Starting phenix.real_space_refine on Wed Sep 17 07:23:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ga1_29884/09_2025/8ga1_29884.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ga1_29884/09_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_29884/09_2025/8ga1_29884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ga1_29884/09_2025/8ga1_29884.map" model { file = "/net/cci-nas-00/data/ceres_data/8ga1_29884/09_2025/8ga1_29884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ga1_29884/09_2025/8ga1_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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, 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: 1.72, per 1000 atoms: 0.25 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: 0.54 Conformation dependent library (CDL) restraints added in 383.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.17 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: 1.04 Time building geometry restraints manager: 0.74 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.560 Find NCS groups from input model: 0.100 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:7.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.590 ------------------------------------------------------------------------------- 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 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 aren 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 covalent geometry : bond 0.00501 ( 6886) covalent geometry : angle 0.84554 ( 9346) SS BOND : bond 0.00215 ( 2) SS BOND : angle 3.83170 ( 4) hydrogen bonds : bond 0.26878 ( 493) hydrogen bonds : angle 10.22363 ( 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 : 0.242 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: 0.6776 time to fit residues: 92.3916 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 : 0.186 ------------------------------------------------------------------------------- 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... 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 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 = 0.3674 r_free = 0.3674 target = 0.155616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.132379 restraints weight = 6424.120| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.04 r_work: 0.3285 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 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 : 0.004 0.048 6888 Z= 0.159 Angle : 0.641 7.656 9350 Z= 0.332 Chirality : 0.042 0.158 1100 Planarity : 0.007 0.058 1174 Dihedral : 5.258 23.266 958 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.81 % Allowed : 13.46 % Favored : 83.73 % 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 aren not related in a simple way. whole: -1.23 (0.26), residues: 896 helix: -0.47 (0.18), residues: 680 sheet: None (None), residues: 0 loop : -1.49 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.016 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 covalent geometry : bond 0.00352 ( 6886) covalent geometry : angle 0.63764 ( 9346) SS BOND : bond 0.00626 ( 2) SS BOND : angle 3.44041 ( 4) hydrogen bonds : bond 0.04654 ( 493) hydrogen bonds : angle 4.85043 ( 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 : 0.240 Fit side-chains REVERT: A 19 ARG cc_start: 0.7361 (mtm-85) cc_final: 0.6404 (mmm160) REVERT: A 167 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.6880 (mmt90) REVERT: A 423 LEU cc_start: 0.8096 (tp) cc_final: 0.7881 (tt) REVERT: B 20 GLN cc_start: 0.7724 (mt0) cc_final: 0.7101 (mm110) REVERT: B 55 LYS cc_start: 0.8345 (mttt) cc_final: 0.7727 (mptm) REVERT: B 321 PRO cc_start: 0.7744 (Cg_exo) cc_final: 0.7403 (Cg_endo) outliers start: 19 outliers final: 6 residues processed: 120 average time/residue: 0.5905 time to fit residues: 74.2264 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 : 0.219 ------------------------------------------------------------------------------- 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: 2.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 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 = 0.3669 r_free = 0.3669 target = 0.154914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.132845 restraints weight = 6374.812| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 0.96 r_work: 0.3292 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6888 Z= 0.156 Angle : 0.610 8.034 9350 Z= 0.314 Chirality : 0.043 0.173 1100 Planarity : 0.006 0.054 1174 Dihedral : 5.048 23.353 958 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.11 % Allowed : 15.53 % Favored : 81.36 % 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 aren not related in a simple way. whole: 0.46 (0.28), residues: 896 helix: 0.85 (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 0.005 0.000 ARG B 23 TYR 0.022 0.002 TYR A 419 PHE 0.016 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 covalent geometry : bond 0.00354 ( 6886) covalent geometry : angle 0.60614 ( 9346) SS BOND : bond 0.00594 ( 2) SS BOND : angle 3.33242 ( 4) hydrogen bonds : bond 0.04270 ( 493) hydrogen bonds : angle 4.45258 ( 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: 21 poor density : 109 time to evaluate : 0.249 Fit side-chains REVERT: A 19 ARG cc_start: 0.7388 (mtm-85) cc_final: 0.7171 (mtt180) REVERT: A 167 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6852 (mmt90) REVERT: A 224 MET cc_start: 0.8692 (mmm) cc_final: 0.8274 (mpp) REVERT: A 423 LEU cc_start: 0.8183 (tp) cc_final: 0.7891 (tp) REVERT: B 17 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.7041 (ttp-170) REVERT: B 55 LYS cc_start: 0.8389 (mttt) cc_final: 0.7851 (mptm) REVERT: B 321 PRO cc_start: 0.7778 (Cg_exo) cc_final: 0.7392 (Cg_endo) REVERT: B 322 ILE cc_start: 0.7866 (mt) cc_final: 0.7576 (mt) outliers start: 21 outliers final: 5 residues processed: 120 average time/residue: 0.6074 time to fit residues: 76.3734 Evaluate side-chains 108 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.158868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.137326 restraints weight = 6355.600| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 0.95 r_work: 0.3342 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6888 Z= 0.136 Angle : 0.571 6.306 9350 Z= 0.292 Chirality : 0.041 0.164 1100 Planarity : 0.005 0.052 1174 Dihedral : 4.837 22.460 958 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.40 % Allowed : 15.68 % Favored : 80.92 % 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 aren not related in a simple way. whole: 1.20 (0.29), residues: 896 helix: 1.45 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -1.19 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.011 0.001 TYR B 419 PHE 0.013 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 covalent geometry : bond 0.00304 ( 6886) covalent geometry : angle 0.56811 ( 9346) SS BOND : bond 0.00357 ( 2) SS BOND : angle 2.68850 ( 4) hydrogen bonds : bond 0.03897 ( 493) hydrogen bonds : angle 4.21935 ( 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 133 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7403 (mtm-85) cc_final: 0.7163 (mtt180) REVERT: A 167 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6806 (mmt90) REVERT: A 224 MET cc_start: 0.8656 (mmm) cc_final: 0.8234 (mpp) REVERT: A 423 LEU cc_start: 0.8248 (tp) cc_final: 0.7916 (tp) REVERT: B 20 GLN cc_start: 0.7627 (mt0) cc_final: 0.7014 (mm-40) REVERT: B 55 LYS cc_start: 0.8388 (mttt) cc_final: 0.7922 (mptm) REVERT: B 215 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8220 (tp) REVERT: B 304 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8327 (mt) REVERT: B 321 PRO cc_start: 0.7606 (Cg_exo) cc_final: 0.7191 (Cg_endo) REVERT: B 322 ILE cc_start: 0.7854 (mt) cc_final: 0.7633 (mt) outliers start: 23 outliers final: 6 residues processed: 122 average time/residue: 0.6089 time to fit residues: 77.9056 Evaluate side-chains 112 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.155921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.134097 restraints weight = 6454.342| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 0.95 r_work: 0.3308 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6888 Z= 0.179 Angle : 0.628 8.414 9350 Z= 0.321 Chirality : 0.044 0.207 1100 Planarity : 0.006 0.052 1174 Dihedral : 5.015 22.520 958 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.70 % Allowed : 16.72 % 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 aren not related in a simple way. whole: 1.30 (0.29), residues: 896 helix: 1.46 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.98 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 23 TYR 0.016 0.002 TYR B 419 PHE 0.021 0.002 PHE A 357 TRP 0.005 0.001 TRP A 124 HIS 0.004 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6886) covalent geometry : angle 0.62433 ( 9346) SS BOND : bond 0.00224 ( 2) SS BOND : angle 3.47084 ( 4) hydrogen bonds : bond 0.04209 ( 493) hydrogen bonds : angle 4.32632 ( 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 131 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7184 (mtt180) REVERT: A 65 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6265 (ppp) REVERT: A 224 MET cc_start: 0.8709 (mmm) cc_final: 0.8225 (mpp) REVERT: B 17 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.7036 (ttp-170) REVERT: B 55 LYS cc_start: 0.8364 (mttt) cc_final: 0.7913 (mptm) REVERT: B 215 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8249 (tp) REVERT: B 322 ILE cc_start: 0.7926 (mt) cc_final: 0.7675 (mt) outliers start: 25 outliers final: 7 residues processed: 123 average time/residue: 0.5960 time to fit residues: 76.7508 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 : 0.241 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 71 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.158846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.137022 restraints weight = 6455.410| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 0.96 r_work: 0.3343 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2479 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= 0.138 Angle : 0.571 7.621 9350 Z= 0.293 Chirality : 0.042 0.176 1100 Planarity : 0.005 0.050 1174 Dihedral : 4.800 22.183 958 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.11 % Allowed : 17.16 % 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 aren not related in a simple way. whole: 1.60 (0.29), residues: 896 helix: 1.75 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.05 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 23 TYR 0.011 0.001 TYR B 419 PHE 0.013 0.001 PHE A 307 TRP 0.005 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6886) covalent geometry : angle 0.56744 ( 9346) SS BOND : bond 0.00498 ( 2) SS BOND : angle 3.07796 ( 4) hydrogen bonds : bond 0.03841 ( 493) hydrogen bonds : angle 4.15911 ( 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 129 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6683 (mm) REVERT: A 224 MET cc_start: 0.8611 (mmm) cc_final: 0.8117 (mpp) REVERT: B 17 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7045 (ttp-170) REVERT: B 20 GLN cc_start: 0.7584 (mt0) cc_final: 0.6946 (mm-40) REVERT: B 30 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7938 (mttp) REVERT: B 55 LYS cc_start: 0.8332 (mttt) cc_final: 0.7869 (mptm) REVERT: B 167 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7343 (mtt180) REVERT: B 215 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8203 (tp) REVERT: B 415 MET cc_start: 0.8621 (mtp) cc_final: 0.8392 (mtm) outliers start: 21 outliers final: 6 residues processed: 121 average time/residue: 0.5955 time to fit residues: 75.3867 Evaluate side-chains 114 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 83 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.160556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.138392 restraints weight = 6565.961| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.02 r_work: 0.3279 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2531 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= 0.144 Angle : 0.576 6.641 9350 Z= 0.294 Chirality : 0.042 0.197 1100 Planarity : 0.005 0.050 1174 Dihedral : 4.781 21.755 958 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.40 % Allowed : 17.16 % 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 aren not related in a simple way. whole: 1.72 (0.29), residues: 896 helix: 1.82 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -0.95 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 23 TYR 0.017 0.002 TYR A 419 PHE 0.015 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 covalent geometry : bond 0.00331 ( 6886) covalent geometry : angle 0.57353 ( 9346) SS BOND : bond 0.00490 ( 2) SS BOND : angle 2.82934 ( 4) hydrogen bonds : bond 0.03861 ( 493) hydrogen bonds : angle 4.15835 ( 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 132 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6503 (mm) REVERT: A 65 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6108 (ppp) REVERT: A 224 MET cc_start: 0.8739 (mmm) cc_final: 0.8219 (mpp) REVERT: A 423 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8375 (tt) REVERT: B 17 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6950 (ttp-170) REVERT: B 30 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7899 (mttp) REVERT: B 55 LYS cc_start: 0.8269 (mttt) cc_final: 0.7786 (mptm) REVERT: B 167 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7157 (mtt180) REVERT: B 215 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8206 (tp) REVERT: B 321 PRO cc_start: 0.7613 (Cg_exo) cc_final: 0.7179 (Cg_endo) REVERT: B 415 MET cc_start: 0.8553 (mtp) cc_final: 0.8307 (mtm) outliers start: 23 outliers final: 6 residues processed: 123 average time/residue: 0.5938 time to fit residues: 76.5693 Evaluate side-chains 115 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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 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 167 ARG Chi-restraints excluded: chain B residue 178 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: 0.7980 chunk 76 optimal weight: 0.0170 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.156756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.132949 restraints weight = 6803.818| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.09 r_work: 0.3298 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6888 Z= 0.130 Angle : 0.570 9.288 9350 Z= 0.290 Chirality : 0.041 0.180 1100 Planarity : 0.005 0.048 1174 Dihedral : 4.719 21.604 958 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.66 % Allowed : 18.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.29), residues: 896 helix: 1.95 (0.21), residues: 674 sheet: None (None), residues: 0 loop : -0.94 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 23 TYR 0.023 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 covalent geometry : bond 0.00292 ( 6886) covalent geometry : angle 0.56290 ( 9346) SS BOND : bond 0.00722 ( 2) SS BOND : angle 4.50425 ( 4) hydrogen bonds : bond 0.03708 ( 493) hydrogen bonds : angle 4.10342 ( 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 126 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6417 (mm) REVERT: A 224 MET cc_start: 0.8736 (mmm) cc_final: 0.8234 (mpp) REVERT: A 423 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8346 (tt) REVERT: B 17 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6866 (ttp-170) REVERT: B 20 GLN cc_start: 0.7492 (mt0) cc_final: 0.6753 (mm-40) REVERT: B 30 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7906 (mttp) REVERT: B 55 LYS cc_start: 0.8243 (mttt) cc_final: 0.7754 (mptm) REVERT: B 167 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7339 (mtt180) REVERT: B 215 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8167 (tp) REVERT: B 304 LEU cc_start: 0.8453 (tp) cc_final: 0.8252 (mt) REVERT: B 322 ILE cc_start: 0.7822 (mt) cc_final: 0.7545 (mt) REVERT: B 415 MET cc_start: 0.8544 (mtp) cc_final: 0.8314 (mtm) outliers start: 18 outliers final: 8 residues processed: 120 average time/residue: 0.6141 time to fit residues: 77.2890 Evaluate side-chains 116 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 167 ARG Chi-restraints excluded: chain B residue 178 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: 0.7980 chunk 83 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.155956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.131792 restraints weight = 6787.883| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.11 r_work: 0.3271 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6888 Z= 0.139 Angle : 0.583 8.616 9350 Z= 0.296 Chirality : 0.042 0.215 1100 Planarity : 0.005 0.051 1174 Dihedral : 4.740 21.142 958 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.81 % Allowed : 18.49 % 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 aren not related in a simple way. 