Starting phenix.real_space_refine on Sun Apr 5 03:01:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x05_66420/04_2026/9x05_66420.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x05_66420/04_2026/9x05_66420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x05_66420/04_2026/9x05_66420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x05_66420/04_2026/9x05_66420.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x05_66420/04_2026/9x05_66420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x05_66420/04_2026/9x05_66420.map" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 606 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4339 2.51 5 N 1195 2.21 5 O 1434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6991 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1484 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "C" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1451 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 194} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "E" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1505 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1088 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 140} Chain breaks: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1460 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 12, 'TRANS': 207} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 6, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 111 Conformer: "B" Number of residues, atoms: 220, 1460 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 12, 'TRANS': 207} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 6, 'GLN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 111 bond proxies already assigned to first conformer: 1487 Time building chain proxies: 2.02, per 1000 atoms: 0.29 Number of scatterers: 6991 At special positions: 0 Unit cell: (64.452, 88.0844, 171.872, 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 23 16.00 O 1434 8.00 N 1195 7.00 C 4339 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 338.5 milliseconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 25 sheets defined 7.8% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.611A pdb=" N LYS B 65 " --> pdb=" O ASP B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 181 through 188 removed outlier: 3.914A pdb=" N HIS C 188 " --> pdb=" O GLN C 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.567A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 167 through 171 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.123A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.764A pdb=" N VAL B 111 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 129 through 132 removed outlier: 4.782A pdb=" N LYS B 152 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU B 187 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 160 removed outlier: 3.545A pdb=" N CYS B 205 " --> pdb=" O LYS B 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AA7, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.796A pdb=" N VAL C 10 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 83 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP C 34 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.796A pdb=" N VAL C 10 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 83 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AB1, first strand: chain 'C' and resid 114 through 118 Processing sheet with id=AB2, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.775A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.626A pdb=" N GLU E 105 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE E 85 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 118 removed outlier: 4.255A pdb=" N SER E 174 " --> pdb=" O THR E 164 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 145 through 150 removed outlier: 3.517A pdb=" N ALA E 193 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR E 192 " --> pdb=" O PHE E 209 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N CYS E 194 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS E 207 " --> pdb=" O CYS E 194 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.792A pdb=" N THR A 120 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 122 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU A 182 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS A 227 " --> pdb=" O MET A 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AB9, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=AC1, first strand: chain 'A' and resid 192 through 197 Processing sheet with id=AC2, first strand: chain 'A' and resid 238 through 243 Processing sheet with id=AC3, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AC4, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'D' and resid 49 through 51 Processing sheet with id=AC6, first strand: chain 'D' and resid 133 through 134 removed outlier: 5.275A pdb=" N LYS D 156 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU D 191 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 162 through 164 261 hydrogen bonds defined for protein. 