Starting phenix.real_space_refine on Wed Mar 12 06:54:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gse_34233/03_2025/8gse_34233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gse_34233/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gse_34233/03_2025/8gse_34233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gse_34233/03_2025/8gse_34233.map" model { file = "/net/cci-nas-00/data/ceres_data/8gse_34233/03_2025/8gse_34233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gse_34233/03_2025/8gse_34233.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.53, per 1000 atoms: 0.74 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.96 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: 2.24 Time building geometry restraints manager: 2.25 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.160 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.430 ------------------------------------------------------------------------------- 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 7681 Z= 0.311 Angle : 0.676 10.354 10471 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 : 5.81 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.032 0.002 TRP H 36 HIS 0.007 0.001 HIS 1 223 PHE 0.053 0.002 PHE 3 220 TYR 0.025 0.002 TYR 3 107 ARG 0.007 0.001 ARG 2 208 *********************** 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 : 0.789 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: 0.8301 (ptm) REVERT: 3 35 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8553 (tttp) REVERT: H 91 SER cc_start: 0.4209 (m) cc_final: 0.3478 (t) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2060 time to fit residues: 29.1524 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 : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 30.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 109 HIS L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.164141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.126749 restraints weight = 9566.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.123976 restraints weight = 25108.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.120767 restraints weight = 24260.112| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7681 Z= 0.211 Angle : 0.524 9.616 10471 Z= 0.275 Chirality : 0.043 0.209 1139 Planarity : 0.005 0.047 1351 Dihedral : 4.522 16.801 1034 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.73 % Allowed : 5.33 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.26), residues: 942 helix: -1.67 (0.70), residues: 50 sheet: -0.01 (0.34), residues: 266 loop : -1.73 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.005 0.001 HIS 1 292 PHE 0.028 0.001 PHE 3 220 TYR 0.013 0.001 TYR 3 107 ARG 0.004 0.000 ARG 2 262 *********************** 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 104 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.867 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8096 (p-90) cc_final: 0.7605 (p-90) REVERT: 2 303 GLN cc_start: 0.5172 (tt0) cc_final: 0.4941 (pp30) REVERT: 3 220 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.6672 (m-80) outliers start: 6 outliers final: 4 residues processed: 100 average time/residue: 0.2323 time to fit residues: 31.3438 Evaluate side-chains 96 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 L residue 82 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 10 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.0770 chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.168184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.131044 restraints weight = 9480.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.129504 restraints weight = 21899.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.129676 restraints weight = 21789.086| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7681 Z= 0.112 Angle : 0.451 8.374 10471 Z= 0.234 Chirality : 0.041 0.161 1139 Planarity : 0.004 0.043 1351 Dihedral : 3.941 13.809 1034 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.97 % Allowed : 8.48 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.27), residues: 942 helix: -1.45 (0.69), residues: 49 sheet: 0.22 (0.33), residues: 279 loop : -1.47 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 148 HIS 0.004 0.001 HIS 1 223 PHE 0.018 0.001 PHE 3 220 TYR 0.011 0.001 TYR 3 107 ARG 0.004 0.000 ARG 1 94 *********************** 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 110 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.798 Fit side-chains REVERT: 2 133 TYR cc_start: 0.9055 (m-80) cc_final: 0.8821 (m-80) REVERT: 2 148 TRP cc_start: 0.7930 (p-90) cc_final: 0.7701 (p-90) REVERT: 2 303 GLN cc_start: 0.5611 (tt0) cc_final: 0.5017 (pp30) REVERT: 3 33 GLU cc_start: 0.8188 (pm20) cc_final: 0.7912 (pm20) REVERT: 3 220 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.6523 (m-80) REVERT: H 91 SER cc_start: 0.4031 (m) cc_final: 0.3422 (t) outliers start: 8 outliers final: 3 residues processed: 107 average time/residue: 0.2080 time to fit residues: 30.0372 Evaluate side-chains 100 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 27 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 77 optimal weight: 0.0570 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.165959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.124105 restraints weight = 9536.