Starting phenix.real_space_refine on Tue Feb 13 15:38:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga1_29884/02_2024/8ga1_29884.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga1_29884/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga1_29884/02_2024/8ga1_29884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga1_29884/02_2024/8ga1_29884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga1_29884/02_2024/8ga1_29884.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ga1_29884/02_2024/8ga1_29884.pdb" } 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 Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ASP 29": "OD1" <-> "OD2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B ASP 171": "OD1" <-> "OD2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "B PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B ASP 417": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.23, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 2.61 Conformation dependent library (CDL) restraints added in 1.5 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: 0.65 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: 1.86 Time building geometry restraints manager: 2.85 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: 99.77 - 106.63: 202 106.63 - 113.49: 3727 113.49 - 120.35: 2783 120.35 - 127.21: 2567 127.21 - 134.08: 67 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 2.440 nonbonded pdb=" O ARG B 147 " pdb=" OG1 THR B 151 " model vdw 2.294 2.440 nonbonded pdb=" OE1 GLU A 148 " pdb=" O HOH A 601 " model vdw 2.304 2.440 nonbonded pdb=" O VAL A 144 " pdb=" O HOH A 602 " model vdw 2.320 2.440 nonbonded pdb=" OH TYR B 94 " pdb=" OG SER B 350 " model vdw 2.320 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 3.680 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.430 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.910 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.651 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: 1.4748 time to fit residues: 201.2772 Evaluate side-chains 91 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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: 0.8980 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 81 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6886 Z= 0.205 Angle : 0.621 7.453 9346 Z= 0.322 Chirality : 0.041 0.154 1100 Planarity : 0.007 0.056 1174 Dihedral : 5.218 23.119 958 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.51 % Allowed : 14.35 % Favored : 83.14 % 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: -1.16 (0.26), residues: 896 helix: -0.42 (0.18), residues: 678 sheet: None (None), residues: 0 loop : -1.45 (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 B 219 TYR 0.015 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 128 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.744 Fit side-chains REVERT: A 19 ARG cc_start: 0.7048 (mtm-85) cc_final: 0.6694 (mmm160) REVERT: A 167 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6705 (mmt90) REVERT: B 55 LYS cc_start: 0.8170 (mttt) cc_final: 0.7898 (mmtp) outliers start: 17 outliers final: 6 residues processed: 120 average time/residue: 1.2645 time to fit residues: 159.3739 Evaluate side-chains 108 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 65 optimal weight: 0.0870 chunk 80 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 20 GLN B 157 ASN B 191 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6886 Z= 0.186 Angle : 0.575 7.487 9346 Z= 0.295 Chirality : 0.041 0.166 1100 Planarity : 0.005 0.052 1174 Dihedral : 4.886 23.264 958 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.40 % Allowed : 14.94 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.28), residues: 896 helix: 1.01 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.41 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 124 HIS 0.002 0.001 HIS B 284 PHE 0.013 0.001 PHE A 357 TYR 0.014 0.001 TYR B 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 132 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.853 Fit side-chains REVERT: A 19 ARG cc_start: 0.7074 (mtm-85) cc_final: 0.6848 (mtt180) REVERT: A 224 MET cc_start: 0.8306 (mmm) cc_final: 0.7899 (mpp) REVERT: B 17 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7157 (ttp-170) REVERT: B 55 LYS cc_start: 0.8215 (mttt) cc_final: 0.7859 (mptm) REVERT: B 177 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8142 (mp) REVERT: B 321 PRO cc_start: 0.7582 (Cg_exo) cc_final: 0.7285 (Cg_endo) REVERT: B 322 ILE cc_start: 0.7842 (mt) cc_final: 0.7614 (mt) outliers start: 23 outliers final: 6 residues processed: 123 average time/residue: 1.2523 time to fit residues: 161.7500 Evaluate side-chains 111 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 17 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 329 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.1522 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.2315 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= 0.248 Angle : 0.608 6.510 9346 Z= 0.310 Chirality : 0.043 0.181 1100 Planarity : 0.005 0.053 1174 Dihedral : 4.955 20.575 958 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.88 % Allowed : 14.20 % 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 (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: 1.12 (0.29), residues: 896 helix: 1.32 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.04 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 124 HIS 0.004 0.001 HIS B 284 PHE 0.020 0.002 PHE A 357 TYR 0.021 0.002 TYR A 419 ARG 0.005 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 139 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6880 (mm) REVERT: A 65 MET