Starting phenix.real_space_refine on Wed Mar 4 01:39:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pry_71816/03_2026/9pry_71816.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pry_71816/03_2026/9pry_71816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pry_71816/03_2026/9pry_71816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pry_71816/03_2026/9pry_71816.map" model { file = "/net/cci-nas-00/data/ceres_data/9pry_71816/03_2026/9pry_71816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pry_71816/03_2026/9pry_71816.cif" } resolution = 3.28 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= 0.038 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 71 5.16 5 C 6112 2.51 5 N 1672 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9691 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1617 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 193} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1617 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 193} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1617 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 193} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1617 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 193} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1613 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 207, 1613 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 193} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1610 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 207, 1610 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 193} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.00, per 1000 atoms: 0.21 Number of scatterers: 9691 At special positions: 0 Unit cell: (109.08, 117.72, 79.92, 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 71 16.00 O 1836 8.00 N 1672 7.00 C 6112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.78 Conformation dependent library (CDL) restraints added in 367.8 milliseconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 0 sheets defined 73.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 42 removed outlier: 3.769A pdb=" N MET A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 59 removed outlier: 4.163A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.640A pdb=" N ALA A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 removed outlier: 3.582A pdb=" N MET A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.766A pdb=" N ALA A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'B' and resid 16 through 30 Processing helix chain 'B' and resid 35 through 44 removed outlier: 3.662A pdb=" N MET B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.776A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 193 Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.676A pdb=" N GLY B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 30 Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.551A pdb=" N MET C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 59 removed outlier: 4.209A pdb=" N VAL C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 120 removed outlier: 3.577A pdb=" N MET C 118 " --> pdb=" O GLN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 174 removed outlier: 3.781A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.536A pdb=" N ASN C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 203 Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 31 removed outlier: 3.890A pdb=" N ALA D 31 " --> pdb=" O VAL D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 removed outlier: 3.575A pdb=" N MET D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 43 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 44 " --> pdb=" O PHE D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.690A pdb=" N MET D 118 " --> pdb=" O GLN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 175 Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.952A pdb=" N ALA D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 removed outlier: 3.845A pdb=" N ALA E 31 " --> pdb=" O VAL E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 44 removed outlier: 3.855A pdb=" N MET E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 