 2.34e-02 9.60e+00 pdb=" CG PHE 3 220 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE 3 220 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE 3 220 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE 3 220 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE 3 220 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE 3 220 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR 3 228 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO 3 229 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO 3 229 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO 3 229 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " -0.012 2.00e-02 2.50e+03 1.18e-02 3.47e+00 pdb=" CG TRP H 36 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " 0.001 2.00e-02 2.50e+03 ... (remaining 1348 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1546 2.78 - 3.31: 6334 3.31 - 3.84: 11250 3.84 - 4.37: 12980 4.37 - 4.90: 23811 Nonbonded interactions: 55921 Sorted by model distance: nonbonded pdb=" OD1 ASP 2 280 " pdb=" N ASN 2 281 " model vdw 2.246 3.120 nonbonded pdb=" OG1 THR 2 252 " pdb=" O ASP 3 50 " model vdw 2.261 3.040 nonbonded pdb=" OE2 GLU 3 66 " pdb=" NH1 ARG 3 69 " model vdw 2.274 3.120 nonbonded pdb=" OD2 ASP 3 182 " pdb=" OH TYR 3 184 " model vdw 2.276 3.040 nonbonded pdb=" NH2 ARG 2 262 " pdb=" O VAL 3 158 " model vdw 2.300 3.120 ... (remaining 55916 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 5.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.630 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.005 0.040 7683 Z= 0.212 Angle : 0.676 10.354 10475 Z= 0.396 Chirality : 0.046 0.292 1139 Planarity : 0.005 0.052 1351 Dihedral : 13.931 87.533 2734 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: -1.94 (0.26), residues: 942 helix: -1.62 (0.70), residues: 48 sheet: -0.04 (0.34), residues: 257 loop : -1.92 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 2 208 TYR 0.025 0.002 TYR 3 107 PHE 0.053 0.002 PHE 3 220 TRP 0.032 0.002 TRP H 36 HIS 0.007 0.001 HIS 1 223 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 7681) covalent geometry : angle 0.67634 (10471) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.48744 ( 4) hydrogen bonds : bond 0.16697 ( 173) hydrogen bonds : angle 6.90860 ( 486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.196 Fit side-chains REVERT: 2 148 TRP cc_start: 0.7953 (p-90) cc_final: 0.7414 (p-90) REVERT: 2 303 GLN cc_start: 0.5311 (tt0) cc_final: 0.4833 (pp30) REVERT: 3 34 MET cc_start: 0.8738 (ptm) cc_final: 0.8299 (ptm) REVERT: 3 35 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8554 (tttp) REVERT: H 91 SER cc_start: 0.4209 (m) cc_final: 0.3477 (t) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.0766 time to fit residues: 10.9187 Evaluate side-chains 89 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 109 HIS ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.161681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.125216 restraints weight = 9663.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.123980 restraints weight = 24235.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.119338 restraints weight = 25263.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.115684 restraints weight = 18101.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.115682 restraints weight = 15995.420| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7683 Z= 0.215 Angle : 0.591 9.280 10475 Z= 0.314 Chirality : 0.045 0.209 1139 Planarity : 0.005 0.051 1351 Dihedral : 4.857 17.219 1034 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.85 % Allowed : 6.67 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: -1.98 (0.26), residues: 942 helix: -1.79 (0.69), residues: 50 sheet: -0.14 (0.34), residues: 256 loop : -1.91 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 2 262 TYR 0.014 0.002 TYR 3 107 PHE 0.033 0.002 PHE 3 220 TRP 0.014 0.002 TRP H 36 HIS 0.006 0.001 HIS 1 292 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 7681) covalent geometry : angle 0.59068 (10471) SS BOND : bond 0.00151 ( 2) SS BOND : angle 0.56427 ( 4) hydrogen bonds : bond 0.04294 ( 173) hydrogen bonds : angle 5.45151 ( 486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.339 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8089 (p-90) cc_final: 0.7551 (p-90) REVERT: 2 303 GLN cc_start: 0.5471 (tt0) cc_final: 0.4878 (pp30) REVERT: 3 220 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.7348 (m-80) outliers start: 7 outliers final: 5 residues processed: 100 average time/residue: 0.0796 time to fit residues: 10.7531 Evaluate side-chains 93 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain 3 residue 222 VAL Chi-restraints excluded: chain L residue 82 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.162684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.125580 restraints weight = 9509.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.123523 restraints weight = 24888.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.123120 restraints weight = 23298.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.122334 restraints weight = 13795.