Starting phenix.real_space_refine on Fri Apr 5 19:26:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/04_2024/7pag_13269.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/04_2024/7pag_13269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/04_2024/7pag_13269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/04_2024/7pag_13269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/04_2024/7pag_13269.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/04_2024/7pag_13269.pdb" } resolution = 4.0 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 971 atoms to isotropic. 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 Ca 3 9.91 5 S 28 5.16 5 C 2504 2.51 5 N 746 2.21 5 O 759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 308": "OD1" <-> "OD2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 489": "OD1" <-> "OD2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4040 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4040 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'peptide': 509, 'undetermined': 4} Link IDs: {'PTRANS': 23, 'TRANS': 485, None: 4} Not linked: pdbres="GLY A 540 " pdbres=" CA A 601 " Not linked: pdbres=" CA A 601 " pdbres=" CA A 602 " Not linked: pdbres=" CA A 602 " pdbres=" CA A 603 " Not linked: pdbres=" CA A 603 " pdbres="NAG A 604 " Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.54, per 1000 atoms: 0.63 Number of scatterers: 4040 At special positions: 0 Unit cell: (91.12, 71.02, 171.52, 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) Ca 3 19.99 S 28 16.00 O 759 8.00 N 746 7.00 C 2504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 256 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 380 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 396 " - pdb=" SG CYS A 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 509 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 533 " 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 Links applied NAG-ASN " NAG A 604 " - " ASN A 204 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 680.4 milliseconds 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 956 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 6 sheets defined 15.1% alpha, 54.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 189 through 199 Processing helix chain 'A' and resid 204 through 219 removed outlier: 4.372A pdb=" N HIS A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.726A pdb=" N PHE A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 346 through 349 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 356 through 373 removed outlier: 3.773A pdb=" N GLN A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 3.564A pdb=" N HIS A 221 " --> pdb=" O MET A 47 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 134 removed outlier: 10.294A pdb=" N PHE A 180 " --> pdb=" O PRO A 96 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N SER A 98 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N TYR A 178 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS A 100 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET A 142 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER A 264 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 144 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN A 262 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL A 146 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU A 260 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY A 148 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN A 258 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N HIS A 150 " --> pdb=" O CYS A 256 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N CYS A 256 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS A 152 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY A 254 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ALA A 154 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU A 252 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N PHE A 156 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA A 250 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA A 158 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A 248 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS A 160 " --> pdb=" O ASN A 246 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASN A 246 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR A 162 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR A 244 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP A 164 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN A 242 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR A 166 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR A 240 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N PHE A 168 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU A 238 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER A 170 