Starting phenix.real_space_refine on Fri Sep 11 03:33:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12es_76385/09_2026/12es_76385.cif Found real_map, /net/cci-nas-00/data/ceres_data/12es_76385/09_2026/12es_76385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/12es_76385/09_2026/12es_76385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12es_76385/09_2026/12es_76385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/12es_76385/09_2026/12es_76385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12es_76385/09_2026/12es_76385.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 36 5.16 5 C 4416 2.51 5 N 1172 2.21 5 O 1425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7049 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1692 Classifications: {'peptide': 223} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 208} Chain: "B" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1644 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "C" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 335 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "D" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1730 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 216} Chain: "E" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1648 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202} Time building chain proxies: 1.59, per 1000 atoms: 0.23 Number of scatterers: 7049 At special positions: 0 Unit cell: (67.08, 102.34, 140.18, 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 36 16.00 O 1425 8.00 N 1172 7.00 C 4416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 21 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 37 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 41 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS E 215 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 208 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " 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: 0.59 Conformation dependent library (CDL) restraints added in 420.7 milliseconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 21 sheets defined 8.7% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.719A pdb=" N LYS A 64 " --> pdb=" O PRO A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.511A pdb=" N THR A 90 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.977A pdb=" N VAL B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 183 through 189 removed outlier: 3.759A pdb=" N HIS B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'C' and resid 24 through 28 Processing helix chain 'C' and resid 34 through 46 removed outlier: 4.450A pdb=" N ARG C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 168 through 170 No H-bonds generated for 'chain 'D' and resid 168 through 170' Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.100A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.535A pdb=" N SER E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.601A pdb=" N TRP A 34 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU A 50 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.676A pdb=" N VAL A 110 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N THR A 99 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET A 108 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 132 removed outlier: 3.603A pdb=" N LEU A 132 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 147 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR A 183 " --> pdb=" O GLY A 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 132 removed outlier: 3.603A pdb=" N LEU A 132 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 147 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR A 183 " --> pdb=" O GLY A 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.513A pdb=" N THR B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.625A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LYS