Starting phenix.real_space_refine on Mon Mar 11 02:57:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnx_24582/03_2024/7rnx_24582.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnx_24582/03_2024/7rnx_24582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnx_24582/03_2024/7rnx_24582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnx_24582/03_2024/7rnx_24582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnx_24582/03_2024/7rnx_24582.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnx_24582/03_2024/7rnx_24582.pdb" } resolution = 3.42 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= 0.061 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4438 2.51 5 N 1140 2.21 5 O 1140 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 ARG 18": "NH1" <-> "NH2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 385": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6758 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3379 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain: "B" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3379 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Time building chain proxies: 4.03, per 1000 atoms: 0.60 Number of scatterers: 6758 At special positions: 0 Unit cell: (76.65, 75.6, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1140 8.00 N 1140 7.00 C 4438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.33 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: 44 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 removed outlier: 3.739A pdb=" N ARG A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 71 removed outlier: 4.182A pdb=" N THR A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 101 removed outlier: 4.101A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 115 through 118 removed outlier: 3.512A pdb=" N ASP A 118 " --> pdb=" O ALA A 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 115 through 118' Processing helix chain 'A' and resid 123 through 126 Processing helix chain 'A' and resid 127 through 141 Processing helix chain 'A' and resid 148 through 166 Processing helix chain 'A' and resid 170 through 191 removed outlier: 4.144A pdb=" N ARG A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 removed outlier: 3.749A pdb=" N GLY A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 233 removed outlier: 3.945A pdb=" N ILE A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 280 removed outlier: 3.885A pdb=" N TYR A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 4.007A pdb=" N ASP A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.972A pdb=" N HIS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 Processing helix chain 'A' and resid 329 through 348 Processing helix chain 'A' and resid 357 through 379 removed outlier: 4.430A pdb=" N LEU A 363 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 387 through 393 Processing helix chain 'A' and resid 393 through 401 removed outlier: 4.369A pdb=" N LEU A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 421 through 438 Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.503A pdb=" N LEU A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 26 Processing helix chain 'B' and resid 32 through 71 removed outlier: 4.124A pdb=" N LEU B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 4.389A pdb=" N LEU B 89 " --> pdb=" O CYS B 85 " (cutoff:3.500A) 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 167 removed outlier: 4.126A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 191 removed outlier: 3.719A pdb=" N HIS B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 201 removed outlier: 3.681A pdb=" N ILE B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 233 removed outlier: 3.542A pdb=" N VAL B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 251 removed outlier: 3.516A pdb=" N THR B 251 " --> pdb=" O PRO B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 252 through 280 Proline residue: B 267 - end of helix removed outlier: 4.355A pdb=" N ASP B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.936A pdb=" N HIS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 308 Processing helix chain 'B' and resid 319 through 324 removed outlier: 3.713A pdb=" N THR B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 349 removed outlier: 3.795A pdb=" N VAL B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 379 removed outlier: 4.119A pdb=" N ALA B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 363 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 