125 through 145 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.863A pdb=" N GLU E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 203 Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'L' and resid 16 through 31 removed outlier: 3.997A pdb=" N ALA L 31 " --> pdb=" O VAL L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 43 removed outlier: 3.629A pdb=" N MET L 39 " --> pdb=" O GLU L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 58 Processing helix chain 'L' and resid 62 through 84 Processing helix chain 'L' and resid 100 through 105 Processing helix chain 'L' and resid 110 through 118 Processing helix chain 'L' and resid 125 through 145 removed outlier: 3.579A pdb=" N TYR L 130 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS L 131 " --> pdb=" O GLY L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 153 removed outlier: 3.532A pdb=" N ILE L 153 " --> pdb=" O ILE L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 175 Processing helix chain 'L' and resid 178 through 193 Processing helix chain 'L' and resid 195 through 204 Processing helix chain 'L' and resid 210 through 218 602 hydrogen bonds defined for protein. 1782 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: 1.36 Time building geometry restraints manager: 1.05 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: 3222 1.34 - 1.46: 1839 1.46 - 1.58: 4692 1.58 - 1.69: 0 1.69 - 1.81: 130 Bond restraints: 9883 Sorted by residual: bond pdb=" CB THR B 58 " pdb=" CG2 THR B 58 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" C ILE D 124 " pdb=" O ILE D 124 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.09e-01 bond pdb=" CA PRO E 125 " pdb=" C PRO E 125 " ideal model delta sigma weight residual 1.527 1.519 0.008 1.07e-02 8.73e+03 6.18e-01 bond pdb=" CB THR E 216 " pdb=" CG2 THR E 216 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.30e-01 bond pdb=" CA PRO L 125 " pdb=" C PRO L 125 " ideal model delta sigma weight residual 1.527 1.520 0.007 1.07e-02 8.73e+03 4.66e-01 ... (remaining 9878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 13061 1.15 - 2.30: 262 2.30 - 3.46: 79 3.46 - 4.61: 2 4.61 - 5.76: 7 Bond angle restraints: 13411 Sorted by residual: angle pdb=" CA PRO E 125 " pdb=" C PRO E 125 " pdb=" O PRO E 125 " ideal model delta sigma weight residual 123.16 120.26 2.90 1.49e+00 4.50e-01 3.80e+00 angle pdb=" CA PRO L 125 " pdb=" C PRO L 125 " pdb=" O PRO L 125 " ideal model delta sigma weight residual 123.16 120.42 2.74 1.49e+00 4.50e-01 3.39e+00 angle pdb=" N ILE L 135 " pdb=" CA ILE L 135 " pdb=" C ILE L 135 " ideal model delta sigma weight residual 110.62 112.42 -1.80 1.02e+00 9.61e-01 3.13e+00 angle pdb=" CA ILE L 135 " pdb=" C ILE L 135 " pdb=" O ILE L 135 " ideal model delta sigma weight residual 120.95 119.18 1.77 1.04e+00 9.25e-01 2.90e+00 angle pdb=" C ILE L 135 " pdb=" CA ILE L 135 " pdb=" CB ILE L 135 " ideal model delta sigma weight residual 112.14 109.97 2.17 1.35e+00 5.49e-01 2.59e+00 ... (remaining 13406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5695 17.95 - 35.90: 296 35.90 - 53.85: 49 53.85 - 71.80: 13 71.80 - 89.76: 8 Dihedral angle restraints: 6061 sinusoidal: 2473 harmonic: 3588 Sorted by residual: dihedral pdb=" CA ASP E 103 " pdb=" CB ASP E 103 " pdb=" CG ASP E 103 " pdb=" OD1 ASP E 103 " ideal model delta sinusoidal sigma weight residual -30.00 -87.27 57.27 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA LEU D 189 " pdb=" C LEU D 189 " pdb=" N LEU D 190 " pdb=" CA LEU D 190 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB GLU D 79 " pdb=" CG GLU D 79 " pdb=" CD GLU D 79 " pdb=" OE1 GLU D 79 " ideal model delta sinusoidal sigma weight residual 0.00 -89.76 89.76 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 843 0.025 - 0.050: 381 0.050 - 0.076: 186 0.076 - 0.101: 79 0.101 - 0.126: 35 Chirality restraints: 1524 Sorted by residual: chirality pdb=" CA PRO D 196 " pdb=" N PRO D 196 " pdb=" C PRO D 196 " pdb=" CB PRO D 196 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE D 124 " pdb=" N ILE D 124 " pdb=" C ILE D 124 " pdb=" CB ILE D 124 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA PRO C 196 " pdb=" N