B 107 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA B 13 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 118 removed outlier: 5.849A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154 removed outlier: 6.268A pdb=" N HIS B 198 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER B 203 " --> pdb=" O HIS B 198 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 12 through 15 Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.772A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP D 73 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.741A pdb=" N TRP D 33 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET D 34 " --> pdb=" O MET D 51 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET D 51 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.931A pdb=" N CYS D 96 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TRP D 115 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG D 98 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP D 113 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP D 111 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR D 102 " --> pdb=" O TYR D 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 132 through 136 removed outlier: 3.574A pdb=" N SER D 192 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR D 188 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 132 through 136 removed outlier: 3.574A pdb=" N SER D 192 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR D 188 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 163 through 166 removed outlier: 4.432A pdb=" N TYR D 206 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.535A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 12 removed outlier: 7.080A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 115 through 119 removed outlier: 6.204A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 146 through 151 311 hydrogen bonds defined for protein. 795 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: 1.03 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2252 1.34 - 1.46: 1785 1.46 - 1.58: 3134 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 7215 Sorted by residual: bond pdb=" N ILE E 97 " pdb=" CA ILE E 97 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.24e-02 6.50e+03 8.81e+00 bond pdb=" N THR E 94 " pdb=" CA THR E 94 " ideal model delta sigma weight residual 1.462 1.485 -0.023 8.50e-03 1.38e+04 7.12e+00 bond pdb=" N TYR E 92 " pdb=" CA TYR E 92 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 6.10e+00 bond pdb=" N SER E 93 " pdb=" CA SER E 93 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.24e-02 6.50e+03 5.28e+00 bond pdb=" CA SER E 93 " pdb=" CB SER E 93 " ideal model delta sigma weight residual 1.527 1.498 0.029 1.38e-02 5.25e+03 4.51e+00 ... (remaining 7210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 9544 1.57 - 3.13: 242 3.13 - 4.70: 34 4.70 - 6.26: 11 6.26 - 7.83: 2 Bond angle restraints: 9833 Sorted by residual: angle pdb=" C PRO E 95 " pdb=" CA PRO E 95 " pdb=" CB PRO E 95 " ideal model delta sigma weight residual 110.92 115.79 -4.87 1.22e+00 6.72e-01 1.59e+01 angle pdb=" C THR B 30 " pdb=" CA THR B 30 " pdb=" CB THR B 30 " ideal model delta sigma weight residual 115.89 110.84 5.05 1.32e+00 5.74e-01 1.46e+01 angle pdb=" CA PRO E 95 " pdb=" C PRO E 95 " pdb=" N PRO E 96 " ideal model delta sigma weight residual 117.93 122.37 -4.44 1.20e+00 6.94e-01 1.37e+01 angle pdb=" N SER D 56 " pdb=" CA SER D 56 " pdb=" C SER D 56 " ideal model delta sigma weight residual 114.56 110.61 3.95 1.27e+00 6.20e-01 9.66e+00 angle pdb=" CB GLU A 42 " pdb=" CG GLU A 42 " pdb=" CD GLU A 42 " ideal model delta sigma weight residual 112.60 117.82 -5.22 1.70e+00 3.46e-01 9.43e+00 ... (remaining 9828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 3901 17.54 - 35.09: 326 35.09 - 52.63: 82 52.63 - 