Starting phenix.real_space_refine on Tue Feb 3 19:25:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hqo_52345/02_2026/9hqo_52345.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hqo_52345/02_2026/9hqo_52345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hqo_52345/02_2026/9hqo_52345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hqo_52345/02_2026/9hqo_52345.map" model { file = "/net/cci-nas-00/data/ceres_data/9hqo_52345/02_2026/9hqo_52345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hqo_52345/02_2026/9hqo_52345.cif" } resolution = 2.97 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= 0.049 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 30 5.16 5 C 4128 2.51 5 N 1032 2.21 5 O 1140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6330 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2114 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 250} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2114 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 250} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2102 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 13, 'TRANS': 250} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 33 Time building chain proxies: 1.64, per 1000 atoms: 0.26 Number of scatterers: 6330 At special positions: 0 Unit cell: (79.23, 82.01, 123.71, 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 30 16.00 O 1140 8.00 N 1032 7.00 C 4128 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: 0.49 Conformation dependent library (CDL) restraints added in 364.5 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1524 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 9 sheets defined 30.8% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 72 through 98 removed outlier: 4.245A pdb=" N LEU A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.822A pdb=" N SER A 225 " --> pdb=" O GLN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 4.280A pdb=" N SER A 277 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 331 Processing helix chain 'B' and resid 72 through 98 removed outlier: 4.238A pdb=" N LEU B 76 " --> pdb=" O PHE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 removed outlier: 3.608A pdb=" N PHE B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.766A pdb=" N SER B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 removed outlier: 4.263A pdb=" N SER B 277 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 331 Processing helix chain 'C' and resid 72 through 98 removed outlier: 4.243A pdb=" N LEU C 76 " --> pdb=" O PHE C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 215 through 227 removed outlier: 3.701A pdb=" N SER C 225 " --> pdb=" O GLN C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 removed outlier: 4.281A pdb=" N SER C 277 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 331 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107 removed outlier: 13.306A pdb=" N PHE A 291 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N MET A 242 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N GLN A 293 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A 244 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL A 295 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU A 246 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ASP A 297 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N LYS A 248 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG A 188 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU A 125 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 107 removed outlier: 13.306A pdb=" N PHE A 291 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N MET A 242 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N GLN A 293 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A 244 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL A 295 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU A 246 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ASP A 297 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N LYS A 248 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 157 removed outlier: 4.078A pdb=" N ASP A 200 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 107 removed outlier: 13.327A pdb=" N PHE B 291 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N