Starting phenix.real_space_refine on Thu Jul 2 04:26:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ga1_29884/07_2026/8ga1_29884.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ga1_29884/07_2026/8ga1_29884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ga1_29884/07_2026/8ga1_29884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ga1_29884/07_2026/8ga1_29884.map" model { file = "/net/cci-nas-00/data/ceres_data/8ga1_29884/07_2026/8ga1_29884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ga1_29884/07_2026/8ga1_29884.cif" } resolution = 2.6 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= 0.005 sd= 0.136 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: 5 Type Number sf(0) Gaussians S 42 5.16 5 Cl 4 4.86 5 C 4426 2.51 5 N 1134 2.21 5 O 1175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6781 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3371 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain: "B" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3371 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CL': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CL': 2} Chain breaks: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 1.51, per 1000 atoms: 0.22 Number of scatterers: 6781 At special positions: 0 Unit cell: (75.9, 70.125, 111.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 42 16.00 O 1175 8.00 N 1134 7.00 C 4426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS B 249 " distance=2.03 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS B 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 310.6 milliseconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 81.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 removed outlier: 3.759A pdb=" N ARG A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 71 removed outlier: 3.568A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 101 removed outlier: 3.885A pdb=" N SER A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 105 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 123 through 141 Proline residue: A 129 - end of helix removed outlier: 4.855A pdb=" N PHE A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.538A pdb=" N GLN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 191 removed outlier: 3.557A pdb=" N ARG A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 203 removed outlier: 3.738A pdb=" N ILE A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 233 Processing helix chain 'A' and resid 253 through 285 Proline residue: A 267 - end of helix removed outlier: 3.578A pdb=" N ARG A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.523A pdb=" N TRP A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.723A pdb=" N SER A 313 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.952A pdb=" N ILE A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 349 Processing helix chain 'A' and resid 356 through 379 removed outlier: 3.502A pdb=" N GLU A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 removed outlier: 3.502A pdb=" N ALA A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.544A pdb=" N ALA A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 27 removed outlier: 4.475A pdb=" N ARG B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 67 removed outlier: 3.512A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 100 removed outlier: 3.502A pdb=" N LEU B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 123 through 141 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 148 through 165 removed outlier: 4.123A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 165 " --> pdb=" O MET B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 191 removed outlier: 3.557A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 203 removed outlier: 3.674A pdb=" N ILE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 232 removed outlier: 3.727A pdb=" N CYS B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 285 removed outlier: 4.049A pdb=" N TYR B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Proline residue: B 267 - end of helix removed outlier: 3.523A pdb=" N HIS B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 308 removed outlier: 3.577A pdb=" N PHE B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.524A pdb=" N SER B 313 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.931A pdb=" N ILE B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 349 Processing helix chain 'B' and resid 356 through 379 removed outlier: 3.724A pdb=" N GLU B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 383 Processing helix chain 'B' and resid 385 through 395 removed outlier: 4.372A pdb=" N PHE B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 404 through 417 removed outlier: 3.517A pdb=" N ASP B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 421 through 439 Processing helix