70.18: 17 70.18 - 87.72: 10 Dihedral angle restraints: 4336 sinusoidal: 1649 harmonic: 2687 Sorted by residual: dihedral pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " pdb=" SG CYS C 37 " pdb=" CB CYS C 37 " ideal model delta sinusoidal sigma weight residual -86.00 -170.38 84.38 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS C 8 " pdb=" SG CYS C 8 " pdb=" SG CYS C 21 " pdb=" CB CYS C 21 " ideal model delta sinusoidal sigma weight residual 93.00 147.39 -54.39 1 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" CA CYS C 8 " pdb=" C CYS C 8 " pdb=" N SER C 9 " pdb=" CA SER C 9 " ideal model delta harmonic sigma weight residual 180.00 150.63 29.37 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 4333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 727 0.033 - 0.065: 258 0.065 - 0.098: 74 0.098 - 0.130: 53 0.130 - 0.163: 4 Chirality restraints: 1116 Sorted by residual: chirality pdb=" CA ILE E 97 " pdb=" N ILE E 97 " pdb=" C ILE E 97 " pdb=" CB ILE E 97 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CA PRO E 95 " pdb=" N PRO E 95 " pdb=" C PRO E 95 " pdb=" CB PRO E 95 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE C 22 " pdb=" N ILE C 22 " pdb=" C ILE C 22 " pdb=" CB ILE C 22 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1113 not shown) Planarity restraints: 1255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 42 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C GLU A 42 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU A 42 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS A 43 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 8 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.33e+00 pdb=" C CYS C 8 " 0.032 2.00e-02 2.50e+03 pdb=" O CYS C 8 " -0.012 2.00e-02 2.50e+03 pdb=" N SER C 9 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 160 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO D 161 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 161 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 161 " -0.022 5.00e-02 4.00e+02 ... (remaining 1252 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 2817 2.91 - 3.41: 5920 3.41 - 3.91: 11049 3.91 - 4.40: 11930 4.40 - 4.90: 21309 Nonbonded interactions: 53025 Sorted by model distance: nonbonded pdb=" O GLU A 42 " pdb=" OE1 GLU A 42 " model vdw 2.417 3.040 nonbonded pdb=" N ASP A 31 " pdb=" OD1 ASP A 31 " model vdw 2.532 3.120 nonbonded pdb=" O ASP A 107 " pdb=" OD1 ASP A 107 " model vdw 2.588 3.040 nonbonded pdb=" N THR B 30 " pdb=" OG1 THR B 30 " model vdw 2.593 2.496 nonbonded pdb=" C SER D 17 " pdb=" OG SER D 17 " model vdw 2.600 2.616 ... (remaining 53020 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.960 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.003 0.037 7229 Z= 0.156 Angle : 0.623 7.827 9861 Z= 0.361 Chirality : 0.042 0.163 1116 Planarity : 0.004 0.044 1255 Dihedral : 14.357 87.721 2572 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.96 % Favored : 96.71 % Rotamer: Outliers : 1.12 % Allowed : 17.35 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.29), residues: 913 helix: 1.05 (0.85), residues: 38 sheet: 1.34 (0.25), residues: 431 loop : 0.31 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 72 TYR 0.020 0.001 TYR E 32 PHE 0.014 0.001 PHE E 140 TRP 0.012 0.001 TRP D 33 HIS 0.002 0.000 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.16 ( 7215) covalent geometry : angle 0.62248 / 0.36 ( 9833) SS BOND : bond 0.00248 / 0.17 ( 14) SS BOND : angle 0.86326 / 0.55 ( 28) hydrogen bonds : bond 0.23719 / 15.99 ( 274) hydrogen bonds : angle 9.04192 / 6.42 ( 795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.278 Fit side-chains REVERT: B 123 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8020 (mt-10) REVERT: B 153 SER cc_start: 0.7194 (m) cc_final: 0.6940 (p) REVERT: B 165 ASP cc_start: 0.8404 (m-30) cc_final: 0.8185 (m-30) REVERT: B 188 ARG cc_start: 0.7409 (mmm160) cc_final: 0.6698 (mtp180) REVERT: C 4 MET cc_start: 0.4646 (mtt) cc_final: 0.4131 (mtp) REVERT: D 3 GLN cc_start: 0.8058 (mm110) cc_final: 0.7716 (mm-40) REVERT: D 60 TYR cc_start: 0.8038 (m-10) cc_final: 0.7073 (m-80) REVERT: D 147 THR cc_start: 0.8059 (m) cc_final: 0.7789 (p) REVERT: E 3 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7146 (mt0) REVERT: E 32 TYR cc_start: 0.8168 (m-10) cc_final: 0.7940 (m-10) REVERT: E 168 ASP cc_start: 0.7658 (t70) cc_final: 0.7107 (t0) REVERT: E 200 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7802 (tt0) outliers start: 9 outliers final: 9 residues processed: 107 average time/residue: 0.0741 time to fit residues: 11.2110 Evaluate side-chains 93 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0870 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.0020 chunk 74 optimal weight: 6.9990 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 GLN A 58 ASN B 6 GLN B 38 GLN B 138 ASN D 183 GLN D 209 ASN E 101 GLN E 156 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107531 restraints weight = 11327.514| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.12 r_work: 0.3253 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7229 Z= 0.099 Angle : 0.527 6.984 9861 Z= 0.279 Chirality : 0.042 0.140 1116 Planarity : 0.004 0.043 1255 Dihedral : 4.432 35.464 1007 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.96 % Favored : 96.93 % Rotamer: Outliers : 3.22 % Allowed : 15.12 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.29), residues: 913 helix: 1.05 (0.82), residues: 39 sheet: 1.59 (0.25), residues: 428 loop : 0.32 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 72 TYR 0.012 0.001 TYR B 93 PHE 0.012 0.001 PHE E 140 TRP 0.012 0.001 TRP D 33 HIS 0.001 0.000 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 7215) covalent geometry : angle 0.52468 / 0.28 ( 9833) SS BOND : bond 0.00455 / 0.30 ( 14) SS BOND : angle 1.02381 / 0.71 ( 28) hydrogen bonds : bond 0.03137 / 2.12 ( 274) hydrogen bonds : angle 5.75515 / 4.07 ( 795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.270 Fit side-chains REVERT: B 123 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8024 (mt-10) REVERT: B 142 LYS cc_start: 0.8136 (ptpp) cc_final: 0.7809 (ptpt) REVERT: B 165 ASP cc_start: 0.8735 (m-30) cc_final: 0.8411 (m-30) REVERT: B 188 ARG cc_start: 0.7492 (mmm160) cc_final: 0.6622 (mtp180) REVERT: B 210 ASN cc_start: 0.7397 (m-40) cc_final: 0.6614 (p0) REVERT: C 4 MET cc_start: 0.4783 (mtt) cc_final: 0.4344 (mtp) REVERT: D 32 PHE cc_start: 0.7917 (m-10) cc_final: 0.7705 (m-10) REVERT: D 73 ASP cc_start: 0.7743 (t0) cc_final: 0.7474 (t0) REVERT: D 80 TYR cc_start: 0.7248 (m-80) cc_final: 0.7001 (m-80) REVERT: D 127 SER cc_start: 0.8529 (m) cc_final: 0.8178 (p) REVERT: D 183 GLN cc_start: 0.8613 (mt0) cc_final: 0.8382 (mt0) REVERT: E 3 GLN cc_start: 0.7880 (mm-40) cc_final: 0.6772 (mt0) REVERT: E 168 ASP cc_start: 0.7383 (t70) cc_final: 0.6609 (t70) REVERT: E 200 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7758 (tt0) outliers start: 26 outliers final: 17 residues processed: 117 average time/residue: 0.0810 time to fit residues: 13.1911 Evaluate side-chains 94 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 151 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098881 restraints weight = 10938.183| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.69 r_work: 0.3132 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7229 Z= 0.130 Angle : 0.559 7.368 9861 Z= 0.298 Chirality : 0.043 0.137 1116 Planarity : 0.004 0.046 1255 Dihedral : 4.614 37.675 1002 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 3.84 % Allowed : 17.22 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.29), residues: 913 helix: 1.00 (0.78), residues: 38 sheet: 1.78 (0.27), residues: 415 loop : 0.17 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 