597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.87 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: 2321 1.34 - 1.46: 1669 1.46 - 1.58: 3121 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 7139 Sorted by residual: bond pdb=" N ARG C 189 " pdb=" CA ARG C 189 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.33e-02 5.65e+03 7.57e+00 bond pdb=" CA SER A 166 " pdb=" CB SER A 166 " ideal model delta sigma weight residual 1.528 1.485 0.043 1.61e-02 3.86e+03 7.11e+00 bond pdb=" N SER C 190 " pdb=" CA SER C 190 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.18e-02 7.18e+03 6.83e+00 bond pdb=" CA SER C 190 " pdb=" CB SER C 190 " ideal model delta sigma weight residual 1.531 1.488 0.043 1.67e-02 3.59e+03 6.74e+00 bond pdb=" CA SER C 192 " pdb=" CB SER C 192 " ideal model delta sigma weight residual 1.533 1.492 0.041 1.72e-02 3.38e+03 5.69e+00 ... (remaining 7134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 9305 1.56 - 3.12: 381 3.12 - 4.68: 51 4.68 - 6.24: 7 6.24 - 7.80: 3 Bond angle restraints: 9747 Sorted by residual: angle pdb=" N SER A 166 " pdb=" CA SER A 166 " pdb=" C SER A 166 " ideal model delta sigma weight residual 110.53 103.65 6.88 1.29e+00 6.01e-01 2.84e+01 angle pdb=" CA SER A 166 " pdb=" C SER A 166 " pdb=" O SER A 166 " ideal model delta sigma weight residual 121.94 117.11 4.83 1.15e+00 7.56e-01 1.76e+01 angle pdb=" C LYS A 190 " pdb=" N ASP A 191 " pdb=" CA ASP A 191 " ideal model delta sigma weight residual 121.54 127.79 -6.25 1.91e+00 2.74e-01 1.07e+01 angle pdb=" N SER C 192 " pdb=" CA SER C 192 " pdb=" C SER C 192 " ideal model delta sigma weight residual 108.75 114.22 -5.47 1.71e+00 3.42e-01 1.02e+01 angle pdb=" C SER A 166 " pdb=" N GLN A 167 " pdb=" CA GLN A 167 " ideal model delta sigma weight residual 121.70 116.37 5.33 1.80e+00 3.09e-01 8.77e+00 ... (remaining 9742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 3926 16.29 - 32.59: 245 32.59 - 48.88: 49 48.88 - 65.17: 8 65.17 - 81.47: 8 Dihedral angle restraints: 4236 sinusoidal: 1340 harmonic: 2896 Sorted by residual: dihedral pdb=" CA PHE D 159 " pdb=" C PHE D 159 " pdb=" N PRO D 160 " pdb=" CA PRO D 160 " ideal model delta harmonic sigma weight residual -180.00 -123.64 -56.36 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual 93.00 46.31 46.69 1 1.00e+01 1.00e-02 3.02e+01 dihedral pdb=" CA VAL D 165 " pdb=" C VAL D 165 " pdb=" N SER D 166 " pdb=" CA SER D 166 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 4233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 725 0.034 - 0.068: 242 0.068 - 0.102: 88 0.102 - 0.136: 54 0.136 - 0.170: 3 Chirality restraints: 1112 Sorted by residual: chirality pdb=" CA PRO D 160 " pdb=" N PRO D 160 " pdb=" C PRO D 160 " pdb=" CB PRO D 160 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CA GLU A 165 " pdb=" N GLU A 165 " pdb=" C GLU A 165 " pdb=" CB GLU A 165 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA ASP A 131 " pdb=" N ASP A 131 " pdb=" C ASP A 131 " pdb=" CB ASP A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1109 not shown) Planarity restraints: 1284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 159 " 0.083 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO D 160 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO D 160 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO D 160 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 105 " -0.015 2.00e-02 2.50e+03 1.37e-02 4.69e+00 pdb=" CG TRP B 105 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 105 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 105 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 105 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 105 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 105 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 105 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 105 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 105 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 29 " -0.017 2.00e-02 2.50e+03 1.45e-02 3.70e+00 pdb=" CG PHE B 29 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 29 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 29 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 29 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 29 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 29 " -0.003 2.00e-02 2.50e+03 ... (remaining 1281 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1066 2.76 - 3.29: 7018 3.29 - 3.83: 11224 3.83 - 4.36: 12579 4.36 - 4.90: 21771 Nonbonded interactions: 53658 Sorted by model distance: nonbonded pdb=" OH TYR C 2 " pdb=" O GLU C 25 " model vdw 2.220 3.040 nonbonded pdb=" NH2 ARG B 67 " pdb=" OD2 ASP B 90 " model vdw 2.305 3.120 nonbonded pdb=" OH TYR A 122 " pdb=" OH TYR A 163 " model vdw 2.314 3.040 nonbonded pdb=" O SER E 171 " pdb=" OG SER E 171 " model vdw 2.323 3.040 nonbonded pdb=" O ASP E 82 " pdb=" OH TYR E 86 " model vdw 2.332 3.040 ... (remaining 53653 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=0.43 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.770 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 0.045 7145 Z= 0.254 Angle : 0.730 7.800 9759 Z= 0.433 Chirality : 0.045 0.170 1112 Planarity : 0.005 0.127 1284 Dihedral : 12.195 81.466 2362 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.96 