removed outlier: 4.020A pdb=" N PHE B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 404 through 415 Processing helix chain 'B' and resid 421 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.723A pdb=" N GLN B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1425 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: 1.82 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1714 1.33 - 1.45: 1284 1.45 - 1.57: 3830 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6902 Sorted by residual: bond pdb=" C TYR B 75 " pdb=" N PRO B 76 " ideal model delta sigma weight residual 1.335 1.387 -0.051 1.36e-02 5.41e+03 1.43e+01 bond pdb=" CB CYS B 347 " pdb=" SG CYS B 347 " ideal model delta sigma weight residual 1.808 1.706 0.102 3.30e-02 9.18e+02 9.48e+00 bond pdb=" CG LEU A 430 " pdb=" CD2 LEU A 430 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.30e+00 bond pdb=" CB THR A 407 " pdb=" CG2 THR A 407 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.15e+00 bond pdb=" CB VAL B 42 " pdb=" CG2 VAL B 42 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.72e+00 ... (remaining 6897 not shown) Histogram of bond angle deviations from ideal: 97.42 - 104.93: 145 104.93 - 112.43: 3424 112.43 - 119.94: 2862 119.94 - 127.44: 2869 127.44 - 134.95: 66 Bond angle restraints: 9366 Sorted by residual: angle pdb=" C LYS B 30 " pdb=" N THR B 31 " pdb=" CA THR B 31 " ideal model delta sigma weight residual 120.69 134.95 -14.26 2.95e+00 1.15e-01 2.34e+01 angle pdb=" C ASN B 74 " pdb=" N TYR B 75 " pdb=" CA TYR B 75 " ideal model delta sigma weight residual 120.09 125.38 -5.29 1.25e+00 6.40e-01 1.79e+01 angle pdb=" C PHE B 232 " pdb=" N ASN B 233 " pdb=" CA ASN B 233 " ideal model delta sigma weight residual 122.67 117.67 5.00 1.47e+00 4.63e-01 1.16e+01 angle pdb=" CG1 ILE A 426 " pdb=" CB ILE A 426 " pdb=" CG2 ILE A 426 " ideal model delta sigma weight residual 110.70 100.76 9.94 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CA LEU A 198 " pdb=" CB LEU A 198 " pdb=" CG LEU A 198 " ideal model delta sigma weight residual 116.30 105.13 11.17 3.50e+00 8.16e-02 1.02e+01 ... (remaining 9361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 3550 16.82 - 33.63: 373 33.63 - 50.45: 72 50.45 - 67.27: 11 67.27 - 84.09: 6 Dihedral angle restraints: 4012 sinusoidal: 1524 harmonic: 2488 Sorted by residual: dihedral pdb=" CA PRO A 359 " pdb=" C PRO A 359 " pdb=" N MET A 360 " pdb=" CA MET A 360 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA LEU B 435 " pdb=" C LEU B 435 " pdb=" N ALA B 436 " pdb=" CA ALA B 436 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA THR B 211 " pdb=" C THR B 211 " pdb=" N LEU B 212 " pdb=" CA LEU B 212 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 668 0.049 - 0.098: 304 0.098 - 0.148: 93 0.148 - 0.197: 29 0.197 - 0.246: 8 Chirality restraints: 1102 Sorted by residual: chirality pdb=" CB ILE A 356 " pdb=" CA ILE A 356 " pdb=" CG1 ILE A 356 " pdb=" CG2 ILE A 356 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+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 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE A 112 " pdb=" CA ILE A 112 " pdb=" CG1 ILE A 112 " pdb=" CG2 ILE A 112 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1099 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 31 " -0.051 5.00e-02 4.00e+02 7.64e-02 9.33e+00 pdb=" N PRO A 32 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 109 " 0.051 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO B 110 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 266 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO B 267 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " 0.038 5.00e-02 4.00e+02 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1763 2.79 - 3.32: 6193 3.32 - 3.85: 11338 3.85 - 4.37: 13230 4.37 - 4.90: 23378 Nonbonded interactions: 55902 Sorted by model distance: nonbonded pdb=" OH TYR A 94 " pdb=" OG SER A 350 " model vdw 2.266 2.440 nonbonded pdb=" OG SER A 86 " pdb=" O GLY A 141 " model vdw 2.279 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OE1 GLU B 385 " model vdw 2.281 2.440 nonbonded pdb=" O VAL B 412 " pdb=" OG1 THR B 416 " model vdw 2.308 2.440 nonbonded pdb=" OH TYR A 419 " pdb=" OE1 GLU B 414 " model vdw 2.313 2.440 ... (remaining 55897 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: 0.400 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: 1.930 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.890 Find NCS groups from input model: 0.320 