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.122734 restraints weight = 12380.385| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7683 Z= 0.146 Angle : 0.516 8.870 10475 Z= 0.272 Chirality : 0.043 0.158 1139 Planarity : 0.005 0.047 1351 Dihedral : 4.532 16.406 1034 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.33 % Allowed : 9.45 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: -1.82 (0.26), residues: 942 helix: -1.77 (0.70), residues: 49 sheet: 0.03 (0.34), residues: 269 loop : -1.84 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 2 208 TYR 0.012 0.001 TYR 2 240 PHE 0.029 0.001 PHE 3 220 TRP 0.013 0.001 TRP H 36 HIS 0.004 0.001 HIS 1 223 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7681) covalent geometry : angle 0.51647 (10471) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.32963 ( 4) hydrogen bonds : bond 0.03525 ( 173) hydrogen bonds : angle 5.10490 ( 486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.187 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8134 (p-90) cc_final: 0.7659 (p-90) REVERT: 2 303 GLN cc_start: 0.5452 (tt0) cc_final: 0.4862 (pp30) REVERT: 3 33 GLU cc_start: 0.8275 (pm20) cc_final: 0.8054 (pm20) REVERT: 3 184 TYR cc_start: 0.7703 (m-80) cc_final: 0.7451 (m-80) REVERT: 3 220 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: H 35 GLN cc_start: 0.4370 (OUTLIER) cc_final: 0.0071 (tp40) outliers start: 11 outliers final: 5 residues processed: 104 average time/residue: 0.0701 time to fit residues: 9.9170 Evaluate side-chains 98 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 82 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 10 optimal weight: 10.0000 chunk 39 optimal weight: 0.0270 chunk 63 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.164805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.123020 restraints weight = 9639.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.120485 restraints weight = 19593.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.121825 restraints weight = 18360.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.121472 restraints weight = 10854.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.121744 restraints weight = 10010.102| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7683 Z= 0.102 Angle : 0.480 8.489 10475 Z= 0.250 Chirality : 0.042 0.158 1139 Planarity : 0.004 0.042 1351 Dihedral : 4.178 16.269 1034 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.09 % Allowed : 12.36 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: -1.65 (0.26), residues: 942 helix: -1.72 (0.69), residues: 48 sheet: 0.10 (0.34), residues: 271 loop : -1.70 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 208 TYR 0.016 0.001 TYR 3 184 PHE 0.026 0.001 PHE 3 220 TRP 0.010 0.001 TRP 2 148 HIS 0.004 0.001 HIS 1 223 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7681) covalent geometry : angle 0.48036 (10471) SS BOND : bond 0.00119 ( 2) SS BOND : angle 0.18612 ( 4) hydrogen bonds : bond 0.02879 ( 173) hydrogen bonds : angle 4.83801 ( 486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.277 Fit side-chains REVERT: 2 148 TRP cc_start: 0.7996 (p-90) cc_final: 0.7763 (p-90) REVERT: 2 303 GLN cc_start: 0.5492 (tt0) cc_final: 0.4910 (pp30) REVERT: 3 33 GLU cc_start: 0.8252 (pm20) cc_final: 0.8037 (pm20) REVERT: 3 184 TYR cc_start: 0.7429 (m-80) cc_final: 0.7131 (m-80) REVERT: 3 220 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: H 35 GLN cc_start: 0.3647 (OUTLIER) cc_final: -0.0244 (tp40) outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 0.0729 time to fit residues: 10.4860 Evaluate side-chains 102 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 263 ASN Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 82 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 105 ASN L 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.163380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.128856 restraints weight = 9613.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.127072 restraints weight = 20833.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.123380 restraints weight = 21258.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.120140 restraints weight = 19180.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.120705 restraints weight = 17787.559| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7683 Z= 0.135 Angle : 0.494 8.006 10475 Z= 0.258 Chirality : 0.042 0.164 1139 Planarity : 0.004 0.041 1351 Dihedral : 4.204 17.667 1034 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.30 % Allowed : 13.21 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: -1.62 (0.26), residues: 942 helix: -1.69 (0.70), residues: 47 sheet: 0.18 (0.34), residues: 273 loop : -1.72 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 208 TYR 0.015 0.001 TYR 3 184 PHE 0.029 0.001 PHE 3 220 TRP 0.011 0.001 TRP H 36 HIS 0.004 0.001 HIS 1 223 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7681) covalent geometry : angle 0.49431 (10471) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.28348 ( 4) hydrogen bonds : bond 0.03169 ( 173) hydrogen bonds : angle 4.78185 ( 486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.172 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8101 (p-90) cc_final: 0.7850 (p-90) REVERT: 2 303 GLN cc_start: 0.5532 (tt0) cc_final: 0.4940 (pp30) REVERT: 3 33 GLU cc_start: 0.8280 (pm20) cc_final: 0.8039 (pm20) REVERT: 3 184 TYR cc_start: 0.7458 (m-80) cc_final: 0.7031 (m-80) REVERT: 3 220 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7424 (m-80) REVERT: H 35 GLN cc_start: 0.4117 (OUTLIER) cc_final: -0.0005 (tp40) REVERT: L 34 ASN cc_start: 0.7231 (OUTLIER) cc_final: 0.7012 (p0) REVERT: L 112 ILE cc_start: 0.2190 (OUTLIER) cc_final: 0.1945 (tt) outliers start: 19 outliers final: 9 residues processed: 109 average time/residue: 0.0711 time to fit residues: 10.4848 Evaluate side-chains 106 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 263 ASN Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 238 VAL Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 2 residue 302 GLU Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain 3 residue 222 VAL Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 112 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 0.0670 chunk 10 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.164939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.121951 restraints weight = 9598.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.119768 restraints weight = 19336.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.120610 restraints weight = 18533.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.118874 restraints weight = 10658.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.119573 restraints weight = 10669.742| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7683 Z= 0.105 Angle : 0.470 8.165 10475 Z= 0.244 Chirality : 0.042 0.156 1139 Planarity : 0.004 0.041 1351 Dihedral : 4.071 15.811 1034 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.82 % Allowed : 14.91 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: -1.54 (0.26), residues: 942 helix: -1.71 (0.69), residues: 48 sheet: 0.28 (0.34), residues: 272 loop : -1.68 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 208 TYR 0.012 0.001 TYR 3 184 PHE 0.027 0.001 PHE 3 220 TRP 0.008 0.001 TRP 2 148 HIS 0.003 0.001 HIS 1 223 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7681) covalent geometry : angle 0.47015 (10471) SS BOND : bond 0.00114 ( 2) SS BOND : angle 0.21040 ( 4) hydrogen bonds : bond 0.02884 ( 173) hydrogen bonds : angle 4.63762 ( 486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.270 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8079 (p-90) cc_final: 0.7878 (p-90) REVERT: 2 303 GLN cc_start: 0.5492 (tt0) cc_final: 0.4885 (pp30) REVERT: 3 33 GLU cc_start: 0.8278 (pm20) cc_final: 0.8016 (pm20) REVERT: 3 184 TYR cc_start: 0.7543 (m-80) cc_final: 0.7116 (m-80) REVERT: 3 220 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: H 35 GLN cc_start: 0.3624 (OUTLIER) cc_final: -0.0278 (tt0) REVERT: L 34 ASN cc_start: 0.7270 (OUTLIER) cc_final: 0.7044 (p0) outliers start: 15 outliers final: 9 residues processed: 99 average time/residue: 0.0749 time to fit residues: 10.2112 Evaluate side-chains 101 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 263 ASN Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 238 VAL Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain 3 residue 222 VAL Chi-restraints excluded: chain 3 residue 228 THR Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 82 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 15 optimal weight: 10.0000 chunk 53 optimal weight: 0.0670 chunk 27 optimal weight: 0.3980 chunk 46 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 overall best weight: 4.8924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 201 HIS 2 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.160173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.115916 restraints weight = 9651.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.113800 restraints weight = 16910.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.115024 restraints weight = 16866.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.114427 restraints weight = 10020.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.114712 restraints weight = 10001.561| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 7683 Z= 0.244 Angle : 0.592 7.906 10475 Z= 0.314 Chirality : 0.046 0.154 1139 Planarity : 0.005 0.049 1351 Dihedral : 4.704 17.531 1034 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 1.94 % Allowed : 15.76 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: -1.91 (0.26), residues: 942 helix: -1.90 (0.69), residues: 49 sheet: 0.03 (0.35), residues: 259 loop : -1.91 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 2 208 TYR 0.013 0.002 TYR 2 240 PHE 0.034 0.002 PHE 3 220 TRP 0.011 0.002 TRP H 36 HIS 0.005 0.001 HIS 1 223 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 7681) covalent geometry : angle 0.59167 (10471) SS BOND : bond 0.00183 ( 2) SS BOND : angle 0.66346 ( 4) hydrogen bonds : bond 0.04031 ( 173) hydrogen bonds : angle 5.06402 ( 