PRO C 196 " pdb=" C PRO C 196 " pdb=" CB PRO C 196 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 1521 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 186 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C THR B 186 " 0.030 2.00e-02 2.50e+03 pdb=" O THR B 186 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU B 187 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 186 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C THR A 186 " 0.026 2.00e-02 2.50e+03 pdb=" O THR A 186 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU A 187 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 48 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO L 49 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO L 49 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 49 " -0.020 5.00e-02 4.00e+02 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 6478 3.05 - 3.52: 10238 3.52 - 3.98: 14376 3.98 - 4.44: 18097 4.44 - 4.90: 27096 Nonbonded interactions: 76285 Sorted by model distance: nonbonded pdb=" N THR D 188 " pdb=" OG1 THR D 188 " model vdw 2.593 2.496 nonbonded pdb=" N THR B 110 " pdb=" OG1 THR B 110 " model vdw 2.619 2.496 nonbonded pdb=" N THR E 110 " pdb=" OG1 THR E 110 " model vdw 2.625 2.496 nonbonded pdb=" N ALA E 177 " pdb=" O ALA E 177 " model vdw 2.635 2.496 nonbonded pdb=" N ALA B 177 " pdb=" O ALA B 177 " model vdw 2.641 2.496 ... (remaining 76280 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 87 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 through 198 or (resid 199 and (name N or na \ me CA or name C or name O or name CB )) or resid 200 through 221)) selection = (chain 'B' and (resid 1 through 87 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 through 198 or (resid 199 and (name N or na \ me CA or name C or name O or name CB )) or resid 200 through 221)) selection = (chain 'C' and (resid 1 through 87 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 through 198 or (resid 199 and (name N or na \ me CA or name C or name O or name CB )) or resid 200 through 221)) selection = (chain 'D' and (resid 1 through 87 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 through 198 or (resid 199 and (name N or na \ me CA or name C or name O or name CB )) or resid 200 through 221)) selection = (chain 'E' and (resid 1 through 87 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 through 221)) selection = chain 'L' } 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 9.480 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 0.033 9883 Z= 0.117 Angle : 0.459 5.759 13411 Z= 0.242 Chirality : 0.040 0.126 1524 Planarity : 0.004 0.035 1728 Dihedral : 11.783 89.756 3721 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.76 % Allowed : 5.67 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.96 (0.24), residues: 1206 helix: 1.92 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.13 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 TYR 0.011 0.001 TYR C 169 PHE 0.009 0.001 PHE B 161 TRP 0.011 0.001 TRP A 80 HIS 0.002 0.000 HIS L 62 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9883) covalent geometry : angle 0.45865 (13411) hydrogen bonds : bond 0.13263 ( 602) hydrogen bonds : angle 4.17453 ( 1782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 189 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 96 MET cc_start: 0.7102 (mmm) cc_final: 0.6889 (mmm) REVERT: A 117 TRP cc_start: 0.7264 (m-10) cc_final: 0.6528 (m-10) REVERT: A 184 TRP cc_start: 0.7256 (t60) cc_final: 0.7046 (t60) REVERT: B 79 GLU cc_start: 0.7005 (tp30) cc_final: 0.6769 (tp30) REVERT: B 83 LEU cc_start: 0.8543 (tp) cc_final: 0.8092 (mp) REVERT: B 213 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6934 (mt-10) REVERT: C 75 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7304 (mt-10) REVERT: C 82 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7451 (ttt-90) REVERT: C 144 MET cc_start: 0.8000 (ttp) cc_final: 0.7689 (ttp) REVERT: C 198 CYS cc_start: 0.7215 (m) cc_final: 0.6578 (m) REVERT: D 97 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.3142 (ppt170) REVERT: E 183 ASN cc_start: 0.8455 (m110) cc_final: 0.8148 (m-40) outliers start: 8 outliers