MET B 242 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N GLN B 293 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 244 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL B 295 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU B 246 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ASP B 297 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N LYS B 248 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 131 removed outlier: 5.931A pdb=" N LEU B 125 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG B 188 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE B 236 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 265 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 157 removed outlier: 4.076A pdb=" N ASP B 200 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 107 removed outlier: 13.295A pdb=" N PHE C 291 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N MET C 242 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N GLN C 293 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU C 244 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL C 295 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU C 246 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASP C 297 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LYS C 248 " --> pdb=" O ASP C 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 124 through 131 removed outlier: 5.997A pdb=" N LEU C 125 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG C 188 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE C 236 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 265 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 151 through 157 removed outlier: 4.108A pdb=" N ASP C 200 " --> pdb=" O TYR C 119 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1989 1.34 - 1.46: 1570 1.46 - 1.58: 2891 1.58 - 1.70: 0 1.70 - 1.81: 48 Bond restraints: 6498 Sorted by residual: bond pdb=" CG LEU C 182 " pdb=" CD2 LEU C 182 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.54e-01 bond pdb=" CG LEU B 182 " pdb=" CD2 LEU B 182 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.11e-01 bond pdb=" CB ASP C 289 " pdb=" CG ASP C 289 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.97e-01 bond pdb=" CG LEU A 182 " pdb=" CD2 LEU A 182 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.38e-01 bond pdb=" CG ARG B 110 " pdb=" CD ARG B 110 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.12e-01 ... (remaining 6493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 8514 1.34 - 2.67: 242 2.67 - 4.01: 54 4.01 - 5.35: 7 5.35 - 6.68: 3 Bond angle restraints: 8820 Sorted by residual: angle pdb=" CB MET C 220 " pdb=" CG MET C 220 " pdb=" SD MET C 220 " ideal model delta sigma weight residual 112.70 119.38 -6.68 3.00e+00 1.11e-01 4.97e+00 angle pdb=" CB MET A 90 " pdb=" CG MET A 90 " pdb=" SD MET A 90 " ideal model delta sigma weight residual 112.70 119.25 -6.55 3.00e+00 1.11e-01 4.77e+00 angle pdb=" CG ARG B 110 " pdb=" CD ARG B 110 " pdb=" NE ARG B 110 " ideal model delta sigma weight residual 112.00 116.30 -4.30 2.20e+00 2.07e-01 3.82e+00 angle pdb=" N TYR C 132 " pdb=" CA TYR C 132 " pdb=" C TYR C 132 " ideal model delta sigma weight residual 110.80 106.72 4.08 2.13e+00 2.20e-01 3.67e+00 angle pdb=" C ASP C 289 " pdb=" CA ASP C 289 " pdb=" CB ASP C 289 " ideal model delta sigma weight residual 110.22 112.71 -2.49 1.32e+00 5.74e-01 3.55e+00 ... (remaining 8815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 3473 16.93 - 33.87: 294 33.87 - 50.80: 71 50.80 - 67.74: 11 67.74 - 84.67: 12 Dihedral angle restraints: 3861 sinusoidal: 1515 harmonic: 2346 Sorted by residual: dihedral pdb=" CA PHE A 204 " pdb=" C PHE A 204 " pdb=" N SER A 205 " pdb=" CA SER A 205 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA PHE B 204 " pdb=" C PHE B 204 " pdb=" N SER B 205 " pdb=" CA SER B 205 " ideal model delta harmonic sigma weight residual -180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA PHE C 204 " pdb=" C PHE C 204 " pdb=" N SER C 205 " pdb=" CA SER C 205 " ideal model delta harmonic sigma weight residual 180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 3858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 554 0.027 - 0.054: 247 0.054 - 0.081: 98 0.081 - 