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.27), residues: 991 helix: -3.48 (0.46), residues: 27 sheet: -0.76 (0.26), residues: 392 loop : -0.55 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 108 TYR 0.025 0.002 TYR D 95 PHE 0.033 0.002 PHE B 29 TRP 0.037 0.002 TRP B 105 HIS 0.002 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 7139) covalent geometry : angle 0.73017 ( 9747) SS BOND : bond 0.00224 ( 6) SS BOND : angle 0.68960 ( 12) hydrogen bonds : bond 0.26363 ( 253) hydrogen bonds : angle 10.68692 ( 597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.306 Fit side-chains REVERT: C 204 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7962 (mttm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0862 time to fit residues: 12.5274 Evaluate side-chains 81 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 184 GLN D 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.059313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.051505 restraints weight = 66506.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.053251 restraints weight = 28861.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054417 restraints weight = 16492.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.055250 restraints weight = 10958.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.055827 restraints weight = 8030.462| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7145 Z= 0.228 Angle : 0.648 6.473 9759 Z= 0.352 Chirality : 0.046 0.225 1112 Planarity : 0.005 0.100 1284 Dihedral : 6.003 46.256 1056 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.05 % Allowed : 7.82 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.96 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.27), residues: 991 helix: -2.39 (0.64), residues: 35 sheet: -0.73 (0.25), residues: 391 loop : -0.44 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 108 TYR 0.028 0.002 TYR E 192 PHE 0.016 0.002 PHE B 29 TRP 0.024 0.002 TRP D 167 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 7139) covalent geometry : angle 0.64834 ( 9747) SS BOND : bond 0.00295 ( 6) SS BOND : angle 0.45309 ( 12) hydrogen bonds : bond 0.04170 ( 253) hydrogen bonds : angle 7.28453 ( 597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.187 Fit side-chains REVERT: C 59 GLU cc_start: 0.7401 (tp30) cc_final: 0.7195 (tp30) REVERT: C 198 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8645 (mp0) REVERT: C 204 LYS cc_start: 0.8034 (mmtm) cc_final: 0.7755 (mmmm) REVERT: A 140 ASP cc_start: 0.8745 (t0) cc_final: 0.8171 (t0) REVERT: A 141 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8622 (pm20) REVERT: A 163 TYR cc_start: 0.8981 (m-80) cc_final: 0.8480 (m-10) REVERT: A 191 ASP cc_start: 0.8212 (t0) cc_final: 0.7896 (t0) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 0.0740 time to fit residues: 9.8064 Evaluate side-chains 88 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 0.0270 chunk 35 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 0.0170 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.061396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.053372 restraints weight = 70270.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.055206 restraints weight = 29311.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.056454 restraints weight = 16461.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.057305 restraints weight = 10822.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.057923 restraints weight = 7883.571| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7145 Z= 0.114 Angle : 0.568 6.291 9759 Z= 0.304 Chirality : 0.044 0.173 1112 Planarity : 0.004 0.077 1284 Dihedral : 5.137 37.069 1056 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.60 % Allowed : 10.38 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.96 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.27), residues: 991 helix: -1.96 (0.70), residues: 41 sheet: -0.56 (0.25), residues: 409 loop : -0.39 (0.29), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 108 TYR 0.025 0.001 TYR D 95 PHE 0.010 0.001 PHE B 175 TRP 0.018 0.001 TRP D 167 HIS 0.002 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7139) covalent geometry : angle 0.56850 ( 9747) SS BOND : bond 0.00227 ( 6) SS BOND : angle 0.41115 ( 12) hydrogen bonds : bond 0.03138 ( 253) hydrogen bonds : angle 6.22792 ( 597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 ASP cc_start: 0.8610 (p0) cc_final: 0.8272 (p0) REVERT: C 198 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8555 (mp0) REVERT: C 204 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7771 (mmmm) REVERT: E 55 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 191 ASP cc_start: 0.8059 (t0) cc_final: 0.7724 (t0) outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 0.0861 time to fit residues: 12.2270 Evaluate side-chains 85 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain A residue 141 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.060301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.053080 restraints weight = 47091.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.054627 restraints weight = 23288.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055674 restraints weight = 14181.