chain 'B' and resid 443 through 460 removed outlier: 3.544A pdb=" N GLU B 459 " --> pdb=" O LYS B 455 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1461 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: 1.19 Time building geometry restraints manager: 0.55 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: 2054 1.34 - 1.46: 1260 1.46 - 1.58: 3496 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 6886 Sorted by residual: bond pdb=" C LEU B 128 " pdb=" N PRO B 129 " ideal model delta sigma weight residual 1.336 1.371 -0.035 1.25e-02 6.40e+03 8.00e+00 bond pdb=" C LEU A 128 " pdb=" N PRO A 129 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.53e+00 bond pdb=" CB PRO B 424 " pdb=" CG PRO B 424 " ideal model delta sigma weight residual 1.492 1.421 0.071 5.00e-02 4.00e+02 2.01e+00 bond pdb=" CG1 ILE B 356 " pdb=" CD1 ILE B 356 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.91e+00 bond pdb=" C LEU B 423 " pdb=" N PRO B 424 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.28e-02 6.10e+03 1.84e+00 ... (remaining 6881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 8964 1.80 - 3.60: 302 3.60 - 5.39: 53 5.39 - 7.19: 20 7.19 - 8.99: 7 Bond angle restraints: 9346 Sorted by residual: angle pdb=" C ALA A 237 " pdb=" N LEU A 238 " pdb=" CA LEU A 238 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C ASN A 74 " pdb=" N TYR A 75 " pdb=" CA TYR A 75 " ideal model delta sigma weight residual 120.09 124.47 -4.38 1.25e+00 6.40e-01 1.23e+01 angle pdb=" C VAL B 162 " pdb=" N LEU B 163 " pdb=" CA LEU B 163 " ideal model delta sigma weight residual 121.52 127.59 -6.07 1.74e+00 3.30e-01 1.22e+01 angle pdb=" C CYS B 230 " pdb=" CA CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sigma weight residual 110.95 105.58 5.37 1.55e+00 4.16e-01 1.20e+01 angle pdb=" CA CYS A 230 " pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " ideal model delta sigma weight residual 114.40 121.86 -7.46 2.30e+00 1.89e-01 1.05e+01 ... (remaining 9341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3585 17.91 - 35.82: 360 35.82 - 53.73: 49 53.73 - 71.64: 8 71.64 - 89.55: 4 Dihedral angle restraints: 4006 sinusoidal: 1518 harmonic: 2488 Sorted by residual: dihedral pdb=" CA ASP A 118 " pdb=" C ASP A 118 " pdb=" N GLN A 119 " pdb=" CA GLN A 119 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ASP B 118 " pdb=" C ASP B 118 " pdb=" N GLN B 119 " pdb=" CA GLN B 119 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA GLU A 235 " pdb=" C GLU A 235 " pdb=" N VAL A 236 " pdb=" CA VAL A 236 " ideal model delta harmonic sigma weight residual -180.00 -156.44 -23.56 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 4003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 875 0.060 - 0.120: 206 0.120 - 0.180: 17 0.180 - 0.240: 1 0.240 - 0.300: 1 Chirality restraints: 1100 Sorted by residual: chirality pdb=" CB ILE B 356 " pdb=" CA ILE B 356 " pdb=" CG1 ILE B 356 " pdb=" CG2 ILE B 356 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE A 288 " pdb=" CA ILE A 288 " pdb=" CG1 ILE A 288 " pdb=" CG2 ILE A 288 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA PRO A 150 " pdb=" N PRO A 150 " pdb=" C PRO A 150 " pdb=" CB PRO A 150 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 1097 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 266 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO B 267 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 149 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO B 150 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 149 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO A 150 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.035 5.00e-02 4.00e+02 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1964 2.81 - 3.33: 6268 3.33 - 3.85: 12145 3.85 - 4.38: 14879 4.38 - 4.90: 24324 Nonbonded interactions: 59580 Sorted by model distance: nonbonded pdb=" O MET B 394 " pdb=" O HOH B 601 " model vdw 2.284 3.040 nonbonded pdb=" O ARG B 147 " pdb=" OG1 THR B 151 " model vdw 2.294 3.040 nonbonded pdb=" OE1 GLU A 148 " pdb=" O HOH A 601 " model vdw 2.304 3.040 nonbonded pdb=" O VAL A 144 " pdb=" O HOH A 602 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR B 94 " pdb=" OG SER B 350 " model vdw 2.320 3.040 ... (remaining 59575 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.470 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 6888 Z= 0.216 Angle : 0.849 8.990 9350 Z= 0.461 Chirality : 0.049 0.300 1100 Planarity : 0.008 0.074 1174 Dihedral : 14.039 89.547 2428 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % 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: -5.16 (0.19), residues: 896 helix: -3.63 (0.11), residues: 670 sheet: None (None), residues: 0 loop : -1.78 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 15 TYR 0.026 0.002 TYR B 419 PHE 0.026 0.002 PHE A 357 TRP 0.008 