0.108: 42 0.108 - 0.135: 25 Chirality restraints: 966 Sorted by residual: chirality pdb=" CA ILE B 116 " pdb=" N ILE B 116 " pdb=" C ILE B 116 " pdb=" CB ILE B 116 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE C 292 " pdb=" N ILE C 292 " pdb=" C ILE C 292 " pdb=" CB ILE C 292 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE A 292 " pdb=" N ILE A 292 " pdb=" C ILE A 292 " pdb=" CB ILE A 292 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 963 not shown) Planarity restraints: 1125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 158 " -0.028 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO B 159 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 158 " 0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO C 159 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 159 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 159 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 158 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO A 159 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " 0.015 5.00e-02 4.00e+02 ... (remaining 1122 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1672 2.81 - 3.33: 5375 3.33 - 3.86: 10298 3.86 - 4.38: 11600 4.38 - 4.90: 20803 Nonbonded interactions: 49748 Sorted by model distance: nonbonded pdb=" ND2 ASN A 302 " pdb=" OD2 ASP B 91 " model vdw 2.290 3.120 nonbonded pdb=" ND2 ASN B 302 " pdb=" OD2 ASP C 91 " model vdw 2.295 3.120 nonbonded pdb=" O PRO B 141 " pdb=" NE2 GLN B 186 " model vdw 2.315 3.120 nonbonded pdb=" O PRO A 141 " pdb=" NE2 GLN A 186 " model vdw 2.359 3.120 nonbonded pdb=" OD1 ASN A 266 " pdb=" O GLY B 234 " model vdw 2.396 3.040 ... (remaining 49743 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 69 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 207 or (resid 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 211 or (resid 212 \ and (name N or name CA or name C or name O or name CB )) or resid 213 through 33 \ 2)) selection = (chain 'B' and (resid 69 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 207 or (resid 208 and (name N or n \ ame CA or name C or name O or name CB )) or resid 209 through 211 or (resid 212 \ and (name N or name CA or name C or name O or name CB )) or resid 213 through 33 \ 2)) selection = chain 'C' } 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: 0.570 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.750 Find NCS groups from input model: 0.100 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:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 0.029 6498 Z= 0.127 Angle : 0.557 6.685 8820 Z= 0.289 Chirality : 0.042 0.135 966 Planarity : 0.003 0.043 1125 Dihedral : 14.424 84.670 2337 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.31), residues: 786 helix: 2.05 (0.36), residues: 249 sheet: -0.39 (0.29), residues: 303 loop : -1.04 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 110 TYR 0.013 0.001 TYR B 111 PHE 0.017 0.001 PHE B 204 TRP 0.007 0.001 TRP B 330 HIS 0.001 0.000 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6498) covalent geometry : angle 0.55674 ( 8820) hydrogen bonds : bond 0.10376 ( 343) hydrogen bonds : angle 4.95444 ( 996) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.245 Fit side-chains REVERT: A 93 ARG cc_start: 0.7934 (ttt-90) cc_final: 0.7575 (ttm110) REVERT: A 97 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8219 (ttpp) REVERT: A 148 ASN cc_start: 0.7933 (t0) cc_final: 0.7650 (t0) REVERT: A 180 ARG cc_start: 0.7952 (mtt180) cc_final: 0.7560 (mtm180) REVERT: A 236 PHE cc_start: 0.9114 (m-10) cc_final: 0.8792 (m-80) REVERT: A 291 PHE cc_start: 0.8260 (m-80) cc_final: 0.7969 (m-80) REVERT: B 97 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7967 (ttmt) REVERT: B 148 ASN cc_start: 0.7359 (t0) cc_final: 0.6809 (t0) REVERT: B 215 ASP cc_start: 0.6149 (t0) cc_final: 0.5926 (t0) REVERT: B 220 MET cc_start: 0.8823 (mmt) cc_final: 0.8257 (mmt) REVERT: C 105 TYR cc_start: 0.8570 (m-80) cc_final: 0.8366 (m-80) REVERT: C 188 ARG cc_start: 0.8286 (ttt-90) cc_final: 0.7943 (ttt-90) REVERT: C 236 PHE cc_start: 0.9072 (m-10) cc_final: 0.8684 (m-80) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.6304 time to fit residues: 126.5458 Evaluate side-chains 125 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN C 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.170345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.126686 restraints weight = 7155.542| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.69 r_work: 0.3190 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6498 Z= 0.167 Angle : 0.578 7.801 8820 Z= 0.296 Chirality : 0.043 0.137 966 Planarity : 0.004 0.037 1125 Dihedral : 4.384 20.201 858 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.76 % Allowed : 12.65 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.30), residues: 786 helix: 2.29 (0.35), residues: 243 sheet: -0.27 (0.29), residues: 303 loop : -0.87 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 110 TYR 0.014 0.002 TYR A 111 PHE 0.021 0.002 PHE C 281 TRP 0.007 0.001 TRP A 287 HIS 0.007 0.002 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6498) covalent geometry : angle 0.57791 ( 8820) hydrogen bonds : bond 0.03299 ( 343) hydrogen bonds : angle 4.21214 ( 996) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.289 Fit side-chains REVERT: A 93 ARG cc_start: 0.8176 (ttt-90) cc_final: 0.7583 (ttm110) REVERT: A 97 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8281 (ttpp) REVERT: A 148 ASN cc_start: 0.7942 (t0) cc_final: 0.7391 (t0) REVERT: A 180 ARG cc_start: 0.8531 (mtt180) cc_final: 0.8070 (mtm180) REVERT: A 246 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8413 (mt-10) REVERT: A 291 PHE cc_start: 0.8498 (m-80) cc_final: 0.8287 (m-80) REVERT: B 97 LYS cc_start: 0.8281 (mtmt) cc_final: 0.8003 (ttmt) REVERT: B 101 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8144 (ptp) REVERT: B 148 ASN cc_start: 0.7655 (t0) cc_final: 0.7144 (t0) REVERT: B 215 ASP cc_start: 0.6737 (t0) cc_final: 0.6430 (t0) REVERT: B 220 MET cc_start: 0.8922 (mmt) cc_final: 0.8381 (mmt) REVERT: C 97 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8052 (ttmt) REVERT: C 143 GLN cc_start: 0.6800 (mm-40) cc_final: 0.6407 (mp-120) outliers start: 32 outliers final: 14 residues processed: 126 average time/residue: 0.5462 time to fit residues: 72.4136 Evaluate side-chains 134 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 297 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 0.0070 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 0.0050 chunk 19 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 overall best weight: 0.3612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.172188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127442 restraints weight = 7143.021| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.80 r_work: 0.3221 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6498 Z= 0.105 Angle : 0.506 4.923 8820 Z= 0.261 Chirality : 0.041 0.136 966 Planarity : 0.003 0.033 1125 Dihedral : 4.216 19.652 858 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.27 % Allowed : 16.22 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.30), residues: 786 helix: 2.41 (0.34), residues: 243 sheet: -0.21 (0.30), residues: 300 loop : -0.65 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 110 TYR 0.010 0.001 TYR B 201 PHE 0.012 0.001 PHE B 281 TRP 0.006 0.001 TRP A 287 HIS 0.003 0.001 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6498) covalent geometry : angle 0.50561 ( 8820) hydrogen bonds : bond 0.02921 ( 343) hydrogen bonds : angle 4.13666 ( 996) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.234 Fit side-chains REVERT: A 93 ARG cc_start: 0.8142 (ttt-90) cc_final: 0.7449 (ttm110) REVERT: A 97 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8185 (ttpp) REVERT: A 148 ASN cc_start: 0.8053 (t0) cc_final: 0.7387 (t0) REVERT: A 180 ARG cc_start: 0.8433 (mtt180) cc_final: 0.7891 (mtm180) REVERT: B 97 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7825 (ttmt) REVERT: B 148 ASN cc_start: 0.7747 (t0) cc_final: 0.7513 (t0) REVERT: B 215 ASP cc_start: 0.6821 (t0) cc_final: 0.6539 (t0) REVERT: B 220 MET cc_start: 0.8843 (mmt) cc_final: 0.8412 (mmt) REVERT: C 93 ARG cc_start: 0.8208 (mtp-110) cc_final: 0.7746 (mtp-110) REVERT: C 188 ARG cc_start: 0.8828 (ttt-90) cc_final: 0.8551 (ttt-90) outliers start: 22 outliers final: 9 residues processed: 125 average time/residue: 0.6037 time to fit residues: 78.8916 Evaluate side-chains 114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 69 