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR A 236 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR A 172 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL A 234 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU A 174 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE A 232 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ARG A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY A 230 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER A 341 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL A 226 " --> pdb=" O ASP A 339 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP A 339 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 removed outlier: 4.348A pdb=" N THR A 73 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 459 through 460 removed outlier: 4.182A pdb=" N PHE A 421 " --> pdb=" O TRP A 460 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 418 " --> pdb=" O HIS A 521 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N HIS A 521 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASN A 420 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER A 519 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 464 through 470 removed outlier: 5.188A pdb=" N ASP A 465 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 418 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A 467 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 416 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 523 " --> pdb=" O HIS A 415 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.633A pdb=" N LEU A 477 " --> pdb=" O ASP A 497 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP A 497 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 479 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER A 495 " --> pdb=" O VAL A 479 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 481 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A 491 " --> pdb=" O ASP A 483 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 405 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: 1.03 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 669 1.32 - 1.45: 1180 1.45 - 1.58: 2251 1.58 - 1.71: 0 1.71 - 1.84: 36 Bond restraints: 4136 Sorted by residual: bond pdb=" C7 NAG A 604 " pdb=" N2 NAG A 604 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C1 NAG A 604 " pdb=" O5 NAG A 604 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C5 NAG A 604 " pdb=" O5 NAG A 604 " ideal model delta sigma weight residual 1.413 1.474 -0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" C2 NAG A 604 " pdb=" N2 NAG A 604 " ideal model delta sigma weight residual 1.439 1.499 -0.060 2.00e-02 2.50e+03 9.08e+00 bond pdb=" C3 NAG A 604 " pdb=" O3 NAG A 604 " ideal model delta sigma weight residual 1.403 1.453 -0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 4131 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.19: 117 106.19 - 113.12: 2227 113.12 - 120.05: 1360 120.05 - 126.99: 1837 126.99 - 133.92: 70 Bond angle restraints: 5611 Sorted by residual: angle pdb=" N ARG A 298 " pdb=" CA ARG A 298 " pdb=" C ARG A 298 " ideal model delta sigma weight residual 109.52 101.88 7.64 1.55e+00 4.16e-01 2.43e+01 angle pdb=" CA ARG A 298 " pdb=" C ARG A 298 " pdb=" O ARG A 298 " ideal model delta sigma weight residual 121.44 116.82 4.62 1.17e+00 7.31e-01 1.56e+01 angle pdb=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 111.71 106.85 4.86 1.34e+00 5.57e-01 1.32e+01 angle pdb=" N VAL A 451 " pdb=" CA VAL A 451 " pdb=" C VAL A 451 " ideal model delta sigma weight residual 107.37 111.93 -4.56 1.48e+00 4.57e-01 9.49e+00 angle pdb=" C CYS A 396 " pdb=" N GLN A 397 " pdb=" CA GLN A 397 " ideal model delta sigma weight residual 121.54 126.90 -5.36 1.91e+00 2.74e-01 7.87e+00 ... (remaining 5606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 2246 17.11 - 34.22: 203 34.22 - 51.33: 45 51.33 - 68.44: 7 68.44 - 85.55: 7 Dihedral angle restraints: 2508 sinusoidal: 1030 harmonic: 1478 Sorted by residual: dihedral pdb=" CB CYS A 376 " pdb=" SG CYS A 376 " pdb=" SG CYS A 392 " pdb=" CB CYS A 392 " ideal model delta sinusoidal sigma weight residual -86.00 -4.35 -81.65 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CB CYS A 396 " pdb=" SG CYS A 396 " pdb=" SG CYS A 406 " pdb=" CB CYS A 406 " ideal model delta sinusoidal sigma weight residual 93.00 146.15 -53.15 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CA LEU A 359 " pdb=" C LEU A 359 " pdb=" N ARG A 360 " pdb=" CA ARG A 360 " ideal model delta harmonic sigma weight residual -180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 2505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 370 0.034 - 0.068: 156 0.068 - 0.101: 48 0.101 - 0.135: 26 0.135 - 0.169: 4 Chirality restraints: 604 Sorted by residual: chirality pdb=" CA ARG A 298 " pdb=" N ARG A 298 " pdb=" C ARG A 298 " pdb=" CB ARG