Starting phenix.real_space_refine on Tue Mar 11 20:31:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ga1_29884/03_2025/8ga1_29884.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ga1_29884/03_2025/8ga1_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_29884/03_2025/8ga1_29884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ga1_29884/03_2025/8ga1_29884.map" model { file = "/net/cci-nas-00/data/ceres_data/8ga1_29884/03_2025/8ga1_29884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ga1_29884/03_2025/8ga1_29884.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 4.67, per 1000 atoms: 0.69 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: 1.40 Conformation dependent library (CDL) restraints added in 918.8 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: 0.66 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: 2.09 Time building geometry restraints manager: 1.70 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: 0.03 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: 0.790 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.970 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 6886 Z= 0.312 Angle : 0.846 8.990 9346 Z= 0.460 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 291 HIS 0.004 0.001 HIS B 70 PHE 0.026 0.002 PHE A 357 TYR 0.026 0.002 TYR B 419 ARG 0.005 0.000 ARG A 15 *********************** 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 : 0.742 Fit side-chains revert: symmetry clash REVERT: A 224 MET cc_start: 0.8273 (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: 1.5359 time to fit residues: 209.7641 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 : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 0.0970 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 12 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.156428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.134467 restraints weight = 6308.170| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 0.96 r_work: 0.3312 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6886 Z= 0.213 Angle : 0.631 8.130 9346 Z= 0.327 Chirality : 0.041 0.155 1100 Planarity : 0.007 0.056 1174 Dihedral : 5.220 23.237 958 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.81 % Allowed : 13.61 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.26), residues: 896 helix: -0.42 (0.18), residues: 678 sheet: None (None), residues: 0 loop : -1.44 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 PHE 0.012 0.001 PHE A 219 TYR 0.016 0.002 TYR B 419 ARG 0.003 0.000 ARG A 209 *********************** 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 131 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.720 Fit side-chains REVERT: A 19 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.6456 (mmm160) REVERT: A 167 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.6853 (mmt90) REVERT: B 20 GLN cc_start: 0.7699 (mt0) cc_final: 0.7123 (mm110) REVERT: B 55 LYS cc_start: 0.8326 (mttt) cc_final: 0.7713 (mptm) REVERT: B 321 PRO cc_start: 0.7723 (Cg_exo) cc_final: 0.7389 (Cg_endo) outliers start: 19 outliers final: 6 residues processed: 122 average time/residue: 1.2597 time to fit residues: 161.4308 Evaluate side-chains 107 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 55 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 0.0670 chunk 26 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3693 r_free = 0.3693 target = 0.157263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.135283 restraints weight = 6397.674| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 0.96 r_work: 0.3318 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6886 Z= 0.188 Angle : 0.581 7.512 9346 Z= 0.298 Chirality : 0.041 0.166 1100 Planarity : 0.005 0.052 1174 Dihedral : 4.925 23.385 958 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.96 % Allowed : 15.53 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 896 helix: 0.98 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -1.39 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 124 HIS 0.002 0.001 HIS B 284 PHE 0.012 0.001 PHE A 357 TYR 0.020 0.002 TYR A 419 ARG 0.006 0.000 ARG B 23 *********************** 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 131 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.737 Fit side-chains REVERT: A 19 ARG cc_start: 0.7357 (mtm-85) cc_final: 0.7133 (mtt180) REVERT: A 224 MET cc_start: 0.8617 (mmm) cc_final: 0.8206 (mpp) REVERT: B 55 LYS cc_start: 0.8380 (mttt) cc_final: 0.7841 (mptm) REVERT: B 321 PRO cc_start: 0.7685 (Cg_exo) cc_final: 0.7304 (Cg_endo) REVERT: B 322 ILE cc_start: 0.7830 (mt) cc_final: 0.7562 (mt) outliers start: 20 outliers final: 6 residues processed: 122 average time/residue: 1.2930 time to fit residues: 165.4306 Evaluate side-chains 111 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 78 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 329 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.0170 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 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 = 0.3727 r_free = 0.3727 target = 0.159626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.137921 restraints weight = 6417.994| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 0.96 r_work: 0.3354 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6886 Z= 0.190 Angle : 0.562 6.226 9346 Z= 0.288 Chirality : 0.041 0.165 1100 Planarity : 0.005 0.051 1174 Dihedral : 4.762 22.224 958 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.85 % Allowed : 15.