final: 5 residues processed: 194 average time/residue: 0.1268 time to fit residues: 32.0206 Evaluate side-chains 175 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 110 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.166295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135622 restraints weight = 11132.372| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.05 r_work: 0.3246 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9883 Z= 0.110 Angle : 0.449 5.623 13411 Z= 0.232 Chirality : 0.040 0.138 1524 Planarity : 0.004 0.035 1728 Dihedral : 4.611 59.240 1322 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.13 % Allowed : 8.31 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.30 (0.24), residues: 1206 helix: 2.20 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.03 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 167 TYR 0.011 0.001 TYR C 169 PHE 0.007 0.001 PHE E 32 TRP 0.012 0.001 TRP A 80 HIS 0.001 0.000 HIS L 62 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9883) covalent geometry : angle 0.44948 (13411) hydrogen bonds : bond 0.04313 ( 602) hydrogen bonds : angle 3.57995 ( 1782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.264 Fit side-chains REVERT: A 96 MET cc_start: 0.6977 (mmm) cc_final: 0.6759 (mmm) REVERT: A 117 TRP cc_start: 0.7181 (m-10) cc_final: 0.6524 (m-10) REVERT: B 83 LEU cc_start: 0.8599 (tp) cc_final: 0.8139 (mp) REVERT: B 104 ILE cc_start: 0.8703 (mm) cc_final: 0.8470 (mt) REVERT: C 75 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7090 (mt-10) REVERT: C 144 MET cc_start: 0.7936 (ttp) cc_final: 0.7660 (ttp) REVERT: C 198 CYS cc_start: 0.7385 (m) cc_final: 0.6807 (m) REVERT: D 25 LYS cc_start: 0.8954 (tttt) cc_final: 0.8661 (ttmm) REVERT: D 39 MET cc_start: 0.8577 (tpt) cc_final: 0.8320 (tpt) REVERT: E 183 ASN cc_start: 0.8487 (m110) cc_final: 0.8104 (m-40) outliers start: 12 outliers final: 8 residues processed: 183 average time/residue: 0.1160 time to fit residues: 27.9766 Evaluate side-chains 176 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 58 optimal weight: 0.0070 chunk 87 optimal weight: 0.0470 chunk 85 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 3 optimal weight: 0.0030 overall best weight: 0.2706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.170727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.141824 restraints weight = 11044.647| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.96 r_work: 0.3455 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9883 Z= 0.095 Angle : 0.425 5.551 13411 Z= 0.218 Chirality : 0.039 0.126 1524 Planarity : 0.004 0.033 1728 Dihedral : 4.308 59.003 1317 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.51 % Allowed : 9.07 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.50 (0.24), residues: 1206 helix: 2.34 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.07 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 154 TYR 0.011 0.001 TYR C 169 PHE 0.005 0.001 PHE E 32 TRP 0.012 0.001 TRP A 184 HIS 0.001 0.000 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 9883) covalent geometry : angle 0.42497 (13411) hydrogen bonds : bond 0.03688 ( 602) hydrogen bonds : angle 3.44919 ( 1782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.288 Fit side-chains REVERT: A 96 MET cc_start: 0.6999 (mmm) cc_final: 0.6789 (mmm) REVERT: A 97 ARG cc_start: 0.7567 (ttp80) cc_final: 0.7109 (ttp80) REVERT: A 117 TRP cc_start: 0.7215 (m-10) cc_final: 0.6650 (m-10) REVERT: B 104 ILE cc_start: 0.8743 (mm) cc_final: 0.8518 (mt) REVERT: C 75 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7047 (mt-10) REVERT: C 144 MET cc_start: 0.7962 (ttp) cc_final: 0.7640 (ttp) REVERT: C 198 CYS cc_start: 0.7544 (m) cc_final: 0.6980 (m) REVERT: D 25 LYS cc_start: 0.9099 (tttt) cc_final: 0.8831 (ttmm) REVERT: D 39 MET cc_start: 0.8566 (tpt) cc_final: 0.8335 (tpt) REVERT: D 97 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.3350 (ppt170) REVERT: D 185 MET cc_start: 0.7944 (ttm) cc_final: 0.7714 (ttm) REVERT: E 183 ASN cc_start: 0.8485 (m110) cc_final: 0.8114 (m-40) REVERT: L 124 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7315 (tp) REVERT: L 143 ARG cc_start: 