Starting phenix.real_space_refine on Fri Dec 27 20:33:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ga1_29884/12_2024/8ga1_29884.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ga1_29884/12_2024/8ga1_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_29884/12_2024/8ga1_29884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ga1_29884/12_2024/8ga1_29884.map" model { file = "/net/cci-nas-00/data/ceres_data/8ga1_29884/12_2024/8ga1_29884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ga1_29884/12_2024/8ga1_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-5532/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: 4.90, per 1000 atoms: 0.72 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: 1.78 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.73 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: 2.04 Time building geometry restraints manager: 2.06 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: 0.00 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: 1.070 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.480 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.920 ------------------------------------------------------------------------------- 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 : 0.682 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: 1.6404 time to fit residues: 223.7415 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 : 0.773 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.855 Fit side-chains REVERT: A 19 ARG cc_start: 0.7053 (mtm-85) cc_final: 0.6696 (mmm160) REVERT: A 167 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6722 (mmt90) REVERT: B 55 LYS cc_start: 0.8160 (mttt) cc_final: 0.7714 (mptm) REVERT: B 321 PRO cc_start: 0.7550 (Cg_exo) cc_final: 0.7277 (Cg_endo) outliers start: 19 outliers final: 6 residues processed: 122 average time/residue: 1.3839 time to fit residues: 177.1785 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 : 0.751 ------------------------------------------------------------------------------- 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 45 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 0.0070 chunk 81 optimal weight: 0.0670 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 20 GLN B 157 ASN B 191 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6886 Z= 0.170 Angle : 0.566 7.072 9346 Z= 0.291 Chirality : 0.040 0.162 1100 Planarity : 0.005 0.051 1174 Dihedral : 4.848 23.358 958 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.40 % Allowed : 15.38 % Favored : 81.21 % 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: 0.67 (0.28), residues: 896 helix: 1.07 (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 0.000 HIS B 284 PHE 0.010 0.001 PHE A 357 TYR 0.019 0.001 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 136 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7027 (mtm-85) cc_final: 0.6798 (mtt180) REVERT: A 204 MET cc_start: 0.8238 (mtp) cc_final: 0.8022 (mmt) REVERT: A 224 MET cc_start: 0.8268 (mmm) cc_final: 0.7910 (mpp) REVERT: A 455 LYS cc_start: 0.8335 (ttmt) cc_final: 0.8067 (ttmt) REVERT: B 55 LYS cc_start: 0.8200 (mttt) cc_final: 0.7873 (mptm) REVERT: B 321 PRO cc_start: 0.7499 (Cg_exo) cc_final: 0.7188 (Cg_endo) outliers start: 23 outliers final: 5 residues processed: 126 average time/residue: 1.4032 time to fit residues: 185.6656 Evaluate side-chains 110 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6886 Z= 0.170 Angle : 0.547 6.113 9346 Z= 0.280 Chirality : 0.040 0.162 1100 Planarity : 0.005 0.050 1174 Dihedral : 4.652 22.327 958 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.96 % Allowed : 15.98 % Favored : 81.07 % 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: 1.45 (0.29), residues: 896 helix: 1.65 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -1.17 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 124 HIS 0.002 0.001 HIS B 284 PHE 0.012 0.001 PHE A 357 TYR 0.014 0.001 TYR A 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 129 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7005 (mtm-85) cc_final: 0.6767 (mtt180) REVERT: A 224 MET cc_start: 0.8293 (mmm) cc_final: 0.7900 (mpp) REVERT: A 455 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8055 (ttmt) REVERT: B 55 LYS cc_start: 0.8167 (mttt) cc_final: 0.7900 (mptm) REVERT: B 321 PRO cc_start: 0.7311 (Cg_exo) cc_final: 0.7045 (Cg_endo) outliers start: 20 outliers final: 6 residues processed: 122 average time/residue: 1.3901 time to fit residues: 177.7419 Evaluate side-chains 110 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 