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.29), residues: 896 helix: 1.54 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -1.18 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 PHE 0.013 0.001 PHE A 357 TYR 0.014 0.001 TYR B 419 ARG 0.004 0.000 ARG B 23 *********************** 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: 26 poor density : 106 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.7143 (mtt180) REVERT: A 27 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6779 (pt0) REVERT: A 167 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.6853 (mmt90) REVERT: A 224 MET cc_start: 0.8644 (mmm) cc_final: 0.8198 (mpp) REVERT: A 423 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8339 (tt) REVERT: B 17 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7115 (ttp-170) REVERT: B 20 GLN cc_start: 0.7633 (mt0) cc_final: 0.7042 (mm-40) REVERT: B 55 LYS cc_start: 0.8380 (mttt) cc_final: 0.7878 (mptm) REVERT: B 322 ILE cc_start: 0.7840 (mt) cc_final: 0.7630 (mt) outliers start: 26 outliers final: 7 residues processed: 124 average time/residue: 1.3077 time to fit residues: 170.3961 Evaluate side-chains 112 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 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 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 4 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3711 r_free = 0.3711 target = 0.158313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.136686 restraints weight = 6280.274| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 0.94 r_work: 0.3337 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6886 Z= 0.219 Angle : 0.583 7.513 9346 Z= 0.298 Chirality : 0.042 0.171 1100 Planarity : 0.005 0.051 1174 Dihedral : 4.819 21.961 958 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.11 % Allowed : 17.75 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.29), residues: 896 helix: 1.63 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.84 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 PHE 0.016 0.001 PHE A 357 TYR 0.015 0.002 TYR B 419 ARG 0.007 0.000 ARG B 23 *********************** 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 133 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6712 (mm) REVERT: A 27 GLU cc_start: 0.7500 (mm-30) cc_final: 0.6814 (pt0) REVERT: A 224 MET cc_start: 0.8662 (mmm) cc_final: 0.8206 (mpp) REVERT: A 423 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8282 (tt) REVERT: B 17 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7063 (ttp-170) REVERT: B 55 LYS cc_start: 0.8345 (mttt) cc_final: 0.7864 (mptm) REVERT: B 215 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8219 (tp) REVERT: B 322 ILE cc_start: 0.7835 (mt) cc_final: 0.7632 (mt) outliers start: 21 outliers final: 7 residues processed: 125 average time/residue: 1.2208 time to fit residues: 160.5130 Evaluate side-chains 117 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 65 MET 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 78 LEU Chi-restraints excluded: chain B residue 215 ILE 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 36 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3705 r_free = 0.3705 target = 0.157704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135890 restraints weight = 6332.838| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 0.95 r_work: 0.3330 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6886 Z= 0.231 Angle : 0.591 8.011 9346 Z= 0.302 Chirality : 0.043 0.194 1100 Planarity : 0.005 0.050 1174 Dihedral : 4.837 21.710 958 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.51 % Allowed : 18.