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS C 143 GLN C 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.170260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124994 restraints weight = 7213.511| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.81 r_work: 0.3163 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6498 Z= 0.141 Angle : 0.529 4.961 8820 Z= 0.271 Chirality : 0.042 0.131 966 Planarity : 0.003 0.029 1125 Dihedral : 4.251 20.426 858 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.42 % Allowed : 17.86 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.30), residues: 786 helix: 2.30 (0.34), residues: 249 sheet: -0.22 (0.30), residues: 300 loop : -0.53 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 110 TYR 0.011 0.001 TYR B 111 PHE 0.014 0.002 PHE A 187 TRP 0.005 0.001 TRP A 330 HIS 0.003 0.001 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6498) covalent geometry : angle 0.52864 ( 8820) hydrogen bonds : bond 0.02912 ( 343) hydrogen bonds : angle 4.08847 ( 996) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.246 Fit side-chains REVERT: A 93 ARG cc_start: 0.8198 (ttt-90) cc_final: 0.7452 (ttm110) REVERT: A 96 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8529 (tt) REVERT: A 97 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8183 (ttpp) REVERT: A 148 ASN cc_start: 0.8113 (t0) cc_final: 0.7393 (t0) REVERT: A 241 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8251 (mppt) REVERT: B 97 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7819 (ttmt) REVERT: B 101 MET cc_start: 0.8741 (ptm) cc_final: 0.8517 (ptm) REVERT: B 148 ASN cc_start: 0.7878 (t0) cc_final: 0.7407 (t0) REVERT: B 165 LEU cc_start: 0.8173 (tp) cc_final: 0.7958 (mm) REVERT: B 215 ASP cc_start: 0.6817 (t0) cc_final: 0.6527 (t0) REVERT: B 220 MET cc_start: 0.8848 (mmt) cc_final: 0.8397 (mmt) REVERT: C 111 TYR cc_start: 0.8908 (m-80) cc_final: 0.8676 (m-80) REVERT: C 143 GLN cc_start: 0.6890 (mp10) cc_final: 0.6327 (mp-120) REVERT: C 241 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8323 (mppt) outliers start: 23 outliers final: 14 residues processed: 125 average time/residue: 0.6178 time to fit residues: 80.7166 Evaluate side-chains 127 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 39 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.170571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.125529 restraints weight = 7193.857| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.81 r_work: 0.3166 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6498 Z= 0.124 Angle : 0.517 5.841 8820 Z= 0.264 Chirality : 0.041 0.127 966 Planarity : 0.003 0.028 1125 Dihedral : 4.199 20.066 858 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.98 % Allowed : 19.49 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.30), residues: 786 helix: 2.40 (0.33), residues: 249 sheet: -0.21 (0.30), residues: 300 loop : -0.54 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 110 TYR 0.011 0.001 TYR B 111 PHE 0.013 0.001 PHE C 281 TRP 0.005 0.001 TRP A 330 HIS 0.002 0.001 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6498) covalent geometry : angle 0.51707 ( 8820) hydrogen bonds : bond 0.02812 ( 343) hydrogen bonds : angle 4.05101 ( 996) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.258 Fit side-chains REVERT: A 93 ARG cc_start: 0.8229 (ttt-90) cc_final: 0.7482 (ttm110) REVERT: A 96 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8557 (tt) REVERT: A 97 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8207 (ttpp) REVERT: A 148 ASN cc_start: 0.8127 (t0) cc_final: 0.7419 (t0) REVERT: A 241 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.7949 (mmmm) REVERT: B 97 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7866 (ttmt) REVERT: B 148 ASN cc_start: 0.7872 (t0) cc_final: 0.7429 (t0) REVERT: B 215 ASP cc_start: 0.6817 (t0) cc_final: 0.6534 (t0) REVERT: B 220 MET cc_start: 0.8874 (mmt) cc_final: 0.8441 (mmt) REVERT: C 93 ARG cc_start: 0.8178 (mtp-110) cc_final: 0.7732 (mtp-110) REVERT: C 143 GLN cc_start: 0.7035 (mp10) cc_final: 0.6550 (mp-120) REVERT: C 188 ARG cc_start: 0.8993 (ttp80) cc_final: 0.8731 (ttt-90) REVERT: C 241 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8295 (mppt) outliers start: 20 outliers final: 12 residues processed: 