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 ARG 0.012 0.000 ARG B 23 TYR 0.026 0.002 TYR A 419 PHE 0.014 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 covalent geometry : bond 0.00320 ( 6886) covalent geometry : angle 0.57464 ( 9346) SS BOND : bond 0.00474 ( 2) SS BOND : angle 4.73662 ( 4) hydrogen bonds : bond 0.03779 ( 493) hydrogen bonds : angle 4.11668 ( 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 124 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6384 (mm) REVERT: A 65 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.5989 (ppp) REVERT: A 224 MET cc_start: 0.8729 (mmm) cc_final: 0.8217 (mpp) REVERT: A 423 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8325 (tt) REVERT: B 17 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6926 (ttp-170) REVERT: B 20 GLN cc_start: 0.7478 (mt0) cc_final: 0.6747 (mm-40) REVERT: B 30 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7927 (mttp) REVERT: B 55 LYS cc_start: 0.8191 (mttt) cc_final: 0.7673 (mptm) REVERT: B 177 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8088 (mp) REVERT: B 215 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8146 (tp) REVERT: B 322 ILE cc_start: 0.7804 (mt) cc_final: 0.7530 (mt) REVERT: B 415 MET cc_start: 0.8560 (mtp) cc_final: 0.8320 (mtm) outliers start: 19 outliers final: 6 residues processed: 117 average time/residue: 0.6337 time to fit residues: 77.6506 Evaluate side-chains 116 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 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 177 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.155247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.129354 restraints weight = 6515.479| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.19 r_work: 0.3265 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6888 Z= 0.138 Angle : 0.585 7.722 9350 Z= 0.296 Chirality : 0.042 0.226 1100 Planarity : 0.005 0.055 1174 Dihedral : 4.742 21.111 958 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.22 % Allowed : 19.23 % Favored : 78.55 % 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 aren not related in a simple way. whole: 1.91 (0.29), residues: 896 helix: 1.95 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.87 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 23 TYR 0.023 0.002 TYR A 419 PHE 0.015 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 covalent geometry : bond 0.00315 ( 6886) covalent geometry : angle 0.57795 ( 9346) SS BOND : bond 0.00505 ( 2) SS BOND : angle 4.33375 ( 4) hydrogen bonds : bond 0.03758 ( 493) hydrogen bonds : angle 4.11349 ( 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 119 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6348 (mm) REVERT: A 65 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.5952 (ppp) REVERT: A 224 MET cc_start: 0.8729 (mmm) cc_final: 0.8212 (mpp) REVERT: A 423 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8267 (tt) REVERT: B 17 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6888 (ttp-170) REVERT: B 20 GLN cc_start: 0.7415 (mt0) cc_final: 0.6611 (mm-40) REVERT: B 30 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7882 (mttp) REVERT: B 55 LYS cc_start: 0.8150 (mttt) cc_final: 0.7609 (mptm) REVERT: B 177 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8056 (mp) REVERT: B 215 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8108 (tp) REVERT: B 322 ILE cc_start: 0.7757 (mt) cc_final: 0.7479 (mt) REVERT: B 415 MET cc_start: 0.8533 (mtp) cc_final: 0.8330 (mtm) outliers start: 15 outliers final: 6 residues processed: 116 average time/residue: 0.6171 time to fit residues: 74.9909 Evaluate side-chains 113 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 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 177 LEU Chi-restraints excluded: chain B residue 178 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: 0.4980 chunk 4 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 85 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.156288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.131577 restraints weight = 6754.285| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.14 r_work: 0.3280 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2721 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= 0.134 Angle : 0.586 8.794 9350 Z= 0.294 Chirality : 0.042 0.217 1100 Planarity : 0.005 0.056 1174 Dihedral : 4.711 21.086 958 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.07 % Allowed : 19.38 % Favored : 78.55 % 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 aren not related in a simple way. whole: 1.97 (0.29), residues: 896 helix: 1.98 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.83 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 23 TYR 0.022 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 covalent geometry : bond 0.00302 ( 6886) covalent geometry : angle 0.58067 ( 9346) SS BOND : bond 0.00512 ( 2) SS BOND : angle 4.02247 ( 4) hydrogen bonds : bond 0.03725 ( 493) hydrogen bonds : angle 4.10560 ( 1461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2607.11 seconds wall clock time: 45 minutes 12.73 seconds (2712.73 seconds total)