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.056419 restraints weight = 9841.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.056947 restraints weight = 7439.056| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7145 Z= 0.169 Angle : 0.587 5.811 9759 Z= 0.315 Chirality : 0.044 0.196 1112 Planarity : 0.004 0.074 1284 Dihedral : 5.196 34.969 1056 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.35 % Allowed : 10.83 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.96 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.27), residues: 991 helix: -1.91 (0.71), residues: 41 sheet: -0.55 (0.24), residues: 424 loop : -0.31 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 24 TYR 0.023 0.002 TYR B 154 PHE 0.011 0.001 PHE B 175 TRP 0.019 0.001 TRP D 167 HIS 0.002 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7139) covalent geometry : angle 0.58690 ( 9747) SS BOND : bond 0.00233 ( 6) SS BOND : angle 0.51986 ( 12) hydrogen bonds : bond 0.03119 ( 253) hydrogen bonds : angle 6.07883 ( 597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 36 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: C 84 ASP cc_start: 0.8550 (p0) cc_final: 0.8288 (p0) REVERT: C 198 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8623 (mp0) REVERT: C 204 LYS cc_start: 0.8059 (mmtm) cc_final: 0.7718 (mmmm) REVERT: E 55 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8322 (tm-30) REVERT: A 191 ASP cc_start: 0.8147 (t0) cc_final: 0.7847 (t0) outliers start: 9 outliers final: 7 residues processed: 92 average time/residue: 0.0768 time to fit residues: 9.8153 Evaluate side-chains 86 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 0.0070 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.060595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.052609 restraints weight = 66931.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.054408 restraints weight = 28957.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.055621 restraints weight = 16578.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.056467 restraints weight = 11049.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.057070 restraints weight = 8104.557| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7145 Z= 0.140 Angle : 0.573 6.271 9759 Z= 0.305 Chirality : 0.044 0.177 1112 Planarity : 0.004 0.057 1284 Dihedral : 5.013 31.267 1056 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.50 % Allowed : 11.13 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.96 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.28), residues: 991 helix: -1.83 (0.71), residues: 42 sheet: -0.58 (0.24), residues: 428 loop : -0.19 (0.30), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 24 TYR 0.023 0.002 TYR B 154 PHE 0.013 0.001 PHE E 98 TRP 0.017 0.001 TRP D 167 HIS 0.002 0.000 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7139) covalent geometry : angle 0.57321 ( 9747) SS BOND : bond 0.00219 ( 6) SS BOND : angle 0.47141 ( 12) hydrogen bonds : bond 0.02868 ( 253) hydrogen bonds : angle 5.87701 ( 597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 36 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: C 102 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8889 (mmmt) REVERT: C 138 ASP cc_start: 0.8323 (m-30) cc_final: 0.8093 (m-30) REVERT: C 196 THR cc_start: 0.8390 (m) cc_final: 0.8106 (p) REVERT: C 198 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8584 (mp0) REVERT: E 55 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8284 (tm-30) REVERT: A 191 ASP cc_start: 0.8185 (t0) cc_final: 0.7888 (t0) outliers start: 10 outliers final: 8 residues processed: 92 average time/residue: 0.0768 time to fit residues: 9.8779 Evaluate side-chains 89 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.057501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.049465 restraints weight = 68258.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.051192 restraints weight = 30204.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.052346 restraints weight = 17508.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.053154 restraints weight = 11786.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.053763 restraints weight = 8800.613| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 7145 Z= 0.377 Angle : 0.734 7.558 9759 Z= 0.399 Chirality : 0.047 0.234 1112 Planarity : 0.005 0.084 1284 Dihedral : 6.216 44.290 1056 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.26 % Allowed : 11.88 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.96 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.27), residues: 991 helix: -2.14 (0.69), residues: 36 sheet: -0.90 (0.24), residues: 435 loop : -0.47 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 60 TYR 0.026 0.003 TYR E 192 PHE 0.022 0.002 PHE B 29 TRP 0.024 0.002 TRP D 36 HIS 0.006 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00785 ( 7139) covalent geometry : angle 0.73332 ( 9747) SS BOND : bond 0.00410 ( 6) SS BOND : angle 0.93329 ( 12) hydrogen bonds : bond 0.03948 ( 253) hydrogen bonds : angle 6.69971 ( 597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: C 36 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8696 (tt0) REVERT: C 198 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8990 (mm-30) REVERT: A 191 ASP cc_start: 0.8287 (t0) cc_final: 0.7982 (t0) outliers start: 15 outliers final: 13 residues processed: 83 average time/residue: 0.0750 time to fit residues: 8.7237 Evaluate side-chains 84 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 MET Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 250 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.058981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.052267 restraints weight = 36905.