486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.284 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8172 (p-90) cc_final: 0.7721 (p-90) REVERT: 2 201 MET cc_start: 0.8953 (mmt) cc_final: 0.8578 (mmt) REVERT: 2 230 ASN cc_start: 0.8666 (p0) cc_final: 0.8460 (p0) REVERT: 2 303 GLN cc_start: 0.5514 (tt0) cc_final: 0.4915 (pp30) REVERT: 3 184 TYR cc_start: 0.7643 (m-80) cc_final: 0.7312 (m-80) REVERT: 3 220 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: H 35 GLN cc_start: 0.4055 (OUTLIER) cc_final: -0.0441 (tt0) REVERT: L 34 ASN cc_start: 0.7219 (OUTLIER) cc_final: 0.6930 (p0) REVERT: L 112 ILE cc_start: 0.2421 (OUTLIER) cc_final: 0.2010 (tt) outliers start: 16 outliers final: 10 residues processed: 104 average time/residue: 0.0803 time to fit residues: 11.3359 Evaluate side-chains 104 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 263 ASN Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 238 VAL Chi-restraints excluded: chain 2 residue 244 MET Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 2 residue 302 GLU Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain 3 residue 222 VAL Chi-restraints excluded: chain 3 residue 228 THR Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 112 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 92 optimal weight: 30.0000 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.164716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.122070 restraints weight = 9647.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.120089 restraints weight = 15774.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.119824 restraints weight = 17420.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.116667 restraints weight = 10474.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.117749 restraints weight = 10121.084| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7683 Z= 0.095 Angle : 0.479 9.019 10475 Z= 0.247 Chirality : 0.042 0.156 1139 Planarity : 0.004 0.042 1351 Dihedral : 4.146 18.177 1034 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.70 % Allowed : 15.76 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: -1.68 (0.26), residues: 942 helix: -2.18 (0.62), residues: 54 sheet: 0.19 (0.34), residues: 265 loop : -1.71 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 208 TYR 0.011 0.001 TYR 2 240 PHE 0.027 0.001 PHE 3 220 TRP 0.013 0.001 TRP 2 148 HIS 0.003 0.001 HIS 1 223 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 7681) covalent geometry : angle 0.47909 (10471) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.31549 ( 4) hydrogen bonds : bond 0.02886 ( 173) hydrogen bonds : angle 4.63177 ( 486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.277 Fit side-chains REVERT: 2 201 MET cc_start: 0.8957 (mmt) cc_final: 0.8578 (mmt) REVERT: 2 303 GLN cc_start: 0.5519 (tt0) cc_final: 0.4914 (pp30) REVERT: 3 33 GLU cc_start: 0.8353 (pm20) cc_final: 0.8099 (pm20) REVERT: 3 184 TYR cc_start: 0.7428 (m-80) cc_final: 0.7020 (m-80) REVERT: 3 220 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: H 35 GLN cc_start: 0.3314 (OUTLIER) cc_final: -0.0264 (tm-30) REVERT: L 34 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.7060 (p0) outliers start: 14 outliers final: 8 residues processed: 108 average time/residue: 0.0730 time to fit residues: 10.8277 Evaluate side-chains 104 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 263 ASN Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 238 VAL Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 2 residue 302 GLU Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain 3 residue 222 VAL Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 82 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 48 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 26 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.163880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.121877 restraints weight = 9589.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.119664 restraints weight = 17967.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.118537 restraints weight = 18620.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.116171 restraints weight = 10889.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.116102 restraints weight = 10897.359| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7683 Z= 0.126 Angle : 0.500 8.362 10475 Z= 0.259 Chirality : 0.043 0.164 1139 Planarity : 0.004 0.043 1351 Dihedral : 4.152 17.637 1034 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.70 % Allowed : 16.00 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: -1.60 (0.26), residues: 942 helix: -1.78 (0.69), residues: 48 sheet: 0.30 (0.34), residues: 268 loop : -1.74 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 208 TYR 0.011 0.001 TYR 2 240 PHE 0.029 0.001 PHE 3 220 TRP 0.025 0.001 TRP 2 148 HIS 0.003 0.001 HIS 1 223 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7681) covalent geometry : angle 0.49988 (10471) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.23020 ( 4) hydrogen bonds : bond 0.03052 ( 173) hydrogen bonds : angle 4.59351 ( 486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.290 