128 average time/residue: 0.6264 time to fit residues: 83.7483 Evaluate side-chains 131 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.170194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.125189 restraints weight = 7185.701| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.81 r_work: 0.3154 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6498 Z= 0.127 Angle : 0.511 6.267 8820 Z= 0.263 Chirality : 0.041 0.125 966 Planarity : 0.003 0.045 1125 Dihedral : 4.184 20.310 858 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.27 % Allowed : 19.79 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.30), residues: 786 helix: 2.45 (0.33), residues: 249 sheet: -0.22 (0.30), residues: 300 loop : -0.53 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 110 TYR 0.011 0.001 TYR B 111 PHE 0.014 0.001 PHE C 204 TRP 0.005 0.001 TRP A 330 HIS 0.002 0.000 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6498) covalent geometry : angle 0.51108 ( 8820) hydrogen bonds : bond 0.02767 ( 343) hydrogen bonds : angle 4.02012 ( 996) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.247 Fit side-chains REVERT: A 93 ARG cc_start: 0.8247 (ttt-90) cc_final: 0.7471 (ttm110) REVERT: A 96 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8528 (tt) REVERT: A 97 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8191 (ttpp) REVERT: A 148 ASN cc_start: 0.8138 (t0) cc_final: 0.7422 (t0) REVERT: A 241 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8264 (mppt) REVERT: B 97 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7852 (ttmt) REVERT: B 148 ASN cc_start: 0.7707 (t0) cc_final: 0.7262 (t0) REVERT: B 215 ASP cc_start: 0.6842 (t0) cc_final: 0.6569 (t0) REVERT: B 220 MET cc_start: 0.8844 (mmt) cc_final: 0.8511 (mmt) REVERT: C 93 ARG cc_start: 0.8052 (mtp-110) cc_final: 0.7810 (mtp-110) REVERT: C 143 GLN cc_start: 0.7084 (mp10) cc_final: 0.6777 (mp-120) REVERT: C 172 ARG cc_start: 0.8457 (tpt-90) cc_final: 0.8006 (tpp80) REVERT: C 188 ARG cc_start: 0.9011 (ttp80) cc_final: 0.8722 (ttt-90) REVERT: C 241 LYS cc_start: 0.8668 (mmtp) cc_final: 0.8236 (mppt) outliers start: 22 outliers final: 12 residues processed: 130 average time/residue: 0.6122 time to fit residues: 83.1121 Evaluate side-chains 137 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.0870 chunk 48 optimal weight: 0.0040 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.170992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.126439 restraints weight = 7162.837| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.79 r_work: 0.3175 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6498 Z= 0.107 Angle : 0.507 6.958 8820 Z= 0.258 Chirality : 0.041 0.126 966 Planarity : 0.003 0.045 1125 Dihedral : 4.129 20.047 858 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.68 % Allowed : 20.83 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.30), residues: 786 helix: 2.51 (0.33), residues: 249 sheet: -0.18 (0.30), residues: 300 loop : -0.51 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 110 TYR 0.011 0.001 TYR C 111 PHE 0.013 0.001 PHE B 204 TRP 0.005 0.001 TRP A 287 HIS 0.002 0.000 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 6498) covalent geometry : angle 0.50749 ( 8820) hydrogen bonds : bond 0.02679 ( 343) hydrogen bonds : angle 3.98536 ( 996) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.250 Fit side-chains REVERT: A 93 ARG cc_start: 0.8254 (ttt-90) cc_final: 0.7496 (ttm110) REVERT: A 96 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8560 (tt) REVERT: A 97 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8213 (ttpp) REVERT: A 107 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: A 148 ASN cc_start: 0.8111 (t0) cc_final: 0.7433 (t0) REVERT: A 212 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7174 (mp10) REVERT: A 241 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8295 (mppt) REVERT: B 97 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7898 (ttmt) REVERT: B 148 ASN cc_start: 0.7696 (t0) cc_final: 0.7206 (t0) REVERT: B 165 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8004 (tp) REVERT: B 215 ASP cc_start: 0.6837 (t0) cc_final: 0.6561 (t0) REVERT: B 220 MET cc_start: 0.8842 (mmt) cc_final: 0.8524 (mmt) REVERT: C 93 ARG cc_start: 0.8063 (mtp-110) cc_final: 