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.013 0.106 6902 Z= 0.818 Angle : 1.071 14.261 9366 Z= 0.561 Chirality : 0.064 0.246 1102 Planarity : 0.009 0.076 1176 Dihedral : 14.183 84.087 2440 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.44 % Allowed : 10.47 % Favored : 89.09 % 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: -4.11 (0.21), residues: 896 helix: -2.39 (0.14), residues: 670 sheet: None (None), residues: 0 loop : -3.15 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 124 HIS 0.007 0.002 HIS A 284 PHE 0.035 0.003 PHE A 357 TYR 0.038 0.003 TYR A 419 ARG 0.004 0.001 ARG B 120 *********************** 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 95 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.720 Fit side-chains REVERT: A 136 LEU cc_start: 0.8036 (tp) cc_final: 0.7813 (tt) REVERT: A 224 MET cc_start: 0.8224 (mmm) cc_final: 0.7959 (mmt) REVERT: B 240 ASP cc_start: 0.7938 (t0) cc_final: 0.7200 (p0) outliers start: 3 outliers final: 0 residues processed: 95 average time/residue: 0.2159 time to fit residues: 26.8627 Evaluate side-chains 76 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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: 1.9990 chunk 68 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 20 GLN B 157 ASN B 234 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6902 Z= 0.168 Angle : 0.507 5.708 9366 Z= 0.261 Chirality : 0.038 0.128 1102 Planarity : 0.006 0.056 1176 Dihedral : 4.299 22.199 960 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.77 % Allowed : 15.04 % Favored : 83.19 % 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: -1.22 (0.27), residues: 896 helix: -0.12 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -2.89 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 124 HIS 0.003 0.001 HIS A 234 PHE 0.015 0.001 PHE B 307 TYR 0.008 0.001 TYR B 419 ARG 0.005 0.000 ARG B 23 *********************** 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 103 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.701 Fit side-chains REVERT: A 360 MET cc_start: 0.8417 (mtp) cc_final: 0.8189 (mtm) REVERT: B 240 ASP cc_start: 0.7856 (t0) cc_final: 0.7293 (p0) outliers start: 12 outliers final: 5 residues processed: 101 average time/residue: 0.1895 time to fit residues: 25.8361 Evaluate side-chains 84 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain B residue 212 LEU 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: 0.9980 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 0.0050 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6902 Z= 0.177 Angle : 0.492 5.687 9366 Z= 0.251 Chirality : 0.038 0.125 1102 Planarity : 0.005 0.052 1176 Dihedral : 4.010 22.382 960 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.77 % Allowed : 16.67 % Favored : 81.56 % 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: 0.03 (0.29), residues: 896 helix: 0.79 (0.21), residues: 674 sheet: None (None), residues: 0 loop : -2.32 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 59 HIS 0.002 0.000 HIS A 234 PHE 0.021 0.001 PHE A 307 TYR 0.011 0.001 TYR A 419 ARG 0.005 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 94 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.698 Fit side-chains REVERT: A 12 GLN cc_start: 0.3240 (OUTLIER) cc_final: 0.1698 (pp30) REVERT: A 360 MET cc_start: 0.8453 (mtp) cc_final: 0.8235 (mtm) REVERT: B 240 ASP cc_start: 0.7806 (t0) cc_final: 0.7290 (p0) outliers start: 12 outliers final: 11 residues processed: 91 average time/residue: 0.1576 time to fit residues: 20.3065 Evaluate side-chains 91 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 388 THR 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: 0.9990 chunk 9 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 0.0170 chunk 72 optimal weight: 0.0870 chunk 49 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6902 Z= 0.155 Angle : 0.466 5.700 9366 Z= 0.238 Chirality : 0.038 0.125 1102 Planarity : 0.004 0.050 1176 Dihedral : 3.803 21.672 960 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.10 % Allowed : 16.96 % Favored : 79.94 % 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: 0.66 (0.29), residues: 896 helix: 1.24 (0.21), residues: 678 sheet: None (None), residues: 0 loop : -2.11 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 59 HIS 0.003 0.000 HIS A 234 PHE 0.015 0.001 PHE A 307 TYR 0.007 0.001 TYR A 419 ARG 0.006 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 107 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.726 Fit side-chains REVERT: A 12 GLN cc_start: 0.3359 (OUTLIER) cc_final: 0.1876 (pp30) REVERT: A 38 MET cc_start: 0.8156 (mmt) cc_final: 0.7463 (mmt) REVERT: A 111 GLU cc_start: 0.7836 (tp30) cc_final: 0.7419 (tm-30) REVERT: B 100 TYR cc_start: 0.8509 (m-10) cc_final: 0.8139 (m-10) REVERT: B 154 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8220 (mt) REVERT: B 240 ASP cc_start: 0.7784 (t0) cc_final: 0.7280 (p0) outliers start: 21 outliers final: 15 residues processed: 104 average time/residue: 0.1602 time to fit residues: 23.3296 Evaluate side-chains 97 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 0.0170 chunk 17 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6902 Z= 0.173 Angle : 0.474 5.647 9366 Z= 0.240 Chirality : 0.039 0.122 1102 Planarity : 0.004 0.048 1176 Dihedral : 3.734 21.672 960 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.24 % Allowed : 17.26 % Favored : 79.50 % 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: 0.93 (0.30), residues: 896 helix: 1.41 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 59 HIS 0.003 0.000 HIS A 234 PHE 0.016 0.001 PHE A 307 TYR 0.008 0.001 TYR B 419 ARG 0.004 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 105 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.758 Fit side-chains REVERT: A 12 GLN cc_start: 0.3170 (OUTLIER) cc_final: 0.1810 (pp30) REVERT: A 111 GLU cc_start: 0.7838 (tp30) cc_final: 0.7537 (tm-30) REVERT: B 154 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8233 (mt) REVERT: B 240 ASP cc_start: 0.7761 (t0) cc_final: 0.7245 (p0) outliers start: 22 outliers final: 14 residues processed: 101 average time/residue: 0.1717 time to fit residues: 24.0575 Evaluate side-chains 95 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6902 Z= 0.243 Angle : 0.520 5.766 9366 Z= 0.261 Chirality : 0.040 0.140 1102 Planarity : 0.004 0.048 1176 Dihedral : 3.827 23.734 960 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.10 % Allowed : 18.29 % Favored : 78.61 % 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: 0.94 (0.29), residues: 896 helix: 1.40 (0.21), residues: 682 sheet: None (None), residues: 0 loop : -1.92 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 59 HIS 0.004 0.001 HIS A 234 PHE 0.017 0.001 PHE A 307 TYR 0.011 0.001 TYR B 419 ARG 0.004 0.000 ARG A 403 *********************** 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 104 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.768 Fit side-chains REVERT: A 12 GLN cc_start: 0.3174 (OUTLIER) cc_final: 0.1728 (pp30) REVERT: A 38 MET cc_start: 0.8185 (mmt) cc_final: 0.7923 (mmt) REVERT: A 111 GLU cc_start: 0.7847 (tp30) cc_final: 0.7605 (tm-30) REVERT: B 154 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8238 (mt) REVERT: B 240 ASP cc_start: 0.7896 (t0) cc_final: 0.7336 (p0) outliers start: 21 outliers final: 15 residues processed: 101 average time/residue: 0.1505 time to fit residues: 21.7703 Evaluate side-chains 97 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 388 THR 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: 3.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 54 optimal weight: 0.0870 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6902 Z= 0.179 Angle : 0.493 7.267 9366 Z= 0.246 Chirality : 0.039 0.125 1102 Planarity : 0.004 0.047 1176 Dihedral : 3.756 23.920 960 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.54 % Allowed : 17.55 % Favored : 78.91 % 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 (0.29), residues: 896 helix: 1.55 (0.21), residues: 682 sheet: None (None), residues: 0 loop : -1.84 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 59 HIS 0.003 0.000 HIS A 234 PHE 0.019 0.001 PHE A 307 TYR 0.009 0.001 TYR B 100 ARG 0.004 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 107 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.3193 (OUTLIER) cc_final: 0.1831 (pp30) REVERT: A 38 MET cc_start: 0.8156 (mmt) cc_final: 0.7836 (mmt) REVERT: A 103 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7658 (pp20) REVERT: A 111 GLU cc_start: 0.7854 (tp30) cc_final: 0.7450 (tm-30) REVERT: B 154 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8211 (mt) REVERT: B 240 ASP cc_start: 0.7920 (t0) cc_final: 0.7368 (p0) outliers start: 24 outliers final: 17 residues processed: 104 average time/residue: 0.1582 time to fit residues: 23.0669 Evaluate side-chains 100 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6902 Z= 0.268 Angle : 0.548 8.293 9366 Z= 0.272 Chirality : 0.041 0.140 1102 Planarity : 0.004 0.047 1176 Dihedral : 