A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA GLU A 446 " pdb=" N GLU A 446 " pdb=" C GLU A 446 " pdb=" CB GLU A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ILE A 232 " pdb=" N ILE A 232 " pdb=" C ILE A 232 " pdb=" CB ILE A 232 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 601 not shown) Planarity restraints: 739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 499 " 0.050 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO A 500 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 95 " -0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO A 96 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 407 " 0.041 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 408 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 408 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 408 " 0.034 5.00e-02 4.00e+02 ... (remaining 736 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 184 2.72 - 3.27: 3973 3.27 - 3.81: 6105 3.81 - 4.36: 6879 4.36 - 4.90: 12259 Nonbonded interactions: 29400 Sorted by model distance: nonbonded pdb=" OG1 THR A 320 " pdb=" OE1 GLN A 323 " model vdw 2.177 2.440 nonbonded pdb=" O TYR A 366 " pdb=" OG SER A 369 " model vdw 2.185 2.440 nonbonded pdb=" OH TYR A 366 " pdb=" NH1 ARG A 370 " model vdw 2.215 2.520 nonbonded pdb=" OE2 GLU A 395 " pdb=" OG SER A 399 " model vdw 2.222 2.440 nonbonded pdb=" O GLN A 361 " pdb=" OG SER A 364 " model vdw 2.247 2.440 ... (remaining 29395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 2.950 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.890 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 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 0.117 4136 Z= 0.316 Angle : 0.746 7.641 5611 Z= 0.411 Chirality : 0.046 0.169 604 Planarity : 0.006 0.077 738 Dihedral : 13.809 85.555 1525 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -1.70 (0.35), residues: 505 helix: -1.61 (0.67), residues: 55 sheet: 0.15 (0.33), residues: 207 loop : -2.22 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 327 HIS 0.003 0.001 HIS A 292 PHE 0.016 0.002 PHE A 447 TYR 0.012 0.001 TYR A 437 ARG 0.006 0.001 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8991 (tp) cc_final: 0.8630 (mp) REVERT: A 231 ARG cc_start: 0.7457 (ttm170) cc_final: 0.7176 (ttt180) REVERT: A 479 VAL cc_start: 0.9503 (t) cc_final: 0.9156 (p) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2205 time to fit residues: 24.5909 Evaluate side-chains 48 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.0030 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4136 Z= 0.292 Angle : 0.730 8.366 5611 Z= 0.386 Chirality : 0.047 0.150 604 Planarity : 0.006 0.058 738 Dihedral : 5.399 22.057 579 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.60 % Allowed : 9.82 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.35), residues: 505 helix: -0.06 (0.71), residues: 53 sheet: -0.88 (0.32), residues: 213 loop : -2.14 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 128 HIS 0.010 0.002 HIS A 513 PHE 0.024 0.002 PHE A 156 TYR 0.016 0.002 TYR A 166 ARG 0.008 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8096 (tpt90) cc_final: 0.7740 (tpt90) REVERT: A 169 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7333 (p0) REVERT: A 222 PHE cc_start: 0.8890 (p90) cc_final: 0.8165 (p90) REVERT: A 231 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7306 (ttt90) REVERT: A 251 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.6894 (t70) REVERT: A 343 GLU cc_start: 0.8737 (tp30) cc_final: 0.8357 (tp30) REVERT: A 479 VAL cc_start: 0.9656 (t) cc_final: 0.9147 (t) outliers start: 7 outliers final: 3 residues processed: 71 average time/residue: 0.1850 time to fit residues: 16.1995 Evaluate side-chains 51 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 320 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4136 Z= 0.268 Angle : 0.710 9.503 5611 Z= 0.371 Chirality : 0.046 0.157 604 Planarity : 0.005 0.050 738 Dihedral : 5.255 18.899 579 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.97 % Allowed : 13.01 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.35), residues: 505 helix: 0.11 (0.71), residues: 53 sheet: -1.32 (0.33), residues: 203 loop : -2.08 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 482 HIS 0.007 0.001 HIS A 365 PHE 0.017 0.002 PHE A 156 TYR 0.014 0.002 TYR A 162 ARG 0.006 0.001 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASN cc_start: 0.8251 (m-40) cc_final: 0.8001 (t0) REVERT: A 163 GLN cc_start: 0.7572 (pt0) cc_final: 0.6795 (tm-30) REVERT: A 169 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7305 (p0) REVERT: A 222 PHE cc_start: 0.8909 (p90) cc_final: 0.8249 (p90) REVERT: A 231 ARG cc_start: 0.7758 (ttm170) cc_final: 0.7241 (ttt180) REVERT: A 343 GLU cc_start: 0.8753 (tp30) cc_final: 0.8434 (tp30) REVERT: A 372 ARG cc_start: 0.7578 (ppt170) cc_final: 0.7200 (ppt170) REVERT: A 464 MET cc_start: 