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.29), residues: 896 helix: 1.69 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.82 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 PHE 0.017 0.001 PHE A 357 TYR 0.028 0.002 TYR A 419 ARG 0.008 0.000 ARG B 23 *********************** 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 126 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.731 Fit side-chains REVERT: A 19 ARG cc_start: 0.7432 (mtm-85) cc_final: 0.7155 (mtt180) REVERT: A 27 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6858 (pt0) REVERT: A 224 MET cc_start: 0.8666 (mmm) cc_final: 0.8200 (mpp) REVERT: B 17 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7033 (ttp-170) REVERT: B 20 GLN cc_start: 0.7588 (mt0) cc_final: 0.6956 (mm-40) REVERT: B 30 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7919 (mttp) REVERT: B 55 LYS cc_start: 0.8340 (mttt) cc_final: 0.7889 (mptm) REVERT: B 167 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7359 (mtt180) REVERT: B 215 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8215 (tp) REVERT: B 322 ILE cc_start: 0.7843 (mt) cc_final: 0.7633 (mt) REVERT: B 415 MET cc_start: 0.8573 (mtp) cc_final: 0.8365 (mtm) outliers start: 17 outliers final: 7 residues processed: 119 average time/residue: 1.3248 time to fit residues: 165.4598 Evaluate side-chains 117 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 167 ARG Chi-restraints excluded: chain B residue 215 ILE 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 81 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 80 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3719 r_free = 0.3719 target = 0.158967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.137223 restraints weight = 6318.208| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 0.94 r_work: 0.3339 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6886 Z= 0.204 Angle : 0.569 6.618 9346 Z= 0.290 Chirality : 0.042 0.184 1100 Planarity : 0.005 0.049 1174 Dihedral : 4.741 21.788 958 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.81 % Allowed : 17.90 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.29), residues: 896 helix: 1.82 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.86 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 PHE 0.014 0.001 PHE A 357 TYR 0.026 0.002 TYR A 419 ARG 0.009 0.000 ARG B 23 *********************** 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 133 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6718 (mm) REVERT: A 27 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6919 (pt0) REVERT: A 224 MET cc_start: 0.8659 (mmm) cc_final: 0.8152 (mpp) REVERT: A 455 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7888 (ttmt) REVERT: B 17 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.7074 (ttp-170) REVERT: B 20 GLN cc_start: 0.7669 (mt0) cc_final: 0.7044 (mm-40) REVERT: B 30 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7969 (mttp) REVERT: B 55 LYS cc_start: 0.8349 (mttt) cc_final: 0.7911 (mptm) REVERT: B 167 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7404 (mtt180) REVERT: B 215 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8220 (tp) REVERT: B 415 MET cc_start: 0.8572 (mtp) cc_final: 0.8329 (mtm) outliers start: 19 outliers final: 5 residues processed: 126 average time/residue: 1.2948 time to fit residues: 171.1034 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 : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 167 ARG Chi-restraints excluded: chain B residue 215 ILE 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 33 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 0.0070 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3703 r_free = 0.3703 target = 0.157773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.133322 restraints weight = 6763.994| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.15 r_work: 0.3303 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6886 Z= 0.174 Angle : 0.551 9.729 9346 Z= 0.280 Chirality : 0.041 0.173 1100 Planarity : 0.005 0.047 1174 Dihedral : 4.637 21.261 958 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.92 % Allowed : 19.08 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.29), residues: 896 helix: 2.01 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.89 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 124 HIS 0.002 0.000 HIS B 284 PHE 0.013 0.001 PHE B 328 TYR 0.022 0.002 TYR A 419 ARG 0.011 0.000 ARG B 23 *********************** 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 124 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6345 (mm) REVERT: A 27 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6668 (pt0) REVERT: A 224 MET cc_start: 0.8720 (mmm) cc_final: 0.8206 (mpp) REVERT: A 455 LYS cc_start: 0.7852 (ttmt) cc_final: 0.7586 (ttmt) REVERT: B 17 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6859 (ttp-170) REVERT: B 20 GLN cc_start: 0.7500 (mt0) cc_final: 0.6691 (mm-40) REVERT: B 55 LYS cc_start: 0.8195 (mttt) cc_final: 0.7691 (mptm) REVERT: B 167 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7322 (mtt180) REVERT: B 215 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8169 (tp) REVERT: B 415 MET cc_start: 0.8519 (mtp) cc_final: 0.8297 (mtm) outliers start: 13 outliers final: 5 residues processed: 118 average time/residue: 1.2972 time to fit residues: 160.6823 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 : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 0.0070 chunk 2 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 82 optimal weight: 0.0370 chunk 30 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3706 r_free = 0.3706 target = 0.157989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.134194 restraints weight = 6779.686| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.10 r_work: 0.3305 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6886 Z= 0.178 Angle : 0.554 7.367 9346 Z= 0.281 Chirality : 0.041 0.185 1100 Planarity : 0.005 0.051 1174 Dihedral : 4.585 20.636 958 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.92 % Allowed : 19.