3.883 23.842 960 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.69 % Allowed : 17.70 % Favored : 78.61 % 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: 1.05 (0.29), residues: 896 helix: 1.46 (0.21), residues: 682 sheet: None (None), residues: 0 loop : -1.80 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 59 HIS 0.004 0.001 HIS A 234 PHE 0.019 0.001 PHE A 307 TYR 0.012 0.001 TYR A 419 ARG 0.004 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 108 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.728 Fit side-chains REVERT: A 12 GLN cc_start: 0.3332 (OUTLIER) cc_final: 0.1868 (pp30) REVERT: A 103 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7615 (pp20) REVERT: A 111 GLU cc_start: 0.7929 (tp30) cc_final: 0.7519 (tm-30) REVERT: B 154 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8228 (mt) REVERT: B 219 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7504 (t80) REVERT: B 240 ASP cc_start: 0.7989 (t0) cc_final: 0.7388 (p0) outliers start: 25 outliers final: 16 residues processed: 105 average time/residue: 0.1621 time to fit residues: 24.0432 Evaluate side-chains 102 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6902 Z= 0.180 Angle : 0.507 8.159 9366 Z= 0.252 Chirality : 0.039 0.130 1102 Planarity : 0.004 0.047 1176 Dihedral : 3.792 24.064 960 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.24 % Allowed : 18.44 % Favored : 78.32 % 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: 1.25 (0.29), residues: 896 helix: 1.61 (0.21), residues: 682 sheet: None (None), residues: 0 loop : -1.75 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 59 HIS 0.004 0.000 HIS A 234 PHE 0.020 0.001 PHE A 307 TYR 0.008 0.001 TYR A 419 ARG 0.004 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 106 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.3259 (OUTLIER) cc_final: 0.1817 (pp30) REVERT: A 38 MET cc_start: 0.8019 (mmt) cc_final: 0.7794 (mmm) REVERT: A 103 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7616 (pp20) REVERT: A 111 GLU cc_start: 0.7869 (tp30) cc_final: 0.7479 (tm-30) REVERT: B 154 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8209 (mt) REVERT: B 240 ASP cc_start: 0.8004 (t0) cc_final: 0.7432 (p0) outliers start: 22 outliers final: 18 residues processed: 103 average time/residue: 0.1614 time to fit residues: 23.3377 Evaluate side-chains 103 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 76 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6902 Z= 0.177 Angle : 0.503 7.963 9366 Z= 0.250 Chirality : 0.039 0.130 1102 Planarity : 0.004 0.047 1176 Dihedral : 3.720 23.951 960 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.69 % Allowed : 17.99 % Favored : 78.32 % 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: 1.33 (0.29), residues: 896 helix: 1.67 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -1.76 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 59 HIS 0.005 0.000 HIS A 234 PHE 0.021 0.001 PHE A 307 TYR 0.014 0.001 TYR B 100 ARG 0.004 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 112 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.3466 (OUTLIER) cc_final: 0.1935 (pp30) REVERT: A 103 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7649 (pp20) REVERT: A 111 GLU cc_start: 0.7795 (tp30) cc_final: 0.7397 (tm-30) REVERT: B 154 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8204 (mt) REVERT: B 240 ASP cc_start: 0.7951 (t0) cc_final: 0.7448 (p0) outliers start: 25 outliers final: 20 residues processed: 109 average time/residue: 0.1645 time to fit residues: 25.0227 Evaluate side-chains 106 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.129424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.106880 restraints weight = 8004.136| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.36 r_work: 0.3000 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6902 Z= 0.205 Angle : 0.533 9.510 9366 Z= 0.262 Chirality : 0.040 0.174 1102 Planarity : 0.004 0.047 1176 Dihedral : 3.767 25.946 960 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.24 % Allowed : 18.44 % Favored : 78.32 % 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: 1.31 (0.29), residues: 896 helix: 1.65 (0.21), residues: 682 sheet: None (None), residues: 0 loop : -1.71 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 59 HIS 0.005 0.001 HIS A 234 PHE 0.020 0.001 PHE A 307 TYR 0.009 0.001 TYR A 419 ARG 0.004 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1489.89 seconds wall clock time: 28 minutes 1.83 seconds (1681.83 seconds total)