0.7828 (mtp-110) REVERT: C 111 TYR cc_start: 0.9042 (m-80) cc_final: 0.8740 (m-80) REVERT: C 119 TYR cc_start: 0.9227 (m-80) cc_final: 0.8982 (m-80) REVERT: C 143 GLN cc_start: 0.7096 (mp10) cc_final: 0.6431 (mp-120) REVERT: C 172 ARG cc_start: 0.8453 (tpt-90) cc_final: 0.8042 (tpp80) REVERT: C 188 ARG cc_start: 0.8984 (ttp80) cc_final: 0.8710 (ttt-90) REVERT: C 241 LYS cc_start: 0.8682 (mmtp) cc_final: 0.8276 (mppt) outliers start: 18 outliers final: 10 residues processed: 140 average time/residue: 0.5996 time to fit residues: 87.4508 Evaluate side-chains 137 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 74 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.169669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.126518 restraints weight = 7180.588| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.70 r_work: 0.3178 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6498 Z= 0.139 Angle : 0.534 7.751 8820 Z= 0.271 Chirality : 0.041 0.128 966 Planarity : 0.003 0.040 1125 Dihedral : 4.181 20.467 858 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.87 % Allowed : 20.24 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.30), residues: 786 helix: 2.42 (0.33), residues: 252 sheet: -0.18 (0.30), residues: 297 loop : -0.63 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 110 TYR 0.013 0.002 TYR B 111 PHE 0.015 0.001 PHE C 204 TRP 0.005 0.001 TRP A 304 HIS 0.002 0.000 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6498) covalent geometry : angle 0.53447 ( 8820) hydrogen bonds : bond 0.02780 ( 343) hydrogen bonds : angle 3.99294 ( 996) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.252 Fit side-chains REVERT: A 93 ARG cc_start: 0.8303 (ttt-90) cc_final: 0.7569 (ttm110) REVERT: A 96 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 97 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8270 (ttpp) REVERT: A 107 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: A 148 ASN cc_start: 0.8041 (t0) cc_final: 0.7400 (t0) REVERT: A 212 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7227 (mp10) REVERT: A 241 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8347 (mppt) REVERT: B 97 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7995 (ttmt) REVERT: B 148 ASN cc_start: 0.7678 (t0) cc_final: 0.7384 (t0) REVERT: B 215 ASP cc_start: 0.6810 (t0) cc_final: 0.6553 (t0) REVERT: B 220 MET cc_start: 0.8844 (mmt) cc_final: 0.8521 (mmt) REVERT: C 143 GLN cc_start: 0.7251 (mp10) cc_final: 0.6589 (mp-120) REVERT: C 148 ASN cc_start: 0.8397 (t0) cc_final: 0.7922 (t0) REVERT: C 172 ARG cc_start: 0.8392 (tpt-90) cc_final: 0.8015 (tpp80) REVERT: C 241 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8315 (mppt) outliers start: 26 outliers final: 14 residues processed: 137 average time/residue: 0.5287 time to fit residues: 75.7538 Evaluate side-chains 139 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 GLN C 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.169909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124694 restraints weight = 7284.117| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.84 r_work: 0.3141 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6498 Z= 0.130 Angle : 0.527 8.097 8820 Z= 0.268 Chirality : 0.041 0.125 966 Planarity : 0.003 0.055 1125 Dihedral : 4.186 20.419 858 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.98 % Allowed : 21.13 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.30), residues: 786 helix: 2.46 (0.33), residues: 252 sheet: -0.20 (0.30), residues: 300 loop : -0.58 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 110 TYR 0.011 0.001 TYR B 111 PHE 0.014 0.001 PHE C 204 TRP 0.005 0.001 TRP C 330 HIS 0.002 0.000 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6498) covalent geometry : angle 0.52747 ( 8820) hydrogen bonds : bond 0.02772 ( 343) hydrogen bonds : angle 4.00860 ( 996) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.167 Fit side-chains REVERT: A 93 ARG cc_start: 0.8295 (ttt-90) cc_final: 0.7511 (ttm110) REVERT: A 96 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8551 (tt) REVERT: A 97 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8207 (ttpp) REVERT: A 148 ASN cc_start: 0.8072 (t0) cc_final: 0.7405 (t0) REVERT: A 241 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8323 (mppt) REVERT: B 148 ASN cc_start: 0.7852 (t0) cc_final: 0.7616 (t0) REVERT: B 215 ASP cc_start: 0.6866 (t0) cc_final: 0.6586 (t0) REVERT: B 220 MET cc_start: 0.8825 (mmt) cc_final: 0.8490 (mmt) REVERT: C 93 ARG cc_start: 0.8160 (mtp-110) cc_final: 0.7636 (mtp-110) REVERT: C 143 GLN cc_start: 0.7219 (mp10) cc_final: 0.6532 (mp-120) REVERT: C 172 ARG cc_start: 0.8505 (tpt-90) cc_final: 0.8101 (tpp80) REVERT: C 188 ARG cc_start: 0.8939 (ttp80) cc_final: 0.8668 (ttt-90) REVERT: C 241 LYS cc_start: 0.8727 (mmtp) cc_final: 0.8287 (mppt) outliers start: 20 outliers final: 15 residues processed: 135 average time/residue: 0.5799 time to fit residues: 81.9075 Evaluate side-chains 139 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 14 optimal weight: 0.0010 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 98 HIS B 212 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.170455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.126306 restraints weight = 7145.665| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.78 r_work: 0.3184 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6498 Z= 0.112 Angle : 0.527 8.659 8820 Z= 0.266 Chirality : 0.041 0.126 966 Planarity : 0.003 0.055 1125 Dihedral : 4.170 20.019 858 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.98 % Allowed : 22.17 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.30), residues: 786 helix: 2.45 (0.32), residues: 252 sheet: -0.18 (0.30), residues: 300 loop : -0.55 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 110 TYR 0.011 0.001 TYR C 111 PHE 0.013 0.001 PHE B 204 TRP 0.004 0.001 TRP A 330 HIS 0.001 0.000 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6498) covalent geometry : angle 0.52657 ( 8820) hydrogen bonds : bond 0.02722 ( 343) hydrogen bonds : angle 4.01106 ( 996) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.251 Fit side-chains REVERT: A 87 GLN cc_start: 0.8964 (pp30) cc_final: 0.8541 (pp30) REVERT: A 93 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.7469 (ttm110) REVERT: A 96 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8426 (tt) REVERT: A 97 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8166 (ttpp) REVERT: A 148 ASN cc_start: 0.8059 (t0) cc_final: 0.7385 (t0) REVERT: A 241 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8278 (mppt) REVERT: B 109 ASP cc_start: 0.7738 (p0) cc_final: 0.7479 (p0) REVERT: B 148 ASN cc_start: 0.7802 (t0) cc_final: 0.7381 (t0) REVERT: B 180 ARG cc_start: 0.8622 (mtt180) cc_final: 0.8356 (mtt180) REVERT: B 215 ASP cc_start: 0.6862 (t0) cc_final: 0.6585 (t0) REVERT: B 220 MET cc_start: 0.8800 (mmt) cc_final: 0.8462 (mmt) REVERT: C 93 ARG cc_start: 0.8156 (mtp-110) cc_final: 0.7644 (mtp-110) REVERT: C 111 TYR cc_start: 0.9040 (m-80) cc_final: 0.8820 (m-80) REVERT: C 143 GLN cc_start: 0.7289 (mp10) cc_final: 0.6623 (mp-120) REVERT: C 172 ARG cc_start: 0.8497 (tpt-90) cc_final: 0.8075 (tpp80) REVERT: C 188 ARG cc_start: 0.8952 (ttp80) cc_final: 0.8638 (ttt-90) REVERT: C 241 LYS cc_start: 0.8631 (mmtp) cc_final: 0.8185 (mppt) outliers start: 20 outliers final: 14 residues processed: 131 average time/residue: 0.5701 time to fit residues: 78.1359 Evaluate side-chains 137 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.169202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124578 restraints weight = 7176.053| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.79 r_work: 0.3125 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6498 Z= 0.146 Angle : 0.544 8.485 8820 Z= 0.276 Chirality : 0.041 0.127 966 Planarity : 0.004 0.055 1125 Dihedral : 4.263 20.247 858 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.83 % Allowed : 22.02 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.30), residues: 786 helix: 2.43 (0.32), residues: 252 sheet: -0.19 (0.30), residues: 303 loop : -0.74 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 110 TYR 0.012 0.002 TYR B 111 PHE 0.015 0.002 PHE C 204 TRP 0.006 0.001 TRP C 304 HIS 0.002 0.001 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6498) covalent geometry : angle 0.54394 ( 8820) hydrogen bonds : bond 0.02843 ( 343) hydrogen bonds : angle 4.03869 ( 996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2836.60 seconds wall clock time: 49 minutes 0.81 seconds (2940.81 seconds total)