cc_start: 0.6279 (OUTLIER) cc_final: 0.5909 (ppp) REVERT: A 224 MET cc_start: 0.8339 (mmm) cc_final: 0.7876 (mpp) REVERT: A 423 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8315 (tt) REVERT: A 442 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7893 (mtmt) REVERT: B 18 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7497 (ttp-170) REVERT: B 30 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7970 (mmmm) REVERT: B 55 LYS cc_start: 0.8198 (mttt) cc_final: 0.7906 (mptm) REVERT: B 321 PRO cc_start: 0.7651 (Cg_exo) cc_final: 0.7324 (Cg_endo) REVERT: B 417 ASP cc_start: 0.6841 (m-30) cc_final: 0.6533 (m-30) outliers start: 33 outliers final: 10 residues processed: 129 average time/residue: 1.2289 time to fit residues: 166.7349 Evaluate side-chains 119 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 226 THR 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 A residue 442 LYS Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 164 ASP 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: 1.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8145 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6886 Z= 0.211 Angle : 0.575 7.555 9346 Z= 0.294 Chirality : 0.042 0.173 1100 Planarity : 0.005 0.052 1174 Dihedral : 4.842 21.867 958 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.85 % Allowed : 15.83 % Favored : 80.33 % 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: 1.47 (0.29), residues: 896 helix: 1.58 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.93 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 PHE 0.016 0.001 PHE A 307 TYR 0.029 0.002 TYR A 419 ARG 0.008 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 134 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.771 Fit side-chains REVERT: A 19 ARG cc_start: 0.7043 (mtm-85) cc_final: 0.6790 (mtt180) REVERT: A 224 MET cc_start: 0.8335 (mmm) cc_final: 0.7880 (mpp) REVERT: B 55 LYS cc_start: 0.8191 (mttt) cc_final: 0.7928 (mptm) REVERT: B 321 PRO cc_start: 0.7613 (Cg_exo) cc_final: 0.7250 (Cg_endo) REVERT: B 322 ILE cc_start: 0.7872 (mt) cc_final: 0.7666 (mt) REVERT: B 417 ASP cc_start: 0.6793 (m-30) cc_final: 0.6508 (m-30) outliers start: 26 outliers final: 12 residues processed: 125 average time/residue: 1.2460 time to fit residues: 163.6574 Evaluate side-chains 120 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 226 THR 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 B residue 71 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 164 ASP 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: 0.9980 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.8139 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6886 Z= 0.207 Angle : 0.572 7.486 9346 Z= 0.291 Chirality : 0.042 0.177 1100 Planarity : 0.005 0.051 1174 Dihedral : 4.773 21.816 958 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.11 % Allowed : 16.57 % Favored : 80.33 % 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: 1.69 (0.29), residues: 896 helix: 1.74 (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 0.006 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 PHE 0.015 0.001 PHE A 357 TYR 0.034 0.002 TYR A 419 ARG 0.009 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 129 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.778 Fit side-chains REVERT: A 19 ARG cc_start: 0.7050 (mtm-85) cc_final: 0.6790 (mtt180) REVERT: A 65 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5902 (ppp) REVERT: A 224 MET cc_start: 0.8315 (mmm) cc_final: 0.7893 (mpp) REVERT: B 55 LYS cc_start: 0.8191 (mttt) cc_final: 0.7939 (mptm) REVERT: B 321 PRO cc_start: 0.7607 (Cg_exo) cc_final: 0.7222 (Cg_endo) REVERT: B 415 MET cc_start: 0.8533 (mtp) cc_final: 0.8271 (mtm) outliers start: 21 outliers final: 9 residues processed: 125 average time/residue: 1.2731 time to fit residues: 167.2152 Evaluate side-chains 113 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 226 THR 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 71 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 164 ASP 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: 0.7980 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.0670 chunk 51 optimal weight: 5.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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: 0.8122 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6886 Z= 0.193 Angle : 0.557 6.255 9346 Z= 0.284 Chirality : 0.041 0.186 1100 Planarity : 0.005 0.051 1174 Dihedral : 4.686 21.220 958 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.40 % Allowed : 16.42 % Favored : 80.18 % 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: 1.88 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.88 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 PHE 0.013 0.001 PHE A 357 TYR 0.034 0.002 TYR A 419 ARG 0.010 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 131 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 0.751 Fit side-chains REVERT: A 19 ARG cc_start: 0.7052 (mtm-85) cc_final: 0.6785 (mtt180) REVERT: A 65 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.5914 (ppp) REVERT: A 224 MET cc_start: 0.8313 (mmm) cc_final: 0.7818 (mpp) REVERT: B 55 LYS cc_start: 0.8144 (mttt) cc_final: 0.7915 (mptm) REVERT: B 215 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8018 (tp) REVERT: B 321 PRO cc_start: 0.7537 (Cg_exo) cc_final: 0.7210 (Cg_endo) REVERT: B 415 MET cc_start: 0.8592 (mtp) cc_final: 0.8285 (mtm) outliers start: 23 outliers final: 9 residues processed: 127 average time/residue: 1.3446 time to fit residues: 179.6288 Evaluate side-chains 113 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 226 THR 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 