19 TYR 0.014 0.001 TYR D 80 PHE 0.016 0.002 PHE A 78 TRP 0.014 0.001 TRP B 163 HIS 0.002 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7215) covalent geometry : angle 0.55568 / 0.30 ( 9833) SS BOND : bond 0.00549 / 0.38 ( 14) SS BOND : angle 1.25753 / 0.84 ( 28) hydrogen bonds : bond 0.03535 / 2.39 ( 274) hydrogen bonds : angle 5.39055 / 3.80 ( 795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 28 SER cc_start: 0.9182 (OUTLIER) cc_final: 0.8938 (m) REVERT: B 2 ILE cc_start: 0.9178 (mp) cc_final: 0.8938 (mt) REVERT: B 165 ASP cc_start: 0.8631 (m-30) cc_final: 0.8336 (m-30) REVERT: B 188 ARG cc_start: 0.7880 (mmm160) cc_final: 0.7316 (mtp180) REVERT: B 210 ASN cc_start: 0.7822 (m-40) cc_final: 0.7155 (p0) REVERT: C 4 MET cc_start: 0.5228 (mtt) cc_final: 0.4761 (mtp) REVERT: D 73 ASP cc_start: 0.7986 (t0) cc_final: 0.7784 (t0) REVERT: D 127 SER cc_start: 0.8802 (m) cc_final: 0.8483 (p) REVERT: D 139 CYS cc_start: 0.5748 (t) cc_final: 0.5463 (t) REVERT: E 168 ASP cc_start: 0.8124 (t70) cc_final: 0.7266 (t0) REVERT: E 200 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8058 (tt0) outliers start: 31 outliers final: 20 residues processed: 120 average time/residue: 0.0801 time to fit residues: 13.1187 Evaluate side-chains 99 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.092979 restraints weight = 11599.226| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.08 r_work: 0.3037 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 7229 Z= 0.138 Angle : 0.604 18.430 9861 Z= 0.314 Chirality : 0.044 0.266 1116 Planarity : 0.004 0.042 1255 Dihedral : 4.669 37.832 1002 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 4.09 % Allowed : 17.22 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.29), residues: 913 helix: 0.96 (0.80), residues: 38 sheet: 1.80 (0.26), residues: 423 loop : 0.00 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.013 0.001 TYR D 102 PHE 0.017 0.002 PHE A 78 TRP 0.012 0.001 TRP B 163 HIS 0.002 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 7215) covalent geometry : angle 0.59457 / 0.31 ( 9833) SS BOND : bond 0.00949 / 0.73 ( 14) SS BOND : angle 2.08822 / 1.74 ( 28) hydrogen bonds : bond 0.03330 / 2.29 ( 274) hydrogen bonds : angle 5.25491 / 3.71 ( 795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8507 (mp0) cc_final: 0.8179 (mp0) REVERT: B 2 ILE cc_start: 0.9078 (mp) cc_final: 0.8878 (mt) REVERT: B 165 ASP cc_start: 0.8573 (m-30) cc_final: 0.8234 (m-30) REVERT: B 188 ARG cc_start: 0.7835 (mmm160) cc_final: 0.7328 (mtp180) REVERT: B 192 TYR cc_start: 0.7261 (m-80) cc_final: 0.6880 (m-80) REVERT: B 210 ASN cc_start: 0.7740 (m-40) cc_final: 0.7128 (p0) REVERT: C 4 MET cc_start: 0.5139 (mtt) cc_final: 0.4778 (mtp) REVERT: D 32 PHE cc_start: 0.8021 (m-10) cc_final: 0.7821 (m-10) REVERT: D 43 LYS cc_start: 0.8307 (mptt) cc_final: 0.8100 (mptt) REVERT: D 73 ASP cc_start: 0.7881 (t0) cc_final: 0.7538 (t0) REVERT: D 127 SER cc_start: 0.8617 (m) cc_final: 0.8272 (p) REVERT: D 139 CYS cc_start: 0.5646 (t) cc_final: 0.5347 (t) REVERT: E 4 MET cc_start: 0.7990 (mmm) cc_final: 0.6701 (mmt) REVERT: E 168 ASP cc_start: 0.7750 (t70) cc_final: 0.6821 (t0) REVERT: E 200 GLN cc_start: 0.8455 (tm-30) cc_final: 0.7937 (tt0) outliers start: 33 outliers final: 23 residues processed: 106 average time/residue: 0.0734 time to fit residues: 10.7872 Evaluate side-chains 98 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 3 GLN E 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097602 restraints weight = 11162.257| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.69 r_work: 0.3107 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 7229 Z= 0.118 Angle : 0.567 15.879 9861 Z= 0.295 Chirality : 0.043 0.263 1116 Planarity : 0.004 0.043 1255 Dihedral : 4.471 36.387 1002 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 3.72 % Allowed : 19.08 