0.001 TRP A 291 HIS 0.004 0.001 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 ( 6886) covalent geometry : angle 0.84554 / 0.46 ( 9346) SS BOND : bond 0.00215 / 0.11 ( 2) SS BOND : angle 3.83170 / 2.10 ( 4) hydrogen bonds : bond 0.26878 / 17.87 ( 493) hydrogen bonds : angle 10.22363 / 7.24 ( 1461) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 224 MET cc_start: 0.8272 (mmm) cc_final: 0.7998 (mpp) REVERT: B 394 MET cc_start: 0.8747 (ttm) cc_final: 0.8438 (ttm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.6278 time to fit residues: 85.6131 Evaluate side-chains 91 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN A 418 ASN A 456 GLN B 61 GLN B 62 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 270 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.155648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.133534 restraints weight = 6426.091| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 0.98 r_work: 0.3301 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6888 Z= 0.160 Angle : 0.644 7.560 9350 Z= 0.334 Chirality : 0.042 0.158 1100 Planarity : 0.007 0.057 1174 Dihedral : 5.283 23.262 958 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.81 % Allowed : 13.17 % Favored : 84.02 % 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: -1.21 (0.26), residues: 896 helix: -0.46 (0.18), residues: 678 sheet: None (None), residues: 0 loop : -1.44 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.017 0.002 TYR B 419 PHE 0.013 0.001 PHE B 219 TRP 0.005 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 6886) covalent geometry : angle 0.64022 / 0.33 ( 9346) SS BOND : bond 0.00499 / 0.24 ( 2) SS BOND : angle 3.44307 / 1.85 ( 4) hydrogen bonds : bond 0.04753 / 3.17 ( 493) hydrogen bonds : angle 4.87246 / 3.44 ( 1461) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.259 Fit side-chains REVERT: A 19 ARG cc_start: 0.7362 (mtm-85) cc_final: 0.6420 (mmm160) REVERT: A 167 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6880 (mmt90) REVERT: B 20 GLN cc_start: 0.7688 (mt0) cc_final: 0.7086 (mm110) REVERT: B 55 LYS cc_start: 0.8327 (mttt) cc_final: 0.7933 (mmtp) outliers start: 19 outliers final: 6 residues processed: 119 average time/residue: 0.5285 time to fit residues: 66.2002 Evaluate side-chains 105 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 329 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 GLN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.155200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.133075 restraints weight = 6376.026| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 0.97 r_work: 0.3295 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6888 Z= 0.153 Angle : 0.609 8.184 9350 Z= 0.313 Chirality : 0.042 0.171 1100 Planarity : 0.006 0.053 1174 Dihedral : 5.040 23.473 958 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.25 % Allowed : 15.09 % Favored : 81.66 % 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: 0.47 (0.28), residues: 896 helix: 0.86 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.28 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 23 TYR 0.021 0.002 TYR A 419 PHE 0.015 0.001 PHE A 357 TRP 0.006 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 6886) covalent geometry : angle 0.60564 / 0.31 ( 9346) SS BOND : bond 0.00507 / 0.25 ( 2) SS BOND : angle 3.33181 / 1.79 ( 4) hydrogen bonds : bond 0.04276 / 2.85 ( 493) hydrogen bonds : angle 4.45567 / 3.14 ( 1461) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.172 Fit side-chains REVERT: A 19 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.7160 (mtt180) REVERT: A 167 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6895 (mmt90) REVERT: A 224 MET cc_start: 0.8678 (mmm) cc_final: 0.8272 (mpp) REVERT: A 423 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8339 (tt) REVERT: B 17 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7016 (ttp-170) REVERT: B 55 LYS cc_start: 0.8385 (mttt) cc_final: 0.7832 (mptm) REVERT: B 177 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8169 (mp) REVERT: B 321 PRO cc_start: 0.7768 (Cg_exo) cc_final: 0.7388 (Cg_endo) REVERT: B 322 ILE cc_start: 0.7864 (mt) cc_final: 0.7578 (mt) outliers start: 22 outliers final: 6 residues processed: 120 average time/residue: 0.5172 time to fit residues: 65.1908 Evaluate side-chains 110 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.155149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.132335 restraints weight = 6371.667| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.01 r_work: 0.3281 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6888 Z= 0.151 Angle : 0.593 6.574 9350 Z= 0.303 Chirality : 0.043 0.170 1100 Planarity : 0.005 0.052 1174 Dihedral : 4.936 22.738 958 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.14 % Allowed : 15.38 % Favored : 80.47 % 