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.053617 restraints weight = 19798.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.054551 restraints weight = 12675.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.055228 restraints weight = 9069.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.055707 restraints weight = 7006.040| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7145 Z= 0.177 Angle : 0.602 6.211 9759 Z= 0.322 Chirality : 0.044 0.179 1112 Planarity : 0.004 0.054 1284 Dihedral : 5.495 37.938 1056 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.80 % Allowed : 13.53 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.96 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.28), residues: 991 helix: -1.93 (0.73), residues: 36 sheet: -0.85 (0.24), residues: 438 loop : -0.39 (0.30), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 211 TYR 0.022 0.002 TYR D 95 PHE 0.009 0.001 PHE B 29 TRP 0.017 0.001 TRP D 167 HIS 0.002 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 7139) covalent geometry : angle 0.60162 ( 9747) SS BOND : bond 0.00256 ( 6) SS BOND : angle 0.56142 ( 12) hydrogen bonds : bond 0.03021 ( 253) hydrogen bonds : angle 6.24559 ( 597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: B 154 TYR cc_start: 0.8655 (p90) cc_final: 0.8402 (p90) REVERT: C 36 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8475 (tt0) REVERT: C 59 GLU cc_start: 0.6854 (tp30) cc_final: 0.6531 (tp30) REVERT: E 55 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8413 (tm-30) REVERT: A 163 TYR cc_start: 0.8949 (m-80) cc_final: 0.8665 (m-10) REVERT: A 191 ASP cc_start: 0.8192 (t0) cc_final: 0.7888 (t0) outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 0.0714 time to fit residues: 8.8425 Evaluate side-chains 86 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 232 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 0.0470 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.060516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.053256 restraints weight = 46830.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.054841 restraints weight = 23139.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.055894 restraints weight = 14080.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056648 restraints weight = 9750.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057210 restraints weight = 7353.985| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7145 Z= 0.116 Angle : 0.594 11.277 9759 Z= 0.310 Chirality : 0.044 0.177 1112 Planarity : 0.004 0.047 1284 Dihedral : 4.883 28.295 1056 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.35 % Allowed : 13.68 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.28), residues: 991 helix: -1.41 (0.82), residues: 36 sheet: -0.72 (0.25), residues: 426 loop : -0.15 (0.30), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 108 TYR 0.023 0.001 TYR D 95 PHE 0.014 0.001 PHE E 98 TRP 0.016 0.001 TRP D 167 HIS 0.002 0.000 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7139) covalent geometry : angle 0.59441 ( 9747) SS BOND : bond 0.00223 ( 6) SS BOND : angle 0.54501 ( 12) hydrogen bonds : bond 0.02697 ( 253) hydrogen bonds : angle 5.75439 ( 597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: C 36 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: C 59 GLU cc_start: 0.6793 (tp30) cc_final: 0.6262 (tp30) REVERT: C 138 ASP cc_start: 0.8276 (m-30) cc_final: 0.8034 (m-30) REVERT: E 55 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8215 (tm-30) REVERT: A 163 TYR cc_start: 0.8862 (m-80) cc_final: 0.8634 (m-10) REVERT: A 191 ASP cc_start: 0.8106 (t0) cc_final: 0.7881 (t0) outliers start: 9 outliers final: 7 residues processed: 93 average time/residue: 0.0773 time to fit residues: 9.9060 Evaluate side-chains 89 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 232 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.0370 overall best weight: 1.1060 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.059752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.051625 restraints weight = 70291.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.053458 restraints weight = 30289.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.054704 restraints weight = 17239.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.055573 restraints weight = 11413.