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.30), residues: 896 helix: 2.09 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.82 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 124 HIS 0.003 0.000 HIS B 284 PHE 0.011 0.001 PHE A 357 TYR 0.021 0.002 TYR A 419 ARG 0.012 0.000 ARG B 23 *********************** 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 122 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.746 Fit side-chains REVERT: A 19 ARG cc_start: 0.7300 (mtm-85) cc_final: 0.6987 (mtt180) REVERT: A 27 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6718 (pt0) REVERT: A 224 MET cc_start: 0.8721 (mmm) cc_final: 0.8222 (mpp) REVERT: A 455 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7668 (ttmt) REVERT: B 17 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6843 (ttp-170) REVERT: B 55 LYS cc_start: 0.8231 (mttt) cc_final: 0.7756 (mptm) REVERT: B 65 MET cc_start: 0.6945 (mmt) cc_final: 0.6709 (mmt) REVERT: B 167 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7314 (mtt180) REVERT: B 215 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8169 (tp) REVERT: B 322 ILE cc_start: 0.7775 (mt) cc_final: 0.7465 (mt) REVERT: B 415 MET cc_start: 0.8554 (mtp) cc_final: 0.8323 (mtm) outliers start: 13 outliers final: 7 residues processed: 116 average time/residue: 1.4413 time to fit residues: 176.4111 Evaluate side-chains 116 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 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 78 LEU Chi-restraints excluded: chain B residue 167 ARG 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 24 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3635 r_free = 0.3635 target = 0.151975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.127819 restraints weight = 6860.188| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.10 r_work: 0.3228 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6886 Z= 0.299 Angle : 0.653 8.233 9346 Z= 0.331 Chirality : 0.046 0.270 1100 Planarity : 0.006 0.059 1174 Dihedral : 5.000 21.815 958 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.33 % Allowed : 19.82 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.29), residues: 896 helix: 1.71 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.80 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 291 HIS 0.004 0.001 HIS B 284 PHE 0.023 0.002 PHE A 357 TYR 0.028 0.002 TYR A 419 ARG 0.012 0.001 ARG B 23 ********************** 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 108 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.679 Fit side-chains REVERT: A 19 ARG cc_start: 0.7330 (mtm-85) cc_final: 0.7039 (mtt180) REVERT: A 27 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6813 (pt0) REVERT: A 224 MET cc_start: 0.8781 (mmm) cc_final: 0.8252 (mpp) REVERT: A 423 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8233 (tt) REVERT: B 17 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6895 (ttp-170) REVERT: B 55 LYS cc_start: 0.8290 (mttt) cc_final: 0.7776 (mptm) REVERT: B 215 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8167 (tp) REVERT: B 322 ILE cc_start: 0.7896 (mt) cc_final: 0.7593 (mt) REVERT: B 415 MET cc_start: 0.8638 (mtp) cc_final: 0.8429 (mtm) outliers start: 9 outliers final: 4 residues processed: 105 average time/residue: 1.2663 time to fit residues: 139.7179 Evaluate side-chains 106 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN 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 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 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 0.1980 chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3684 r_free = 0.3684 target = 0.156121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.132451 restraints weight = 6849.664| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.09 r_work: 0.3334 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6886 Z= 0.189 Angle : 0.578 6.695 9346 Z= 0.292 Chirality : 0.042 0.218 1100 Planarity : 0.005 0.054 1174 Dihedral : 4.740 21.856 958 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.33 % Allowed : 19.82 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.29), residues: 896 helix: 1.95 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.88 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 PHE 0.017 0.001 PHE B 37 TYR 0.024 0.002 TYR A 419 ARG 0.013 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5275.19 seconds wall clock time: 90 minutes 44.02 seconds (5444.02 seconds total)