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.29), residues: 913 helix: 1.06 (0.82), residues: 38 sheet: 1.83 (0.26), residues: 428 loop : -0.04 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.011 0.001 TYR B 140 PHE 0.015 0.001 PHE A 78 TRP 0.012 0.001 TRP B 163 HIS 0.002 0.000 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 7215) covalent geometry : angle 0.56011 / 0.29 ( 9833) SS BOND : bond 0.00734 / 0.55 ( 14) SS BOND : angle 1.79648 / 1.49 ( 28) hydrogen bonds : bond 0.03001 / 2.05 ( 274) hydrogen bonds : angle 5.01112 / 3.54 ( 795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: B 165 ASP cc_start: 0.8528 (m-30) cc_final: 0.8229 (m-30) REVERT: B 188 ARG cc_start: 0.7928 (mmm160) cc_final: 0.7599 (mtp180) REVERT: B 210 ASN cc_start: 0.7895 (m-40) cc_final: 0.7468 (p0) REVERT: C 4 MET cc_start: 0.5425 (mtt) cc_final: 0.5018 (mtp) REVERT: D 32 PHE cc_start: 0.8261 (m-10) cc_final: 0.8014 (m-10) REVERT: D 73 ASP cc_start: 0.7990 (t0) cc_final: 0.7674 (t0) REVERT: D 83 MET cc_start: 0.8430 (ptm) cc_final: 0.7982 (ptp) REVERT: D 127 SER cc_start: 0.8816 (m) cc_final: 0.8534 (p) REVERT: E 168 ASP cc_start: 0.8363 (t70) cc_final: 0.7597 (t0) REVERT: E 200 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8079 (tt0) outliers start: 30 outliers final: 24 residues processed: 105 average time/residue: 0.0804 time to fit residues: 11.5686 Evaluate side-chains 97 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 68 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 22 optimal weight: 0.1980 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 189 HIS E 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.095465 restraints weight = 11240.762| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.67 r_work: 0.3073 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7229 Z= 0.137 Angle : 0.589 14.725 9861 Z= 0.307 Chirality : 0.044 0.242 1116 Planarity : 0.004 0.045 1255 Dihedral : 4.621 38.169 1002 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.83 % Favored : 96.06 % Rotamer: Outliers : 3.22 % Allowed : 19.95 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.29), residues: 913 helix: 1.00 (0.84), residues: 38 sheet: 1.80 (0.27), residues: 427 loop : -0.13 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 72 TYR 0.013 0.001 TYR A 94 PHE 0.016 0.002 PHE A 78 TRP 0.011 0.001 TRP B 163 HIS 0.003 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7215) covalent geometry : angle 0.58147 / 0.30 ( 9833) SS BOND : bond 0.00829 / 0.59 ( 14) SS BOND : angle 1.79963 / 1.47 ( 28) hydrogen bonds : bond 0.03261 / 2.23 ( 274) hydrogen bonds : angle 5.14316 / 3.63 ( 795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 210 ASN cc_start: 0.7969 (m-40) cc_final: 0.7531 (p0) REVERT: D 3 GLN cc_start: 0.8153 (mm110) cc_final: 0.7911 (mm-40) REVERT: D 32 PHE cc_start: 0.8290 (m-10) cc_final: 0.8041 (m-10) REVERT: D 57 GLU cc_start: 0.7440 (mp0) cc_final: 0.7136 (mp0) REVERT: D 73 ASP cc_start: 0.8028 (t0) cc_final: 0.7689 (t0) REVERT: D 127 SER cc_start: 0.8823 (m) cc_final: 0.8537 (p) REVERT: D 139 CYS cc_start: 0.5802 (t) cc_final: 0.5599 (t) REVERT: E 168 ASP cc_start: 0.8502 (t70) cc_final: 0.7745 (t0) REVERT: E 200 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8104 (tt0) outliers start: 26 outliers final: 25 residues processed: 96 average time/residue: 0.0832 time to fit residues: 10.9173 Evaluate side-chains 95 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.091621 restraints weight = 11294.066| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.57 r_work: 0.3007 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 7229 Z= 0.218 Angle : 0.670 13.548 9861 Z= 0.355 Chirality : 0.046 0.256 1116 Planarity : 0.005 0.051 1255 Dihedral : 5.166 40.902 1002 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.71 % Favored : 95.18 % Rotamer: Outliers : 4.83 % Allowed : 18.71 