Starting phenix.real_space_refine on Sat Dec 28 02:36:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gse_34233/12_2024/8gse_34233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gse_34233/12_2024/8gse_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_34233/12_2024/8gse_34233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gse_34233/12_2024/8gse_34233.map" model { file = "/net/cci-nas-00/data/ceres_data/8gse_34233/12_2024/8gse_34233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gse_34233/12_2024/8gse_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-5532/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: 5.21, per 1000 atoms: 0.70 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: 1.55 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: 0.83 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: 1.84 Time building geometry restraints manager: 1.90 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: 2.420 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.940 Find NCS groups from input model: 0.100 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.810 ------------------------------------------------------------------------------- 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 : 0.883 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: 0.2145 time to fit residues: 30.3754 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 : 0.824 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.825 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8086 (p-90) cc_final: 0.7642 (p-90) REVERT: 3 220 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.6779 (m-80) outliers start: 6 outliers final: 4 residues processed: 100 average time/residue: 0.2218 time to fit residues: 29.6595 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 : 0.852 ------------------------------------------------------------------------------- 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 46 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.0470 chunk 84 optimal weight: 30.0000 chunk 91 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 225 ASN ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1118 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= 0.230 Angle : 0.515 8.614 10471 Z= 0.271 Chirality : 0.043 0.162 1139 Planarity : 0.004 0.046 1351 Dihedral : 4.395 14.833 1034 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.45 % Allowed : 8.61 % Favored : 89.94 % 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: -1.67 (0.26), residues: 942 helix: -1.77 (0.68), residues: 50 sheet: 0.19 (0.34), residues: 267 loop : -1.75 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.004 0.001 HIS 1 223 PHE 0.028 0.001 PHE 3 220 TYR 0.012 0.001 TYR 3 107 ARG 0.004 0.001 ARG 1 89 *********************** 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 109 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.793 Fit side-chains REVERT: 2 133 TYR cc_start: 0.9141 (m-80) cc_final: 0.8925 (m-80) REVERT: 2 148 TRP cc_start: 0.8126 (p-90) cc_final: 0.7672 (p-90) REVERT: 2 201 MET cc_start: 0.8892 (mmt) cc_final: 0.8490 (mmt) REVERT: 3 33 GLU cc_start: 0.8324 (pm20) cc_final: 0.8091 (pm20) REVERT: 3 220 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.7271 (m-80) REVERT: H 35 GLN cc_start: 0.2444 (OUTLIER) cc_final: -0.1236 (tp40) outliers start: 12 outliers final: 7 residues processed: 105 average time/residue: 0.2185 time to fit residues: 30.4976 Evaluate side-chains 100 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 3 residue 221 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 9 optimal weight: 0.0070 chunk 40 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1353 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= 0.165 Angle : 0.488 8.297 10471 Z= 0.254 Chirality : 0.042 0.165 1139 Planarity : 0.004 0.042 1351 Dihedral : 4.143 15.154 1034 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.21 % Allowed : 11.39 % Favored : 87.39 % 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: -1.54 (0.27), residues: 942 helix: -1.71 (0.69), residues: 49 sheet: 0.18 (0.34), residues: 279 loop : -1.65 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.003 0.001 HIS 1 223 PHE 0.026 0.001 PHE 3 220 TYR 0.011 0.001 TYR 2 240 ARG 0.005 0.000 ARG 2 208 *********************** 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 107 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.840 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8040 (p-90) cc_final: 0.7820 (p-90) REVERT: 2 201 MET cc_start: 0.8910 (mmt) cc_final: 0.8494 (mmt) REVERT: 3 33 GLU cc_start: 0.8277 (pm20) cc_final: 0.8035 (pm20) REVERT: 3 220 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: H 35 GLN cc_start: 0.2176 (OUTLIER) cc_final: -0.1171 (tp40) outliers start: 10 outliers final: 6 residues processed: 103 average time/residue: 0.2177 time to fit residues: 30.0457 Evaluate side-chains 101 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 278 ILE 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 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 