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: 1.14 (0.29), residues: 896 helix: 1.35 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.08 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.028 0.002 TYR A 419 PHE 0.016 0.001 PHE A 357 TRP 0.005 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 6886) covalent geometry : angle 0.59035 / 0.30 ( 9346) SS BOND : bond 0.00422 / 0.20 ( 2) SS BOND : angle 2.93568 / 1.58 ( 4) hydrogen bonds : bond 0.04038 / 2.68 ( 493) hydrogen bonds : angle 4.29734 / 3.02 ( 1461) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.244 Fit side-chains REVERT: A 19 ARG cc_start: 0.7402 (mtm-85) cc_final: 0.7170 (mtt180) REVERT: A 167 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6898 (mmt90) REVERT: A 224 MET cc_start: 0.8708 (mmm) cc_final: 0.8261 (mpp) REVERT: B 17 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6952 (ttp-170) REVERT: B 20 GLN cc_start: 0.7635 (mt0) cc_final: 0.6987 (mm-40) REVERT: B 30 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7945 (mttp) REVERT: B 55 LYS cc_start: 0.8357 (mttt) cc_final: 0.7867 (mptm) REVERT: B 321 PRO cc_start: 0.7706 (Cg_exo) cc_final: 0.7291 (Cg_endo) REVERT: B 322 ILE cc_start: 0.7869 (mt) cc_final: 0.7603 (mt) REVERT: B 417 ASP cc_start: 0.7048 (m-30) cc_final: 0.6668 (m-30) outliers start: 28 outliers final: 7 residues processed: 122 average time/residue: 0.5324 time to fit residues: 68.3592 Evaluate side-chains 113 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 329 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.157137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.135329 restraints weight = 6458.727| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 0.95 r_work: 0.3321 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6888 Z= 0.159 Angle : 0.604 8.052 9350 Z= 0.308 Chirality : 0.043 0.188 1100 Planarity : 0.005 0.051 1174 Dihedral : 4.942 22.318 958 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.55 % Allowed : 16.42 % Favored : 80.03 % 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: 1.37 (0.29), residues: 896 helix: 1.51 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.96 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 23 TYR 0.030 0.002 TYR A 419 PHE 0.017 0.001 PHE A 357 TRP 0.005 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 6886) covalent geometry : angle 0.59988 / 0.31 ( 9346) SS BOND : bond 0.00595 / 0.28 ( 2) SS BOND : angle 3.29876 / 1.84 ( 4) hydrogen bonds : bond 0.04034 / 2.68 ( 493) hydrogen bonds : angle 4.27016 / 3.00 ( 1461) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.245 Fit side-chains REVERT: A 19 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.7158 (mtt180) REVERT: A 224 MET cc_start: 0.8680 (mmm) cc_final: 0.8181 (mpp) REVERT: B 30 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7967 (mttp) REVERT: B 55 LYS cc_start: 0.8367 (mttt) cc_final: 0.7907 (mptm) REVERT: B 147 ARG cc_start: 0.8392 (ptt-90) cc_final: 0.8185 (ptt180) REVERT: B 167 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7144 (mtt180) REVERT: B 215 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8226 (tp) REVERT: B 322 ILE cc_start: 0.7881 (mt) cc_final: 0.7660 (mt) REVERT: B 417 ASP cc_start: 0.7157 (m-30) cc_final: 0.6752 (m-30) outliers start: 24 outliers final: 7 residues processed: 119 average time/residue: 0.5226 time to fit residues: 65.4243 Evaluate side-chains 111 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 329 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN B 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.158864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.137120 restraints weight = 6462.285| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 0.96 r_work: 0.3345 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6888 Z= 0.139 Angle : 0.574 7.114 9350 Z= 0.293 Chirality : 0.042 0.177 1100 Planarity : 0.005 0.050 1174 Dihedral : 4.798 22.162 958 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.96 % Allowed : 17.31 % Favored : 79.73 % 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: 1.58 (0.29), residues: 896 helix: 1.71 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -1.01 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 23 TYR 0.032 0.002 TYR A 419 PHE 0.013 0.001 PHE A 357 TRP 0.005 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6886) covalent geometry : angle 0.57120 / 0.29 ( 9346) SS BOND : bond 0.00431 / 0.21 ( 2) SS BOND : angle 2.98614 / 1.66 ( 4) hydrogen bonds : bond 0.03849 / 2.55 ( 493) hydrogen bonds : angle 4.17453 / 2.93 ( 1461) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.205 Fit side-chains REVERT: A 19 ARG cc_start: 0.7435 (mtm-85) cc_final: 0.7167 (mtt180) REVERT: A 224 MET cc_start: 0.8621 (mmm) cc_final: 0.8122 (mpp) REVERT: B 17 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.7067 (ttp-170) REVERT: B 20 GLN cc_start: 0.7627 (mt0) cc_final: 0.6993 (mm-40) REVERT: B 55 LYS cc_start: 0.8360 (mttt) cc_final: 0.7895 (mptm) REVERT: B 167 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7126 (mtt180) REVERT: B 215 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8183 (tp) outliers start: 20 outliers final: 6 residues processed: 120 average time/residue: 0.5302 time to fit residues: 66.8831 Evaluate side-chains 113 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 329 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.154128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.130586 restraints weight = 6813.020| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.07 r_work: 0.3251 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6888 Z= 0.162 Angle : 0.603 7.129 9350 Z= 0.307 Chirality : 0.043 0.222 1100 Planarity : 0.005 0.051 1174 Dihedral : 4.880 21.852 958 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.81 % Allowed : 17.60 % Favored : 79.59 % 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: 1.61 (0.29), residues: 896 helix: 1.67 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.83 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 23 TYR 0.036 0.002 TYR A 419 PHE 0.018 0.002 PHE A 357 TRP 0.004 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 6886) covalent geometry : angle 0.59930 / 0.31 ( 9346) SS BOND : bond 0.00604 / 0.30 ( 2) SS BOND : angle 3.09179 / 1.73 ( 4) hydrogen bonds : bond 0.04024 / 2.66 ( 493) hydrogen bonds : angle 4.24424 / 2.98 ( 1461) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.227 Fit side-chains REVERT: A 19 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.7112 (mtt180) REVERT: A 224 MET cc_start: 0.8751 (mmm) cc_final: 0.8249 (mpp) REVERT: A 423 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8285 (tt) REVERT: B 17 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6964 (ttp-170) REVERT: B 30 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7925 (mttp) REVERT: B 55 LYS cc_start: 0.8312 (mttt) cc_final: 0.7803 (mptm) REVERT: B 215 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8209 (tp) REVERT: B 321 PRO cc_start: 0.7698 (Cg_exo) cc_final: 0.7224 (Cg_endo) REVERT: B 415 MET cc_start: 0.8710 (mtp) cc_final: 0.8506 (mtm) outliers start: 19 outliers final: 6 residues processed: 120 average time/residue: 0.5198 time to fit residues: 65.5254 Evaluate side-chains 111 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 329 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 18 optimal weight: 0.6980 chunk 76 optimal weight: 0.0570 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.156478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.131984 restraints weight = 6806.288| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.15 r_work: 0.3285 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6888 Z= 0.128 Angle : 0.575 9.948 9350 Z= 0.292 Chirality : 0.041 0.179 1100 Planarity : 0.005 0.048 1174 Dihedral : 4.749 21.952 958 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.96 % Allowed : 17.01 % Favored : 80.03 % 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: 1.82 (0.29), residues: 896 helix: 1.91 (0.21), residues: 674 sheet: None (None), residues: 0 loop : -0.99 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 23 TYR 0.032 0.002 TYR A 419 PHE 0.011 0.001 PHE A 357 TRP 0.005 0.001 TRP A 124 HIS 0.003 0.000 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6886) covalent geometry : angle 0.56783 / 0.29 ( 9346) SS BOND : bond 0.00755 / 0.39 ( 2) SS BOND : angle 4.53267 / 2.43 ( 4) hydrogen bonds : bond 0.03708 / 2.46 ( 493) hydrogen bonds : angle 4.11927 / 2.89 ( 1461) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.242 Fit side-chains REVERT: A 19 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.6982 (mtt180) REVERT: A 224 MET cc_start: 0.8692 (mmm) cc_final: 0.8185 (mpp) REVERT: B 17 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6850 (ttp-170) REVERT: B 20 GLN cc_start: 0.7420 (mt0) cc_final: 0.6650 (mm-40) REVERT: B 30 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7875 (mttp) REVERT: B 55 LYS cc_start: 0.8175 (mttt) cc_final: 0.7643 (mptm) REVERT: B 215 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8144 (tp) REVERT: B 322 ILE cc_start: 0.7780 (mt) cc_final: 0.7496 (mt) REVERT: B 415 MET cc_start: 0.8633 (mtp) cc_final: 0.8407 (mtm) outliers start: 20 outliers final: 7 residues processed: 126 average time/residue: 0.5483 time to fit residues: 72.5642 Evaluate side-chains 114 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain B residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.155072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.130590 restraints weight = 6797.361| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.14 r_work: 0.3317 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6888 