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.122219 restraints weight = 19287.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.122652 restraints weight = 19148.144| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7681 Z= 0.177 Angle : 0.483 7.153 10471 Z= 0.251 Chirality : 0.042 0.169 1139 Planarity : 0.004 0.040 1351 Dihedral : 3.943 13.160 1034 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.45 % Allowed : 11.03 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.27), residues: 942 helix: -1.48 (0.69), residues: 49 sheet: 0.28 (0.33), residues: 278 loop : -1.51 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.004 0.001 HIS 1 223 PHE 0.025 0.001 PHE 3 220 TYR 0.011 0.001 TYR 2 240 ARG 0.004 0.000 ARG 1 94 *********************** 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 110 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.777 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8033 (p-90) cc_final: 0.7827 (p-90) REVERT: 2 303 GLN cc_start: 0.5505 (tt0) cc_final: 0.4928 (pp30) REVERT: 3 33 GLU cc_start: 0.8178 (pm20) cc_final: 0.7857 (pm20) REVERT: 3 220 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: H 35 GLN cc_start: 0.3605 (OUTLIER) cc_final: 0.0164 (tm-30) outliers start: 12 outliers final: 7 residues processed: 104 average time/residue: 0.2206 time to fit residues: 30.2791 Evaluate side-chains 101 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 244 MET Chi-restraints excluded: chain 2 residue 301 THR 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 82 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 201 HIS ** 3 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.158739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.116792 restraints weight = 9634.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.114331 restraints weight = 18518.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.114026 restraints weight = 19496.721| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 7681 Z= 0.540 Angle : 0.682 8.086 10471 Z= 0.364 Chirality : 0.049 0.159 1139 Planarity : 0.006 0.055 1351 Dihedral : 5.137 16.487 1034 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.30 % Allowed : 11.27 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.26), residues: 942 helix: -2.04 (0.66), residues: 49 sheet: 0.04 (0.35), residues: 257 loop : -2.04 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.007 0.002 HIS 3 41 PHE 0.037 0.002 PHE 3 220 TYR 0.017 0.002 TYR 2 240 ARG 0.004 0.001 ARG 1 222 *********************** 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 113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.872 Fit side-chains REVERT: 1 236 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8796 (tp) REVERT: 2 148 TRP cc_start: 0.8242 (p-90) cc_final: 0.7740 (p-90) REVERT: 2 303 GLN cc_start: 0.5479 (tt0) cc_final: 0.4871 (pp30) REVERT: 3 33 GLU cc_start: 0.8372 (pm20) cc_final: 0.8026 (pm20) REVERT: 3 220 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: H 81 MET cc_start: 0.2072 (ttp) cc_final: 0.1654 (ttp) outliers start: 19 outliers final: 11 residues processed: 107 average time/residue: 0.2103 time to fit residues: 30.0801 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 : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 236 LEU Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 227 THR 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 221 SER Chi-restraints excluded: chain 3 residue 222 VAL Chi-restraints excluded: chain L residue 82 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 91 optimal weight: 20.0000 chunk 41 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 168 HIS 3 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.162155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.117496 restraints weight = 9557.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.114330 restraints weight = 19236.