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.29), residues: 913 helix: 0.08 (0.78), residues: 43 sheet: 1.70 (0.27), residues: 419 loop : -0.49 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 72 TYR 0.017 0.002 TYR D 80 PHE 0.023 0.002 PHE B 32 TRP 0.012 0.001 TRP B 163 HIS 0.004 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 ( 7215) covalent geometry : angle 0.66140 / 0.35 ( 9833) SS BOND : bond 0.01023 / 0.72 ( 14) SS BOND : angle 2.13260 / 1.70 ( 28) hydrogen bonds : bond 0.04000 / 2.72 ( 274) hydrogen bonds : angle 5.75707 / 4.07 ( 795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 165 ASP cc_start: 0.8507 (m-30) cc_final: 0.8233 (m-30) REVERT: B 210 ASN cc_start: 0.8261 (m-40) cc_final: 0.7563 (p0) REVERT: D 3 GLN cc_start: 0.8080 (mm110) cc_final: 0.7862 (mm-40) REVERT: D 57 GLU cc_start: 0.7459 (mp0) cc_final: 0.7144 (mp0) REVERT: D 73 ASP cc_start: 0.8150 (t0) cc_final: 0.7865 (t0) REVERT: D 98 ARG cc_start: 0.8225 (ttp-170) cc_final: 0.8013 (ttm170) REVERT: E 24 ARG cc_start: 0.6275 (mtm110) cc_final: 0.5912 (mmm-85) REVERT: E 81 GLU cc_start: 0.8055 (pm20) cc_final: 0.7528 (pp20) REVERT: E 168 ASP cc_start: 0.8655 (t70) cc_final: 0.7937 (t0) outliers start: 39 outliers final: 30 residues processed: 118 average time/residue: 0.0820 time to fit residues: 13.1183 Evaluate side-chains 109 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096577 restraints weight = 11260.923| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.67 r_work: 0.3082 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 7229 Z= 0.112 Angle : 0.579 11.945 9861 Z= 0.301 Chirality : 0.043 0.221 1116 Planarity : 0.004 0.047 1255 Dihedral : 4.581 37.387 1002 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.83 % Favored : 96.06 % Rotamer: Outliers : 3.84 % Allowed : 20.45 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.29), residues: 913 helix: 0.41 (0.80), residues: 43 sheet: 1.81 (0.27), residues: 414 loop : -0.46 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.014 0.001 TYR B 140 PHE 0.013 0.001 PHE A 78 TRP 0.012 0.001 TRP B 163 HIS 0.002 0.000 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 7215) covalent geometry : angle 0.57149 / 0.30 ( 9833) SS BOND : bond 0.00716 / 0.53 ( 14) SS BOND : angle 1.78238 / 1.48 ( 28) hydrogen bonds : bond 0.02901 / 1.95 ( 274) hydrogen bonds : angle 5.07336 / 3.59 ( 795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 210 ASN cc_start: 0.8127 (m-40) cc_final: 0.7614 (p0) REVERT: D 73 ASP cc_start: 0.8001 (t0) cc_final: 0.7643 (t0) REVERT: E 81 GLU cc_start: 0.7944 (pm20) cc_final: 0.7520 (pp20) REVERT: E 168 ASP cc_start: 0.8494 (t70) cc_final: 0.7748 (t0) REVERT: E 200 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8150 (tt0) outliers start: 31 outliers final: 26 residues processed: 103 average time/residue: 0.0800 time to fit residues: 11.4237 Evaluate side-chains 97 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 36 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 0.0070 chunk 62 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.118023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.097165 restraints weight = 11226.360| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.68 r_work: 0.3088 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7229 Z= 0.109 Angle : 0.586 14.384 9861 Z= 0.302 Chirality : 0.043 0.226 1116 Planarity : 0.004 0.046 1255 Dihedral : 4.477 36.924 1002 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.05 % Favored : 95.84 % Rotamer: Outliers : 3.47 % Allowed : 20.94 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.29), residues: 913 helix: 0.45 (0.80), residues: 43 sheet: 1.81 (0.26), residues: 423 loop : -0.47 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.012 0.001 TYR B 49 PHE 0.013 0.001 PHE A 78 TRP 0.011 0.001 TRP B 163 HIS 0.002 0.000 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 