Z= 0.143 Angle : 0.593 8.940 9350 Z= 0.300 Chirality : 0.042 0.215 1100 Planarity : 0.005 0.052 1174 Dihedral : 4.772 21.393 958 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.92 % Allowed : 18.64 % Favored : 79.44 % 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: 1.81 (0.29), residues: 896 helix: 1.88 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.93 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 23 TYR 0.035 0.002 TYR A 419 PHE 0.015 0.001 PHE A 357 TRP 0.004 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6886) covalent geometry : angle 0.58390 / 0.30 ( 9346) SS BOND : bond 0.00490 / 0.24 ( 2) SS BOND : angle 4.90148 / 2.63 ( 4) hydrogen bonds : bond 0.03815 / 2.53 ( 493) hydrogen bonds : angle 4.14519 / 2.91 ( 1461) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.248 Fit side-chains REVERT: A 19 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.7009 (mtt180) REVERT: A 224 MET cc_start: 0.8748 (mmm) cc_final: 0.8233 (mpp) REVERT: B 17 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6933 (ttp-170) REVERT: B 20 GLN cc_start: 0.7483 (mt0) cc_final: 0.6800 (mm-40) REVERT: B 30 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7925 (mttp) REVERT: B 55 LYS cc_start: 0.8251 (mttt) cc_final: 0.7757 (mptm) REVERT: B 215 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8117 (tp) REVERT: B 322 ILE cc_start: 0.7826 (mt) cc_final: 0.7555 (mt) REVERT: B 415 MET cc_start: 0.8685 (mtp) cc_final: 0.8452 (mtm) outliers start: 13 outliers final: 6 residues processed: 113 average time/residue: 0.5974 time to fit residues: 70.7639 Evaluate side-chains 113 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.161605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.138893 restraints weight = 6634.472| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.07 r_work: 0.3287 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6888 Z= 0.140 Angle : 0.590 8.009 9350 Z= 0.298 Chirality : 0.042 0.229 1100 Planarity : 0.005 0.055 1174 Dihedral : 4.766 21.286 958 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.48 % Allowed : 19.82 % Favored : 78.70 % 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: 1.83 (0.29), residues: 896 helix: 1.89 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.90 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 23 TYR 0.035 0.002 TYR A 419 PHE 0.015 0.001 PHE A 357 TRP 0.004 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6886) covalent geometry : angle 0.58292 / 0.29 ( 9346) SS BOND : bond 0.00524 / 0.26 ( 2) SS BOND : angle 4.48894 / 2.42 ( 4) hydrogen bonds : bond 0.03777 / 2.49 ( 493) hydrogen bonds : angle 4.13215 / 2.91 ( 1461) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.177 Fit side-chains REVERT: A 19 ARG cc_start: 0.7330 (mtm-85) cc_final: 0.7026 (mtt180) REVERT: A 65 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6147 (ppp) REVERT: A 224 MET cc_start: 0.8755 (mmm) cc_final: 0.8246 (mpp) REVERT: B 17 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6916 (ttp-170) REVERT: B 20 GLN cc_start: 0.7500 (mt0) cc_final: 0.6789 (mm-40) REVERT: B 30 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7930 (mttp) REVERT: B 55 LYS cc_start: 0.8249 (mttt) cc_final: 0.7765 (mptm) REVERT: B 215 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8145 (tp) REVERT: B 322 ILE cc_start: 0.7827 (mt) cc_final: 0.7559 (mt) REVERT: B 415 MET cc_start: 0.8726 (mtp) cc_final: 0.8508 (mtm) outliers start: 10 outliers final: 4 residues processed: 109 average time/residue: 0.5991 time to fit residues: 68.5198 Evaluate side-chains 109 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 79 optimal weight: 0.0970 chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.162305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.139627 restraints weight = 6612.764| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.06 r_work: 0.3297 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6888 Z= 0.133 Angle : 0.580 7.147 9350 Z= 0.292 Chirality : 0.042 0.224 1100 Planarity : 0.005 0.055 1174 Dihedral : 4.705 21.140 958 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.78 % Allowed : 19.53 % Favored : 78.70 % 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: 1.91 (0.29), residues: 896 helix: 1.94 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.85 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 23 TYR 0.034 0.002 TYR A 419 PHE 0.016 0.001 PHE B 37 TRP 0.005 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6886) covalent geometry : angle 0.57391 / 0.29 ( 9346) SS BOND : bond 0.00535 / 0.27 ( 2) SS BOND : angle 4.05138 / 2.19 ( 4) hydrogen bonds : bond 0.03704 / 2.45 ( 493) hydrogen bonds : angle 4.10027 / 2.89 ( 1461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2382.32 seconds wall clock time: 41 minutes 27.24 seconds (2487.24 seconds total)