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.116354 restraints weight = 16716.667| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7681 Z= 0.256 Angle : 0.539 8.979 10471 Z= 0.282 Chirality : 0.043 0.161 1139 Planarity : 0.005 0.045 1351 Dihedral : 4.581 17.367 1034 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.82 % Allowed : 13.33 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.26), residues: 942 helix: -1.95 (0.68), residues: 49 sheet: 0.15 (0.34), residues: 266 loop : -1.94 (0.22), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.003 0.001 HIS 1 223 PHE 0.031 0.001 PHE 3 220 TYR 0.012 0.001 TYR 2 240 ARG 0.004 0.000 ARG 1 94 *********************** 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 111 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.692 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8040 (p-90) cc_final: 0.7799 (p-90) REVERT: 2 303 GLN cc_start: 0.5474 (tt0) cc_final: 0.4876 (pp30) REVERT: 3 33 GLU cc_start: 0.8247 (pm20) cc_final: 0.7961 (pm20) REVERT: 3 184 TYR cc_start: 0.7894 (m-80) cc_final: 0.7594 (m-80) REVERT: 3 220 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: H 81 MET cc_start: 0.2471 (ttp) cc_final: 0.2086 (ttp) REVERT: L 112 ILE cc_start: 0.2569 (OUTLIER) cc_final: 0.2227 (tt) outliers start: 15 outliers final: 9 residues processed: 105 average time/residue: 0.2010 time to fit residues: 28.3738 Evaluate side-chains 103 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 87 LEU 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 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 Chi-restraints excluded: chain L residue 112 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 32 optimal weight: 9.9990 chunk 83 optimal weight: 30.0000 chunk 68 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 0.0970 chunk 1 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.159649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.116360 restraints weight = 9593.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.114197 restraints weight = 18528.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115554 restraints weight = 17977.100| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 7681 Z= 0.409 Angle : 0.614 8.836 10471 Z= 0.325 Chirality : 0.046 0.156 1139 Planarity : 0.005 0.047 1351 Dihedral : 4.907 18.697 1034 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.06 % Allowed : 14.30 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.26), residues: 942 helix: -2.15 (0.67), residues: 49 sheet: 0.00 (0.35), residues: 250 loop : -2.07 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.005 0.001 HIS 3 41 PHE 0.033 0.002 PHE 3 220 TYR 0.018 0.002 TYR 3 184 ARG 0.006 0.001 ARG 2 208 *********************** 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 110 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.890 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8160 (p-90) cc_final: 0.7744 (p-90) REVERT: 2 230 ASN cc_start: 0.8691 (p0) cc_final: 0.8487 (p0) REVERT: 2 303 GLN cc_start: 0.5520 (tt0) cc_final: 0.4926 (pp30) REVERT: 3 33 GLU cc_start: 0.8296 (pm20) cc_final: 0.8022 (pm20) REVERT: 3 220 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: H 81 MET cc_start: 0.2649 (ttp) cc_final: 0.2153 (ttp) REVERT: L 112 ILE cc_start: 0.2322 (OUTLIER) cc_final: 0.1867 (tt) outliers start: 17 outliers final: 12 residues processed: 105 average time/residue: 0.2091 time to fit residues: 30.0990 Evaluate side-chains 108 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 87 LEU 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 3 residue 53 VAL 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 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 77 optimal weight: 20.0000 chunk 36 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.168524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.131509 restraints weight = 9558.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.128838 restraints weight = 23006.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.124969 restraints weight = 23909.379| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7681 Z= 0.126 Angle : 0.487 9.615 10471 Z= 0.251 Chirality : 0.042 0.156 1139 Planarity : 0.004 0.043 1351 Dihedral : 4.138 16.207 1034 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.58 % Allowed : 14.55 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.26), residues: 942 helix: -2.30 (0.61), residues: 54 sheet: 0.28 (0.34), residues: 267 loop : -1.75 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 2 148 HIS 0.003 0.000 HIS 1 223 PHE 0.026 0.001 PHE 3 220 TYR 0.010 0.001 TYR 1 192 ARG 0.006 0.000 ARG 2 208 *********************** 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 116 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.790 Fit side-chains REVERT: 