245 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7698 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2484 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= 0.207 Angle : 0.574 7.410 9346 Z= 0.293 Chirality : 0.042 0.167 1100 Planarity : 0.005 0.051 1174 Dihedral : 4.741 21.908 958 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.22 % Allowed : 18.05 % 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 (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: 1.68 (0.29), residues: 896 helix: 1.72 (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 130 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6898 (mm) REVERT: A 224 MET cc_start: 0.8341 (mmm) cc_final: 0.7880 (mpp) REVERT: A 455 LYS cc_start: 0.8378 (ttmt) cc_final: 0.8115 (ttmt) REVERT: B 215 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8016 (tp) REVERT: B 321 PRO cc_start: 0.7444 (Cg_exo) cc_final: 0.7096 (Cg_endo) REVERT: B 322 ILE cc_start: 0.7864 (mt) cc_final: 0.7597 (mt) REVERT: B 415 MET cc_start: 0.8440 (mtp) cc_final: 0.8174 (mtm) outliers start: 15 outliers final: 6 residues processed: 124 average time/residue: 1.3368 time to fit residues: 174.2835 Evaluate side-chains 113 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 245 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2493 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= 0.226 Angle : 0.588 7.186 9346 Z= 0.301 Chirality : 0.043 0.184 1100 Planarity : 0.005 0.050 1174 Dihedral : 4.789 21.925 958 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.81 % Allowed : 17.46 % 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 (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: 1.71 (0.29), residues: 896 helix: 1.73 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.76 (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 0.018 0.001 PHE A 357 TYR 0.017 0.002 TYR B 419 ARG 0.005 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 124 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.802 Fit side-chains REVERT: A 19 ARG cc_start: 0.7034 (mtm-85) cc_final: 0.6777 (mtt180) REVERT: A 224 MET cc_start: 0.8359 (mmm) cc_final: 0.7859 (mpp) REVERT: A 423 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8260 (tt) REVERT: B 215 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8020 (tp) REVERT: B 321 PRO cc_start: 0.7550 (Cg_exo) cc_final: 0.7165 (Cg_endo) REVERT: B 322 ILE cc_start: 0.7871 (mt) cc_final: 0.7655 (mt) REVERT: B 415 MET cc_start: 0.8615 (mtp) cc_final: 0.8288 (mtm) outliers start: 19 outliers final: 8 residues processed: 118 average time/residue: 1.2907 time to fit residues: 160.5582 Evaluate side-chains 111 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 245 SER 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 78 LEU 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 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6886 Z= 0.282 Angle : 0.635 8.915 9346 Z= 0.323 Chirality : 0.045 0.233 1100 Planarity : 0.006 0.052 1174 Dihedral : 4.971 22.128 958 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % 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 (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: 1.52 (0.29), residues: 896 helix: 1.60 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.83 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 291 HIS 0.004 0.001 HIS B 284 PHE 0.022 0.002 PHE A 357 TYR 0.021 0.002 TYR A 419 ARG 0.006 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 120 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6913 (mm) REVERT: A 224 MET cc_start: 0.8355 (mmm) cc_final: 0.7853 (mpp) REVERT: A 423 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8269 (tt) REVERT: B 215 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8010 (tp) REVERT: B 321 PRO cc_start: 0.7680 (Cg_exo) cc_final: 0.7311 (Cg_endo) REVERT: B 322 ILE cc_start: 0.7940 (mt) cc_final: 0.7730 (mt) REVERT: B 415 MET cc_start: 0.8523 (mtp) cc_final: 0.8250 (mtm) outliers start: 18 outliers final: 5 residues processed: 116 average time/residue: 1.3564 time to fit residues: 165.8359 Evaluate side-chains 109 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 238 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 423 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6886 Z= 0.209 Angle : 0.581 7.029 9346 Z= 0.296 Chirality : 0.042 0.196 1100 Planarity : 0.005 0.051 1174 Dihedral : 4.792 22.114 958 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.37 % Allowed : 18.49 % 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: 1.73 (0.29), residues: 896 helix: 1.79 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.85 (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 0.031 0.002 TYR A 419 ARG 0.010 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 125 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6896 (mm) REVERT: A 224 MET cc_start: 0.8332 (mmm) cc_final: 0.7815 (mpp) REVERT: A 423 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8271 (tt) REVERT: B 167 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6798 (mtt180) REVERT: B 215 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8005 (tp) REVERT: B 321 PRO cc_start: 0.7592 (Cg_exo) cc_final: 0.7206 (Cg_endo) REVERT: B 415 MET cc_start: 0.8538 (mtp) cc_final: 0.8225 (mtm) outliers start: 16 outliers final: 3 residues processed: 120 average time/residue: 1.3180 time to fit residues: 167.4855 Evaluate side-chains 109 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 423 LEU 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 80 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6886 Z= 0.213 Angle : 0.598 11.831 9346 Z= 0.304 Chirality : 0.042 0.217 1100 Planarity : 0.005 0.051 1174 Dihedral : 4.816 21.749 958 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.07 % Allowed : 18.93 % 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: 1.81 (0.29), residues: 896 helix: 1.87 (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 0.003 0.001 HIS B 284 PHE 0.014 0.001 PHE A 357 TYR 0.036 0.002 TYR A 419 ARG 0.014 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 120 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6882 (mm) REVERT: A 224 MET cc_start: 0.8312 (mmm) cc_final: 0.7822 (mpp) REVERT: B 167 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6763 (mtt180) REVERT: B 215 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7996 (tp) REVERT: B 321 PRO cc_start: 0.7494 (Cg_exo) cc_final: 0.7168 (Cg_endo) REVERT: B 415 MET cc_start: 0.8565 (mtp) cc_final: 0.8276 (mtm) outliers start: 14 outliers final: 4 residues processed: 117 average time/residue: 1.3163 time to fit residues: 161.9818 Evaluate side-chains 110 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 304 LEU 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 249 CYS 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 40 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6886 Z= 0.217 Angle : 0.602 10.788 9346 Z= 0.305 Chirality : 0.043 0.228 1100 Planarity : 0.005 0.056 1174 Dihedral : 4.810 21.639 958 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.18 % Allowed : 19.82 % 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: 1.82 (0.29), residues: 896 helix: 1.87 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.87 (0.45), 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 0.037 0.002 TYR A 419 ARG 0.015 0.000 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 109 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.757 Fit side-chains REVERT: A 19 ARG cc_start: 0.7046 (mtm-85) cc_final: 0.6776 (mtt180) REVERT: A 65 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5893 (ppp) REVERT: A 224 MET cc_start: 0.8317 (mmm) cc_final: 0.7834 (mpp) REVERT: B 215 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7964 (tp) REVERT: B 321 PRO cc_start: 0.7577 (Cg_exo) cc_final: 0.7213 (Cg_endo) REVERT: B 322 ILE cc_start: 0.7910 (mt) cc_final: 0.7673 (mt) REVERT: B 415 MET cc_start: 0.8609 (mtp) cc_final: 0.8323 (mtm) outliers start: 8 outliers final: 3 residues processed: 107 average time/residue: 1.3499 time to fit residues: 151.5905 Evaluate side-chains 108 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.0870 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.157659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.133484 restraints weight = 6730.035| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.12 r_work: 0.3354 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2785 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= 0.182 Angle : 0.565 8.357 9346 Z= 0.287 Chirality : 0.041 0.196 1100 Planarity : 0.005 0.050 1174 Dihedral : 4.648 21.392 958 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.48 % Allowed : 19.38 % 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: 2.01 (0.29), residues: 896 helix: 2.01 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.80 (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 0.016 0.001 PHE B 37 TYR 0.032 0.002 TYR A 419 ARG 0.015 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3078.19 seconds wall clock time: 56 minutes 6.31 seconds (3366.31 seconds total)