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.056161 restraints weight = 8333.062| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7145 Z= 0.161 Angle : 0.619 9.886 9759 Z= 0.323 Chirality : 0.044 0.187 1112 Planarity : 0.004 0.044 1284 Dihedral : 4.931 28.242 1056 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.35 % Allowed : 13.68 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.28), residues: 991 helix: -1.54 (0.77), residues: 36 sheet: -0.65 (0.25), residues: 441 loop : -0.27 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 60 TYR 0.023 0.002 TYR B 154 PHE 0.018 0.001 PHE A 239 TRP 0.017 0.001 TRP D 167 HIS 0.003 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 7139) covalent geometry : angle 0.61938 ( 9747) SS BOND : bond 0.00259 ( 6) SS BOND : angle 0.54181 ( 12) hydrogen bonds : bond 0.02804 ( 253) hydrogen bonds : angle 5.80614 ( 597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: C 36 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8498 (tt0) REVERT: C 59 GLU cc_start: 0.6903 (tp30) cc_final: 0.6605 (tp30) REVERT: C 84 ASP cc_start: 0.8483 (p0) cc_final: 0.8262 (p0) REVERT: C 138 ASP cc_start: 0.8327 (m-30) cc_final: 0.8094 (m-30) REVERT: E 55 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8320 (tm-30) REVERT: A 129 TYR cc_start: 0.8513 (t80) cc_final: 0.8153 (t80) REVERT: A 163 TYR cc_start: 0.8894 (m-80) cc_final: 0.8651 (m-10) REVERT: A 191 ASP cc_start: 0.8241 (t0) cc_final: 0.8006 (t0) outliers start: 9 outliers final: 7 residues processed: 92 average time/residue: 0.0817 time to fit residues: 10.4167 Evaluate side-chains 87 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 232 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.0270 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 99 optimal weight: 0.0040 chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 overall best weight: 0.3850 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.061363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.053366 restraints weight = 66369.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.055206 restraints weight = 29072.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.056453 restraints weight = 16583.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.057320 restraints weight = 10976.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.057914 restraints weight = 8002.126| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7145 Z= 0.113 Angle : 0.617 10.067 9759 Z= 0.319 Chirality : 0.044 0.185 1112 Planarity : 0.004 0.043 1284 Dihedral : 4.606 24.605 1056 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.05 % Allowed : 14.89 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.28), residues: 991 helix: -1.17 (0.83), residues: 36 sheet: -0.51 (0.25), residues: 426 loop : -0.14 (0.30), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 108 TYR 0.019 0.001 TYR B 154 PHE 0.015 0.001 PHE A 239 TRP 0.014 0.001 TRP D 167 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7139) covalent geometry : angle 0.61739 ( 9747) SS BOND : bond 0.00266 ( 6) SS BOND : angle 0.49554 ( 12) hydrogen bonds : bond 0.02615 ( 253) hydrogen bonds : angle 5.51674 ( 597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: C 36 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: C 59 GLU cc_start: 0.6999 (tp30) cc_final: 0.6465 (tp30) REVERT: C 84 ASP cc_start: 0.8396 (p0) cc_final: 0.8053 (p0) REVERT: C 138 ASP cc_start: 0.8174 (m-30) cc_final: 0.7924 (m-30) REVERT: C 196 THR cc_start: 0.8543 (m) cc_final: 0.8285 (p) REVERT: E 55 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8149 (tm-30) REVERT: E 145 LYS cc_start: 0.8765 (tptp) cc_final: 0.8556 (tptp) REVERT: A 191 ASP cc_start: 0.8218 (t0) cc_final: 0.7921 (t0) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.0715 time to fit residues: 9.5285 Evaluate side-chains 88 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 232 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 61 optimal weight: 0.0670 chunk 73 optimal weight: 0.6980 chunk 10 optimal weight: 0.0060 chunk 28 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4534 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.061437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053811 restraints weight = 54860.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.055500 restraints weight = 25578.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.056660 restraints weight = 15095.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.057475 restraints weight = 10209.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.058061 restraints weight = 7564.377| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7145 Z= 0.116 Angle : 0.612 9.936 9759 Z= 0.319 Chirality : 0.043 0.185 1112 Planarity : 0.004 0.044 1284 Dihedral : 4.478 22.614 1056 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.90 % Allowed : 16.09 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.28), residues: 991 helix: -1.19 (0.81), residues: 36 sheet: -0.40 (0.25), residues: 434 loop : -0.19 (0.30), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 18 TYR 0.020 0.001 TYR B 154 PHE 0.014 0.001 PHE A 239 TRP 0.014 0.001 TRP D 167 HIS 0.002 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7139) covalent geometry : angle 0.61255 ( 9747) SS BOND : bond 0.00209 ( 6) SS BOND : angle 0.45947 ( 12) hydrogen bonds : bond 0.02552 ( 253) hydrogen bonds : angle 5.45915 ( 597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1262.82 seconds wall clock time: 22 minutes 30.04 seconds (1350.04 seconds total)