0.8140 (ttm-80) cc_final: 0.7519 (tpm170) outliers start: 16 outliers final: 9 residues processed: 186 average time/residue: 0.1093 time to fit residues: 27.1330 Evaluate side-chains 176 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain L residue 124 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 95 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 0.0020 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN E 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.168432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139075 restraints weight = 11180.356| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.97 r_work: 0.3416 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9883 Z= 0.115 Angle : 0.448 5.576 13411 Z= 0.230 Chirality : 0.040 0.219 1524 Planarity : 0.004 0.035 1728 Dihedral : 4.119 58.709 1313 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.79 % Allowed : 9.16 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.50 (0.24), residues: 1206 helix: 2.33 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.11 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 82 TYR 0.009 0.001 TYR L 169 PHE 0.007 0.001 PHE E 32 TRP 0.012 0.001 TRP A 80 HIS 0.001 0.000 HIS L 62 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9883) covalent geometry : angle 0.44844 (13411) hydrogen bonds : bond 0.03993 ( 602) hydrogen bonds : angle 3.48008 ( 1782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.344 Fit side-chains REVERT: A 97 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7225 (ttp80) REVERT: A 117 TRP cc_start: 0.7252 (m-10) cc_final: 0.6685 (m-10) REVERT: B 33 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8503 (t) REVERT: C 75 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7053 (mt-10) REVERT: C 144 MET cc_start: 0.8011 (ttp) cc_final: 0.7629 (ttp) REVERT: C 198 CYS cc_start: 0.7543 (m) cc_final: 0.6990 (m) REVERT: D 25 LYS cc_start: 0.9106 (tttt) cc_final: 0.8840 (ttmm) REVERT: D 39 MET cc_start: 0.8586 (tpt) cc_final: 0.8374 (tpt) REVERT: D 97 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.3428 (ppt170) REVERT: E 103 ASP cc_start: 0.8413 (m-30) cc_final: 0.7983 (m-30) REVERT: E 183 ASN cc_start: 0.8560 (m110) cc_final: 0.8155 (m-40) REVERT: L 169 TYR cc_start: 0.8652 (m-80) cc_final: 0.8100 (m-80) outliers start: 19 outliers final: 11 residues processed: 185 average time/residue: 0.1124 time to fit residues: 27.6647 Evaluate side-chains 184 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 205 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 62 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 118 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.165545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134698 restraints weight = 11333.237| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.11 r_work: 0.3395 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9883 Z= 0.125 Angle : 0.464 6.634 13411 Z= 0.237 Chirality : 0.040 0.206 1524 Planarity : 0.004 0.036 1728 Dihedral : 4.157 58.549 1313 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.98 % Allowed : 10.10 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.41 (0.24), residues: 1206 helix: 2.27 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.04 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 82 TYR 0.009 0.001 TYR L 169 PHE 0.007 0.001 PHE E 32 TRP 0.014 0.001 TRP A 184 HIS 0.002 0.000 HIS L 62 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9883) covalent geometry : angle 0.46406 (13411) hydrogen bonds : bond 0.04093 ( 602) hydrogen bonds : angle 3.51032 ( 1782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.243 Fit side-chains REVERT: A 97 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7317 (ttp80) REVERT: A 117 TRP cc_start: 0.7306 (m-10) cc_final: 0.6716 (m-10) REVERT: B 33 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8472 (t) REVERT: C 75 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7020 (mt-10) REVERT: C 144 MET cc_start: 0.7986 (ttp) cc_final: 0.7607 (ttp) REVERT: D 25 LYS cc_start: 0.9035 (tttt) cc_final: 0.8759 (ttmm) REVERT: D 39 MET cc_start: 0.8535 (tpt) cc_final: 0.8294 (tpt) REVERT: D 97 