2 262 ARG cc_start: 0.8655 (ttt-90) cc_final: 0.8437 (ttm-80) REVERT: 2 303 GLN cc_start: 0.5551 (tt0) cc_final: 0.4949 (pp30) REVERT: 3 33 GLU cc_start: 0.8007 (pm20) cc_final: 0.7659 (pm20) REVERT: 3 220 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: H 81 MET cc_start: 0.2576 (ttp) cc_final: 0.2292 (ttt) outliers start: 13 outliers final: 7 residues processed: 110 average time/residue: 0.1923 time to fit residues: 28.7812 Evaluate side-chains 107 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 263 ASN Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 1 residue 280 ASP 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 L residue 82 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 80 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 39 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 27 optimal weight: 0.0870 chunk 84 optimal weight: 30.0000 chunk 91 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.179104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.139460 restraints weight = 9469.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.137176 restraints weight = 16713.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.135991 restraints weight = 15934.429| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7681 Z= 0.131 Angle : 0.489 8.229 10471 Z= 0.248 Chirality : 0.042 0.166 1139 Planarity : 0.004 0.044 1351 Dihedral : 3.900 14.943 1034 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.97 % Allowed : 15.88 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.27), residues: 942 helix: -2.15 (0.63), residues: 54 sheet: 0.43 (0.35), residues: 257 loop : -1.64 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 2 148 HIS 0.004 0.001 HIS 1 223 PHE 0.024 0.001 PHE 3 220 TYR 0.014 0.001 TYR 3 184 ARG 0.007 0.000 ARG 2 208 *********************** 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 113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.781 Fit side-chains REVERT: 2 148 TRP cc_start: 0.7833 (p-90) cc_final: 0.7306 (p-90) REVERT: 2 262 ARG cc_start: 0.8538 (ttt-90) cc_final: 0.8264 (ttm-80) REVERT: 2 303 GLN cc_start: 0.5460 (tt0) cc_final: 0.4895 (pp30) REVERT: 3 33 GLU cc_start: 0.8203 (pm20) cc_final: 0.7975 (pm20) REVERT: 3 220 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.6793 (m-80) REVERT: H 81 MET cc_start: 0.2625 (ttp) cc_final: 0.2311 (ttt) REVERT: L 9 SER cc_start: 0.5303 (p) cc_final: 0.4818 (m) outliers start: 8 outliers final: 6 residues processed: 109 average time/residue: 0.2026 time to fit residues: 29.5858 Evaluate side-chains 109 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 220 PHE Chi-restraints excluded: chain L residue 82 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.6622 > 50: distance: 12 - 17: 4.639 distance: 17 - 18: 5.527 distance: 19 - 20: 14.341 distance: 19 - 24: 14.341 distance: 21 - 22: 8.368 distance: 21 - 23: 8.235 distance: 25 - 26: 13.319 distance: 25 - 28: 9.474 distance: 26 - 27: 7.045 distance: 26 - 31: 9.762 distance: 28 - 29: 15.230 distance: 28 - 30: 14.411 distance: 31 - 32: 8.531 distance: 32 - 33: 10.704 distance: 32 - 35: 11.803 distance: 33 - 34: 10.087 distance: 33 - 38: 9.162 distance: 35 - 36: 16.234 distance: 35 - 37: 10.150 distance: 38 - 39: 34.560 distance: 39 - 40: 4.669 distance: 40 - 41: 8.212 distance: 40 - 42: 9.608 distance: 42 - 43: 4.218 distance: 43 - 44: 5.882 distance: 43 - 46: 5.602 distance: 44 - 45: 15.697 distance: 44 - 54: 16.196 distance: 46 - 47: 5.789 distance: 47 - 49: 9.821 distance: 48 - 50: 6.937 distance: 49 - 51: 5.553 distance: 50 - 52: 8.079 distance: 51 - 52: 4.252 distance: 52 - 53: 4.454 distance: 54 - 55: 23.969 distance: 55 - 56: 6.067 distance: 56 - 57: 12.122 distance: 56 - 58: 11.232 distance: 58 - 59: 16.081 distance: 59 - 60: 16.160 distance: 59 - 62: 28.407 distance: 60 - 61: 25.359 distance: 60 - 65: 43.109 distance: 62 - 63: 21.023 distance: 62 - 64: 34.608 distance: 65 - 66: 18.791 distance: 66 - 67: 19.940 distance: 66 - 69: 11.851 distance: 67 - 68: 12.959 distance: 67 - 79: 20.636 distance: 69 - 70: 22.932 distance: 70 - 71: 16.754 distance: 70 - 72: 9.785 distance: 71 - 73: 10.148 distance: 72 - 74: 19.088 distance: 72 - 75: 18.626 distance: 73 - 74: 10.122 distance: 74 - 76: 5.377 distance: 75 - 77: 7.518 distance: 76 - 78: 18.209 distance: 77 - 78: 17.193 distance: 79 - 80: 22.308 distance: 79 - 85: 25.093 distance: 80 - 81: 4.886 distance: 80 - 83: 19.096 distance: 81 - 82: 32.088 distance: 81 - 86: 7.568 distance: 83 - 84: 16.734 distance: 84 - 85: 22.993 distance: 86 - 87: 32.811 distance: 87 - 88: 15.329 distance: 87 - 90: 23.735 distance: 88 - 89: 12.875 distance: 88 - 92: 7.445 distance: 90 - 91: 12.307