74 optimal weight: 30.0000 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 7681 Z= 0.363 Angle : 0.574 8.196 10471 Z= 0.304 Chirality : 0.045 0.161 1139 Planarity : 0.005 0.046 1351 Dihedral : 4.630 18.610 1034 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.94 % Allowed : 12.73 % Favored : 85.33 % 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: -1.83 (0.26), residues: 942 helix: -1.97 (0.68), residues: 49 sheet: 0.15 (0.35), residues: 262 loop : -1.88 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.005 0.001 HIS 3 41 PHE 0.033 0.002 PHE 3 220 TYR 0.014 0.002 TYR 2 240 ARG 0.005 0.001 ARG 2 208 *********************** 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: 16 poor density : 99 time to evaluate : 0.819 Fit side-chains REVERT: 1 181 MET cc_start: 0.8485 (ptp) cc_final: 0.8235 (ptp) REVERT: 2 148 TRP cc_start: 0.8125 (p-90) cc_final: 0.7698 (p-90) REVERT: 2 201 MET cc_start: 0.8895 (mmt) cc_final: 0.8527 (mmt) REVERT: 3 33 GLU cc_start: 0.8340 (pm20) cc_final: 0.8095 (pm20) REVERT: 3 220 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: H 35 GLN cc_start: 0.2410 (OUTLIER) cc_final: -0.1330 (tt0) outliers start: 16 outliers final: 10 residues processed: 110 average time/residue: 0.2003 time to fit residues: 29.8927 Evaluate side-chains 108 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7681 Z= 0.283 Angle : 0.538 8.688 10471 Z= 0.284 Chirality : 0.044 0.158 1139 Planarity : 0.005 0.045 1351 Dihedral : 4.518 19.896 1034 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.82 % Allowed : 14.30 % 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: -1.81 (0.26), residues: 942 helix: -1.98 (0.67), residues: 48 sheet: 0.13 (0.34), residues: 276 loop : -1.90 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 1 248 HIS 0.004 0.001 HIS 3 41 PHE 0.031 0.002 PHE 3 220 TYR 0.012 0.001 TYR 2 240 ARG 0.006 0.001 ARG 2 208 *********************** 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 : 0.750 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8081 (p-90) cc_final: 0.7702 (p-90) REVERT: 2 201 MET cc_start: 0.8898 (mmt) cc_final: 0.8524 (mmt) REVERT: 3 33 GLU cc_start: 0.8345 (pm20) cc_final: 0.8105 (pm20) REVERT: 3 220 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: H 35 GLN cc_start: 0.2412 (OUTLIER) cc_final: -0.1249 (tt0) REVERT: H 81 MET cc_start: 0.1136 (ttp) cc_final: 0.0881 (ttp) REVERT: L 112 ILE cc_start: 0.2078 (OUTLIER) cc_final: 0.1806 (tt) outliers start: 15 outliers final: 9 residues processed: 107 average time/residue: 0.2083 time to fit residues: 30.0405 Evaluate side-chains 105 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 65 optimal weight: 0.0470 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 89 optimal weight: 0.0030 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1910 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= 0.118 Angle : 0.464 8.343 10471 Z= 0.240 Chirality : 0.041 0.158 1139 Planarity : 0.004 0.042 1351 Dihedral : 3.957 18.337 1034 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.33 % Allowed : 14.18 % 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 (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: -1.54 (0.27), residues: 942 helix: -2.17 (0.62), residues: 53 sheet: 0.35 (0.34), residues: 266 loop : -1.65 (0.23), residues: 623 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 0.024 0.001 PHE 3 220 TYR 0.008 0.001 TYR L 55 ARG 0.006 0.000 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 113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.839 Fit side-chains REVERT: 2 262 ARG cc_start: 0.8592 (ttt-90) cc_final: 0.8324 (ttm-80) REVERT: 3 33 GLU cc_start: 0.8315 (pm20) cc_final: 0.8072 (pm20) REVERT: 3 220 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7330 (m-80) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.2027 time to fit residues: 30.0688 Evaluate side-chains 103 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 L residue 82 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 0.0670 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 85 optimal weight: 0.3980 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2044 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= 0.151 Angle : 0.484 7.938 10471 Z= 0.247 Chirality : 0.042 0.170 1139 Planarity : 0.004 0.041 1351 Dihedral : 3.901 17.632 1034 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.33 % Allowed : 15.39 % 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 (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: -1.42 (0.27), residues: 942 helix: -2.08 (0.63), residues: 53 sheet: 0.54 (0.35), residues: 263 loop : -1.60 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 2 148 HIS 0.004 0.001 HIS 1 223 PHE 0.025 0.001 PHE 3 220 TYR 0.011 0.001 TYR 3 184 ARG 0.007 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 108 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.837 Fit side-chains REVERT: 2 86 THR cc_start: 0.7429 (p) cc_final: 0.7223 (m) REVERT: 2 148 TRP cc_start: 0.7825 (p-90) cc_final: 0.7363 (p-90) REVERT: 2 262 ARG cc_start: 0.8561 (ttt-90) cc_final: 0.8258 (ttm-80) REVERT: 3 33 GLU cc_start: 0.8273 (pm20) cc_final: 0.8060 (pm20) REVERT: 3 220 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.6803 (m-80) REVERT: H 35 GLN cc_start: 0.2121 (OUTLIER) cc_final: -0.0873 (tm-30) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.2125 time to fit residues: 29.6792 Evaluate side-chains 104 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 3 residue 228 THR Chi-restraints excluded: chain H residue 35 GLN 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 78 optimal weight: 20.0000 chunk 83 optimal weight: 0.0040 chunk 85 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 75 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 0.0670 overall best weight: 0.6332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7681 Z= 0.119 Angle : 0.456 7.647 10471 Z= 0.232 Chirality : 0.041 0.166 1139 Planarity : 0.004 0.041 1351 Dihedral : 3.688 16.065 1034 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.97 % Allowed : 16.00 % Favored : 83.03 % 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: -1.27 (0.27), residues: 942 helix: -1.97 (0.63), residues: 54 sheet: 0.63 (0.35), residues: 260 loop : -1.48 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP 2 148 HIS 0.003 0.000 HIS 1 223 PHE 0.022 0.001 PHE 3 220 TYR 0.008 0.001 TYR L 55 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 108 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: 2 86 THR cc_start: 0.7579 (p) cc_final: 0.7317 (m) REVERT: 2 148 TRP cc_start: 0.7987 (p-90) cc_final: 0.7619 (p-90) REVERT: 2 215 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8527 (mp) REVERT: 3 33 GLU cc_start: 0.8256 (pm20) cc_final: 0.8026 (pm20) REVERT: 3 220 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.6440 (m-80) outliers start: 8 outliers final: 6 residues processed: 106 average time/residue: 0.2144 time to fit residues: 30.4863 Evaluate side-chains 104 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 215 LEU 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 H residue 35 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 73 optimal weight: 40.0000 chunk 7 optimal weight: 8.9990 chunk 56 optimal weight: 0.4980 chunk 45 optimal weight: 0.0870 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7681 Z= 0.127 Angle : 0.461 7.654 10471 Z= 0.234 Chirality : 0.041 0.177 1139 Planarity : 0.004 0.043 1351 Dihedral : 3.641 15.903 1034 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.09 % Allowed : 16.00 % 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 (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: -1.26 (0.27), residues: 942 helix: -1.84 (0.65), residues: 53 sheet: 0.64 (0.35), residues: 250 loop : -1.46 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 2 148 HIS 0.003 0.001 HIS 1 223 PHE 0.023 0.001 PHE 3 220 TYR 0.016 0.001 TYR 3 184 ARG 0.007 0.000 ARG 2 208 ********************** 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 107 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.826 Fit side-chains REVERT: 2 86 THR cc_start: 0.7578 (p) cc_final: 0.7344 (m) REVERT: 2 148 TRP cc_start: 0.8052 (p-90) cc_final: 0.7680 (p-90) REVERT: 3 33 GLU cc_start: 0.8252 (pm20) cc_final: 0.8019 (pm20) REVERT: 3 184 TYR cc_start: 0.7634 (m-80) cc_final: 0.7170 (m-80) REVERT: 3 220 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.6579 (m-80) REVERT: H 35 GLN cc_start: 0.1926 (OUTLIER) cc_final: -0.0577 (tm-30) REVERT: L 112 ILE cc_start: 0.1367 (OUTLIER) cc_final: 0.1135 (tt) outliers start: 9 outliers final: 5 residues processed: 104 average time/residue: 0.1973 time to fit residues: 28.0423 Evaluate side-chains 105 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 H residue 35 GLN 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 22 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 0.0470 chunk 73 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 9 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.8020 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.165161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.123576 restraints weight = 9476.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.122242 restraints weight = 18733.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.118962 restraints weight = 18828.452| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2227 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= 0.176 Angle : 0.491 7.520 10471 Z= 0.252 Chirality : 0.042 0.172 1139 Planarity : 0.004 0.044 1351 Dihedral : 3.825 17.111 1034 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.09 % Allowed : 16.24 % Favored : 82.67 % 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: -1.27 (0.27), residues: 942 helix: -1.51 (0.70), residues: 47 sheet: 0.67 (0.35), residues: 257 loop : -1.54 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP 2 148 HIS 0.003 0.001 HIS 1 223 PHE 0.026 0.001 PHE 3 220 TYR 0.014 0.001 TYR 3 184 ARG 0.007 0.000 ARG 2 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1659.90 seconds wall clock time: 31 minutes 7.34 seconds (1867.34 seconds total)