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.3475 (ppt170) REVERT: D 185 MET cc_start: 0.8010 (ttm) cc_final: 0.7571 (ttm) REVERT: E 25 LYS cc_start: 0.8700 (tttp) cc_final: 0.8490 (tttm) REVERT: E 103 ASP cc_start: 0.8440 (m-30) cc_final: 0.8017 (m-30) REVERT: E 183 ASN cc_start: 0.8532 (m110) cc_final: 0.8101 (m-40) REVERT: E 195 ASN cc_start: 0.6035 (OUTLIER) cc_final: 0.5770 (p0) REVERT: L 124 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7273 (tp) REVERT: L 169 TYR cc_start: 0.8618 (m-80) cc_final: 0.8083 (m-80) outliers start: 21 outliers final: 14 residues processed: 183 average time/residue: 0.1226 time to fit residues: 29.5914 Evaluate side-chains 185 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 124 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 100 optimal weight: 0.0270 chunk 67 optimal weight: 0.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.146668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.115077 restraints weight = 11365.459| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.10 r_work: 0.3396 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9883 Z= 0.115 Angle : 0.456 6.512 13411 Z= 0.233 Chirality : 0.040 0.193 1524 Planarity : 0.004 0.036 1728 Dihedral : 4.126 58.463 1313 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.89 % Allowed : 11.43 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.42 (0.24), residues: 1206 helix: 2.29 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.01 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 97 TYR 0.009 0.001 TYR A 169 PHE 0.007 0.001 PHE E 32 TRP 0.014 0.001 TRP A 184 HIS 0.001 0.000 HIS L 62 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9883) covalent geometry : angle 0.45556 (13411) hydrogen bonds : bond 0.03943 ( 602) hydrogen bonds : angle 3.49037 ( 1782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.239 Fit side-chains REVERT: A 97 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7184 (ttp80) REVERT: A 117 TRP cc_start: 0.7295 (m-10) cc_final: 0.6670 (m-10) REVERT: B 33 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8431 (t) REVERT: C 75 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7048 (mt-10) REVERT: C 144 MET cc_start: 0.7943 (ttp) cc_final: 0.7586 (ttp) REVERT: D 25 LYS cc_start: 0.9011 (tttt) cc_final: 0.8722 (ttmm) REVERT: D 39 MET cc_start: 0.8495 (tpt) cc_final: 0.8270 (tpt) REVERT: D 97 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.3399 (ppt170) REVERT: D 185 MET cc_start: 0.8022 (ttm) cc_final: 0.7600 (ttm) REVERT: E 25 LYS cc_start: 0.8670 (tttp) cc_final: 0.8470 (tttm) REVERT: E 103 ASP cc_start: 0.8431 (m-30) cc_final: 0.8022 (m-30) REVERT: E 183 ASN cc_start: 0.8498 (m110) cc_final: 0.8050 (m-40) REVERT: L 169 TYR cc_start: 0.8586 (m-80) cc_final: 0.8054 (m-80) outliers start: 20 outliers final: 14 residues processed: 178 average time/residue: 0.1229 time to fit residues: 28.6296 Evaluate side-chains 178 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 205 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 106 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 116 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 74 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.147374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116892 restraints weight = 11372.556| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.99 r_work: 0.3397 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9883 Z= 0.111 Angle : 0.455 6.911 13411 Z= 0.232 Chirality : 0.040 0.197 1524 Planarity : 0.004 0.036 1728 Dihedral : 4.101 58.480 1313 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.98 % Allowed : 11.71 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.44 (0.24), residues: 1206 helix: 2.29 (0.18), residues: 846 sheet: None (None), residues: 0 loop : 0.01 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 82 TYR 0.009 0.001 TYR A 169 PHE 0.007 0.001 PHE E 32 TRP 0.016 0.001 TRP A 184 HIS 0.001 0.000 HIS L 62 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9883) covalent geometry : angle 0.45482 (13411) hydrogen bonds : bond 0.03855 ( 602) hydrogen bonds : angle 3.47422 ( 1782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7763 (ttp80) cc_final: 0.7298 (ttp80) REVERT: A 117 TRP cc_start: 0.7291 (m-10) cc_final: 0.6732 (m-10) REVERT: C 75 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7153 (mt-10) REVERT: C 144 MET cc_start: 0.8044 (ttp) cc_final: 0.7694 (ttp) REVERT: C 198 CYS cc_start: 0.7576 (m) cc_final: 0.7056 (m) REVERT: D 25 LYS cc_start: 0.9130 (tttt) cc_final: 0.8869 (ttmm) REVERT: D 39 MET cc_start: 0.8550 (tpt) cc_final: 0.8328 (tpt) REVERT: D 185 MET cc_start: 0.8080 (ttm) cc_final: 0.7678 (ttm) REVERT: E 103 ASP cc_start: 0.8467 (m-30) cc_final: 0.8041 (m-30) REVERT: E 183 ASN cc_start: 0.8566 (m110) cc_final: 0.8133 (m-40) REVERT: E 189 LEU cc_start: 0.6976 (mm) cc_final: 0.6759 (mm) REVERT: L 169 TYR cc_start: 0.8653 (m-80) cc_final: 0.8133 (m-80) outliers start: 21 outliers final: 17 residues processed: 178 average time/residue: 0.1218 time to fit residues: 28.5986 Evaluate side-chains 180 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 205 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.0040 chunk 37 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 20 optimal weight: 0.0170 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 0.0770 chunk 116 optimal weight: 0.7980 overall best weight: 0.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 GLN E 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.171460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.142502 restraints weight = 10984.129| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.95 r_work: 0.3460 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9883 Z= 0.093 Angle : 0.435 7.312 13411 Z= 0.222 Chirality : 0.039 0.178 1524 Planarity : 0.004 0.035 1728 Dihedral : 3.993 59.680 1313 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.51 % Allowed : 12.37 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.57 (0.24), residues: 1206 helix: 2.41 (0.18), residues: 846 sheet: None (None), residues: 0 loop : 0.01 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 143 TYR 0.006 0.001 TYR A 169 PHE 0.006 0.001 PHE E 168 TRP 0.020 0.001 TRP A 184 HIS 0.001 0.000 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 9883) covalent geometry : angle 0.43462 (13411) hydrogen bonds : bond 0.03324 ( 602) hydrogen bonds : angle 3.37933 ( 1782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.407 Fit side-chains REVERT: A 39 MET cc_start: 0.8519 (tpt) cc_final: 0.8218 (mmt) REVERT: A 97 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7249 (ttp80) REVERT: A 117 TRP cc_start: 0.7309 (m-10) cc_final: 0.6785 (m-10) REVERT: B 144 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7757 (ttm) REVERT: C 75 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7022 (mt-10) REVERT: C 144 MET cc_start: 0.7974 (ttp) cc_final: 0.7625 (ttp) REVERT: D 25 LYS cc_start: 0.9107 (tttt) cc_final: 0.8845 (ttmm) REVERT: D 97 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.3336 (ppt170) REVERT: D 145 TYR cc_start: 0.7487 (m-80) cc_final: 0.6871 (m-10) REVERT: E 103 ASP cc_start: 0.8421 (m-30) cc_final: 0.8016 (m-30) REVERT: E 179 GLN cc_start: 0.8404 (tp40) cc_final: 0.7937 (tp40) REVERT: E 183 ASN cc_start: 0.8509 (m110) cc_final: 0.8039 (m-40) REVERT: L 143 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7729 (tpm170) outliers start: 16 outliers final: 11 residues processed: 178 average time/residue: 0.1133 time to fit residues: 26.5065 Evaluate side-chains 178 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 205 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 80 optimal weight: 0.0270 chunk 72 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.137259 restraints weight = 11122.497| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.07 r_work: 0.3422 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9883 Z= 0.106 Angle : 0.456 6.897 13411 Z= 0.232 Chirality : 0.040 0.179 1524 Planarity : 0.004 0.035 1728 Dihedral : 4.018 59.119 1313 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.42 % Allowed : 12.84 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.58 (0.24), residues: 1206 helix: 2.43 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.02 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 