71 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 164 ASP 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: 0.9980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 0.0170 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6886 Z= 0.193 Angle : 0.570 9.703 9346 Z= 0.288 Chirality : 0.041 0.180 1100 Planarity : 0.005 0.050 1174 Dihedral : 4.701 20.962 958 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.81 % Allowed : 17.16 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.92 (0.29), residues: 896 helix: 1.97 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.92 (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 0.035 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 124 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.779 Fit side-chains REVERT: A 19 ARG cc_start: 0.7062 (mtm-85) cc_final: 0.6789 (mtt180) REVERT: A 65 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.5907 (ppp) REVERT: A 224 MET cc_start: 0.8286 (mmm) cc_final: 0.7825 (mpp) REVERT: B 55 LYS cc_start: 0.8133 (mttt) cc_final: 0.7914 (mptm) REVERT: B 167 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6989 (mtt180) REVERT: B 215 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7998 (tp) REVERT: B 321 PRO cc_start: 0.7519 (Cg_exo) cc_final: 0.7188 (Cg_endo) REVERT: B 415 MET cc_start: 0.8577 (mtp) cc_final: 0.8271 (mtm) outliers start: 19 outliers final: 9 residues processed: 117 average time/residue: 1.2182 time to fit residues: 149.9314 Evaluate side-chains 115 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 414 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 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: 0.8129 moved from start: 0.2635 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= 0.210 Angle : 0.584 8.218 9346 Z= 0.294 Chirality : 0.042 0.213 1100 Planarity : 0.005 0.053 1174 Dihedral : 4.743 21.137 958 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.66 % Allowed : 17.90 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.29), residues: 896 helix: 1.91 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.75 (0.45), 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 0.013 0.001 PHE A 357 TYR 0.037 0.002 TYR A 419 ARG 0.012 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6824 (mm) REVERT: A 65 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.5925 (ppp) REVERT: A 224 MET cc_start: 0.8312 (mmm) cc_final: 0.7848 (mpp) REVERT: B 55 LYS cc_start: 0.8140 (mttt) cc_final: 0.7928 (mptm) REVERT: B 167 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6972 (mtt180) REVERT: B 215 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.7967 (tp) REVERT: B 322 ILE cc_start: 0.7885 (mt) cc_final: 0.7650 (mt) REVERT: B 415 MET cc_start: 0.8596 (mtp) cc_final: 0.8306 (mtm) outliers start: 18 outliers final: 10 residues processed: 119 average time/residue: 1.2263 time to fit residues: 154.6893 Evaluate side-chains 115 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 226 THR 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 71 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 414 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8118 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6886 Z= 0.201 Angle : 0.579 6.610 9346 Z= 0.291 Chirality : 0.042 0.219 1100 Planarity : 0.005 0.055 1174 Dihedral : 4.704 20.930 958 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.51 % Allowed : 17.90 % 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 (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: 1.90 (0.29), residues: 896 helix: 1.95 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.91 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 124 HIS 0.003 0.001 HIS B 284 PHE 0.013 0.001 PHE B 37 TYR 0.036 0.002 TYR A 419 ARG 0.013 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 119 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6812 (mm) REVERT: A 65 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5912 (ppp) REVERT: A 224 MET cc_start: 0.8308 (mmm) cc_final: 0.7863 (mpp) REVERT: B 19 ARG cc_start: 0.7574 (mtt90) cc_final: 0.7366 (mtt-85) REVERT: B 55 LYS cc_start: 0.8133 (mttt) cc_final: 0.7923 (mptm) REVERT: B 167 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6943 (mtt180) REVERT: B 215 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7984 (tp) REVERT: B 322 ILE cc_start: 0.7861 (mt) cc_final: 0.7653 (mt) REVERT: B 415 MET cc_start: 0.8599 (mtp) cc_final: 0.8302 (mtm) outliers start: 17 outliers final: 11 residues processed: 114 average time/residue: 1.3395 time to fit residues: 160.2500 Evaluate side-chains 116 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 226 THR 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 71 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 414 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.7980 chunk 10 optimal weight: 0.0010 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.159513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.138080 restraints weight = 6331.188| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 0.93 r_work: 0.3356 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 0.045 6886 Z= 0.195 Angle : 0.582 8.260 9346 Z= 0.290 Chirality : 0.042 0.221 1100 Planarity : 0.005 0.054 1174 Dihedral : 4.668 20.749 958 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.51 % Allowed : 18.05 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.29), residues: 896 helix: 1.99 (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 0.017 0.001 PHE B 37 TYR 0.037 0.002 TYR A 419 ARG 0.013 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3002.52 seconds wall clock time: 54 minutes 6.87 seconds (3246.87 seconds total)