Fit side-chains REVERT: 2 148 TRP cc_start: 0.7759 (p-90) cc_final: 0.7244 (p-90) REVERT: 2 303 GLN cc_start: 0.5544 (tt0) cc_final: 0.4938 (pp30) REVERT: 3 33 GLU cc_start: 0.8324 (pm20) cc_final: 0.8103 (pm20) REVERT: 3 184 TYR cc_start: 0.7553 (m-80) cc_final: 0.7093 (m-80) REVERT: 3 220 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: H 35 GLN cc_start: 0.2855 (OUTLIER) cc_final: -0.0644 (tm-30) REVERT: L 34 ASN cc_start: 0.7086 (OUTLIER) cc_final: 0.6874 (p0) REVERT: L 112 ILE cc_start: 0.2017 (OUTLIER) cc_final: 0.1728 (tt) outliers start: 14 outliers final: 9 residues processed: 102 average time/residue: 0.1011 time to fit residues: 13.7559 Evaluate side-chains 102 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 263 ASN Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 238 VAL Chi-restraints excluded: chain 2 residue 246 VAL Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 2 residue 302 GLU Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain 3 residue 222 VAL Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 0.0870 chunk 74 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.166486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.124541 restraints weight = 9515.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.122362 restraints weight = 17247.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.122132 restraints weight = 16358.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.119088 restraints weight = 10258.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.120174 restraints weight = 8853.919| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7683 Z= 0.085 Angle : 0.468 8.025 10475 Z= 0.240 Chirality : 0.042 0.167 1139 Planarity : 0.004 0.044 1351 Dihedral : 3.870 16.187 1034 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.82 % Allowed : 15.27 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: -1.45 (0.27), residues: 942 helix: -2.06 (0.63), residues: 53 sheet: 0.46 (0.35), residues: 259 loop : -1.59 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 1 94 TYR 0.009 0.001 TYR 2 240 PHE 0.024 0.001 PHE 3 220 TRP 0.028 0.001 TRP 2 148 HIS 0.003 0.000 HIS 1 223 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 7681) covalent geometry : angle 0.46785 (10471) SS BOND : bond 0.00120 ( 2) SS BOND : angle 0.38616 ( 4) hydrogen bonds : bond 0.02584 ( 173) hydrogen bonds : angle 4.41087 ( 486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.294 Fit side-chains REVERT: 2 86 THR cc_start: 0.7577 (p) cc_final: 0.7295 (m) REVERT: 2 148 TRP cc_start: 0.7822 (p-90) cc_final: 0.7391 (p-90) REVERT: 2 303 GLN cc_start: 0.5623 (tt0) cc_final: 0.5002 (pp30) REVERT: 3 33 GLU cc_start: 0.8281 (pm20) cc_final: 0.8052 (pm20) REVERT: 3 184 TYR cc_start: 0.7864 (m-80) cc_final: 0.7387 (m-80) REVERT: 3 220 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.6740 (m-80) REVERT: H 35 GLN cc_start: 0.3284 (OUTLIER) cc_final: -0.0086 (tm-30) REVERT: L 34 ASN cc_start: 0.7318 (OUTLIER) cc_final: 0.7095 (p0) REVERT: L 112 ILE cc_start: 0.1901 (OUTLIER) cc_final: 0.1598 (tt) outliers start: 15 outliers final: 9 residues processed: 108 average time/residue: 0.0999 time to fit residues: 14.6427 Evaluate side-chains 108 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 263 ASN Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 238 VAL Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 2 residue 302 GLU Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain 3 residue 222 VAL Chi-restraints excluded: chain 3 residue 228 THR Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 81 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 0.0670 chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.167660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.132913 restraints weight = 9598.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.127591 restraints weight = 20808.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.119453 restraints weight = 13162.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.118633 restraints weight = 15027.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.119809 restraints weight = 12609.395| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7683 Z= 0.125 Angle : 0.504 8.151 10475 Z= 0.258 Chirality : 0.042 0.169 1139 Planarity : 0.004 0.046 1351 Dihedral : 3.966 16.446 1034 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.58 % Allowed : 16.00 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: -1.43 (0.27), residues: 942 helix: -1.63 (0.70), residues: 47 sheet: 0.42 (0.34), residues: 268 loop : -1.62 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 208 TYR 0.010 0.001 TYR 2 240 PHE 0.027 0.001 PHE 3 220 TRP 0.031 0.001 TRP 2 148 HIS 0.004 0.001 HIS 1 223 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7681) covalent geometry : angle 0.50358 (10471) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.23387 ( 4) hydrogen bonds : bond 0.02949 ( 173) hydrogen bonds : angle 4.44012 ( 486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1190.72 seconds wall clock time: 21 minutes 18.53 seconds (1278.53 seconds total)