143 TYR 0.009 0.001 TYR A 169 PHE 0.006 0.001 PHE E 32 TRP 0.018 0.001 TRP A 184 HIS 0.001 0.000 HIS L 62 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9883) covalent geometry : angle 0.45627 (13411) hydrogen bonds : bond 0.03604 ( 602) hydrogen bonds : angle 3.40745 ( 1782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7286 (ttp80) REVERT: A 117 TRP cc_start: 0.7274 (m-10) cc_final: 0.6783 (m-10) REVERT: B 144 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7754 (ttm) REVERT: C 75 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6993 (mt-10) REVERT: C 144 MET cc_start: 0.7961 (ttp) cc_final: 0.7641 (ttp) REVERT: C 187 GLU cc_start: 0.6268 (tm-30) cc_final: 0.5783 (tt0) REVERT: D 25 LYS cc_start: 0.9028 (tttt) cc_final: 0.8749 (ttmm) REVERT: D 185 MET cc_start: 0.7810 (ttm) cc_final: 0.7164 (ttm) REVERT: E 179 GLN cc_start: 0.8354 (tp40) cc_final: 0.7850 (tp40) REVERT: E 183 ASN cc_start: 0.8513 (m110) cc_final: 0.8016 (m-40) REVERT: L 169 TYR cc_start: 0.8567 (m-80) cc_final: 0.8002 (m-80) outliers start: 15 outliers final: 12 residues processed: 178 average time/residue: 0.1140 time to fit residues: 26.8108 Evaluate side-chains 179 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 0.5980 chunk 111 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.147910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116635 restraints weight = 11249.673| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.05 r_work: 0.3401 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9883 Z= 0.121 Angle : 0.472 6.742 13411 Z= 0.241 Chirality : 0.040 0.185 1524 Planarity : 0.004 0.037 1728 Dihedral : 4.072 58.445 1313 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.32 % Allowed : 12.65 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.51 (0.24), residues: 1206 helix: 2.38 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.01 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 82 TYR 0.010 0.001 TYR L 169 PHE 0.007 0.001 PHE E 32 TRP 0.024 0.001 TRP A 184 HIS 0.001 0.000 HIS L 62 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9883) covalent geometry : angle 0.47231 (13411) hydrogen bonds : bond 0.03848 ( 602) hydrogen bonds : angle 3.46532 ( 1782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8382 (tppp) cc_final: 0.8163 (ttmt) REVERT: A 39 MET cc_start: 0.8551 (tpt) cc_final: 0.8269 (tpp) REVERT: A 97 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7218 (ttp80) REVERT: A 117 TRP cc_start: 0.7212 (m-10) cc_final: 0.6717 (m-10) REVERT: C 75 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7044 (mt-10) REVERT: C 144 MET cc_start: 0.7931 (ttp) cc_final: 0.7635 (ttm) REVERT: D 25 LYS cc_start: 0.9014 (tttt) cc_final: 0.8737 (ttmm) REVERT: E 179 GLN cc_start: 0.8377 (tp40) cc_final: 0.7871 (tp40) REVERT: E 183 ASN cc_start: 0.8521 (m110) cc_final: 0.8039 (m-40) outliers start: 14 outliers final: 14 residues processed: 177 average time/residue: 0.1234 time to fit residues: 28.6289 Evaluate side-chains 181 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 46 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.170430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.140095 restraints weight = 11170.671| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.07 r_work: 0.3406 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9883 Z= 0.109 Angle : 0.465 6.685 13411 Z= 0.238 Chirality : 0.040 0.181 1524 Planarity : 0.004 0.038 1728 Dihedral : 4.044 58.654 1313 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.42 % Allowed : 13.22 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.54 (0.24), residues: 1206 helix: 2.38 (0.18), residues: 846 sheet: None (None), residues: 0 loop : 0.01 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 82 TYR 0.009 0.001 TYR A 169 PHE 0.006 0.001 PHE E 32 TRP 0.028 0.001 TRP A 184 HIS 0.001 0.000 HIS L 62 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9883) covalent geometry : angle 0.46507 (13411) hydrogen bonds : bond 0.03646 ( 602) hydrogen bonds : angle 3.44202 ( 1782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2184.12 seconds wall clock time: 38 minutes 3.42 seconds (2283.42 seconds total)