7215) covalent geometry : angle 0.57734 / 0.30 ( 9833) SS BOND : bond 0.00793 / 0.60 ( 14) SS BOND : angle 1.97875 / 1.64 ( 28) hydrogen bonds : bond 0.02834 / 1.93 ( 274) hydrogen bonds : angle 4.86055 / 3.43 ( 795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 MET cc_start: 0.8874 (ttt) cc_final: 0.7771 (ttt) REVERT: B 210 ASN cc_start: 0.8124 (m-40) cc_final: 0.7618 (p0) REVERT: D 32 PHE cc_start: 0.8264 (m-10) cc_final: 0.8020 (m-10) REVERT: D 73 ASP cc_start: 0.7989 (t0) cc_final: 0.7610 (t0) REVERT: E 81 GLU cc_start: 0.7860 (pm20) cc_final: 0.7515 (pp20) REVERT: E 168 ASP cc_start: 0.8483 (t70) cc_final: 0.7727 (t0) REVERT: E 200 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8120 (tt0) outliers start: 28 outliers final: 26 residues processed: 95 average time/residue: 0.0707 time to fit residues: 9.6372 Evaluate side-chains 95 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 52 ASN E 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.097252 restraints weight = 11223.375| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.68 r_work: 0.3093 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7229 Z= 0.108 Angle : 0.579 14.428 9861 Z= 0.297 Chirality : 0.043 0.235 1116 Planarity : 0.004 0.046 1255 Dihedral : 4.400 36.699 1002 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.05 % Favored : 95.84 % Rotamer: Outliers : 3.35 % Allowed : 21.19 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.29), residues: 913 helix: 0.56 (0.80), residues: 43 sheet: 1.80 (0.26), residues: 421 loop : -0.48 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.012 0.001 TYR B 49 PHE 0.013 0.001 PHE A 78 TRP 0.010 0.001 TRP B 163 HIS 0.001 0.000 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 7215) covalent geometry : angle 0.57011 / 0.29 ( 9833) SS BOND : bond 0.00683 / 0.49 ( 14) SS BOND : angle 1.92975 / 1.60 ( 28) hydrogen bonds : bond 0.02790 / 1.90 ( 274) hydrogen bonds : angle 4.80364 / 3.39 ( 795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: B 175 MET cc_start: 0.8871 (ttt) cc_final: 0.7758 (ttt) REVERT: B 210 ASN cc_start: 0.8117 (m-40) cc_final: 0.7627 (p0) REVERT: D 32 PHE cc_start: 0.8282 (m-10) cc_final: 0.7920 (m-10) REVERT: D 73 ASP cc_start: 0.7983 (t0) cc_final: 0.7579 (t0) REVERT: E 81 GLU cc_start: 0.7763 (pm20) cc_final: 0.7508 (pp20) REVERT: E 168 ASP cc_start: 0.8483 (t70) cc_final: 0.7745 (t0) REVERT: E 200 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8113 (tt0) outliers start: 27 outliers final: 26 residues processed: 96 average time/residue: 0.0759 time to fit residues: 10.2450 Evaluate side-chains 96 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.0030 chunk 43 optimal weight: 9.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.097020 restraints weight = 11151.283| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.70 r_work: 0.3090 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 7229 Z= 0.218 Angle : 0.988 59.200 9861 Z= 0.579 Chirality : 0.049 0.827 1116 Planarity : 0.004 0.045 1255 Dihedral : 4.488 36.696 1002 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.16 % Favored : 95.73 % Rotamer: Outliers : 3.35 % Allowed : 21.31 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.29), residues: 913 helix: 0.58 (0.80), residues: 43 sheet: 1.80 (0.26), residues: 421 loop : -0.45 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 72 TYR 0.013 0.001 TYR D 114 PHE 0.013 0.001 PHE A 78 TRP 0.010 0.001 TRP B 163 HIS 0.001 0.000 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.22 ( 7215) covalent geometry : angle 0.97973 / 0.58 ( 9833) SS BOND : bond 0.00651 / 0.47 ( 14) SS BOND : angle 2.63068 / 2.22 ( 28) hydrogen bonds : bond 0.02799 / 1.91 ( 274) hydrogen bonds : angle 4.80147 / 3.39 ( 795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1698.58 seconds wall clock time: 29 minutes 54.62 seconds (1794.62 seconds total)