0.6992 (tpp) cc_final: 0.6657 (tpp) outliers start: 13 outliers final: 7 residues processed: 63 average time/residue: 0.1954 time to fit residues: 15.2490 Evaluate side-chains 54 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 4136 Z= 0.329 Angle : 0.795 10.558 5611 Z= 0.425 Chirality : 0.051 0.360 604 Planarity : 0.005 0.045 738 Dihedral : 5.823 20.831 579 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 4.34 % Allowed : 15.98 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.36), residues: 505 helix: 0.23 (0.75), residues: 53 sheet: -1.99 (0.33), residues: 213 loop : -1.93 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 482 HIS 0.007 0.002 HIS A 365 PHE 0.020 0.002 PHE A 156 TYR 0.019 0.002 TYR A 275 ARG 0.004 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 55 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 THR cc_start: 0.0718 (OUTLIER) cc_final: 0.0502 (p) REVERT: A 163 GLN cc_start: 0.7746 (pt0) cc_final: 0.7178 (tm-30) REVERT: A 217 SER cc_start: 0.8816 (t) cc_final: 0.8552 (p) REVERT: A 257 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7718 (mp) REVERT: A 279 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7699 (tm-30) REVERT: A 293 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6589 (mp10) REVERT: A 343 GLU cc_start: 0.8848 (tp30) cc_final: 0.8443 (tp30) REVERT: A 372 ARG cc_start: 0.7951 (ppt170) cc_final: 0.7455 (ppt170) REVERT: A 464 MET cc_start: 0.7266 (tpp) cc_final: 0.6724 (tpp) REVERT: A 488 TRP cc_start: 0.5017 (p90) cc_final: 0.3696 (t60) outliers start: 19 outliers final: 13 residues processed: 69 average time/residue: 0.1998 time to fit residues: 16.9838 Evaluate side-chains 65 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 49 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 0.0570 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 4136 Z= 0.341 Angle : 0.864 14.871 5611 Z= 0.461 Chirality : 0.049 0.174 604 Planarity : 0.005 0.044 738 Dihedral : 6.164 25.672 579 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 4.79 % Allowed : 16.21 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.36), residues: 505 helix: -0.06 (0.74), residues: 57 sheet: -2.41 (0.32), residues: 213 loop : -1.91 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 482 HIS 0.010 0.002 HIS A 285 PHE 0.014 0.002 PHE A 156 TYR 0.017 0.002 TYR A 166 ARG 0.003 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 48 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.6317 (tmt170) cc_final: 0.5575 (ttp80) REVERT: A 114 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: A 163 GLN cc_start: 0.7677 (pt0) cc_final: 0.7260 (tm-30) REVERT: A 217 SER cc_start: 0.8878 (t) cc_final: 0.8659 (p) REVERT: A 258 ASN cc_start: 0.7092 (OUTLIER) cc_final: 0.6441 (t0) REVERT: A 293 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6466 (mp10) REVERT: A 343 GLU cc_start: 0.9001 (tp30) cc_final: 0.8619 (tp30) REVERT: A 372 ARG cc_start: 0.7551 (ppt170) cc_final: 0.7219 (ppt170) REVERT: A 464 MET cc_start: 0.7296 (tpp) cc_final: 0.6530 (tpp) REVERT: A 477 LEU cc_start: 0.9080 (tt) cc_final: 0.8754 (mt) REVERT: A 488 TRP cc_start: 0.5291 (p90) cc_final: 0.3396 (t60) outliers start: 21 outliers final: 13 residues processed: 66 average time/residue: 0.1770 time to fit residues: 14.5531 Evaluate side-chains 61 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 20.0000 chunk 49 optimal weight: 0.0570 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 28 optimal weight: 0.0050 chunk 36 optimal weight: 9.9990 overall best weight: 2.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.6660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4136 Z= 0.271 Angle : 0.815 17.342 5611 Z= 0.430 Chirality : 0.051 0.360 604 Planarity : 0.004 0.041 738 Dihedral : 5.745 23.864 579 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 4.34 % Allowed : 17.81 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.36), residues: 505 helix: -0.14 (0.72), residues: 57 sheet: -2.11 (0.33), residues: 213 loop : -1.88 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 482 HIS 0.005 0.001 HIS A 150 PHE 0.023 0.002 PHE A 518 TYR 0.015 0.002 TYR A 275 ARG 0.004 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 49 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7821 (tt0) cc_final: 0.6956 (tm-30) REVERT: A 163 GLN cc_start: 0.7507 (pt0) cc_final: 0.7003 (tm-30) REVERT: A 169 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7436 (p0) REVERT: A 217 SER cc_start: 0.8967 (t) cc_final: 0.8729 (p) REVERT: A 279 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7486 (mp0) REVERT: A 293 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6436 (mp10) REVERT: A 343 GLU cc_start: 0.8972 (tp30) cc_final: 0.8578 (tp30) REVERT: A 372 ARG cc_start: 0.7839 (ppt170) cc_final: 0.7422 (ppt170) REVERT: A 464 MET cc_start: 0.7203 (tpp) cc_final: 0.6439 (tpp) REVERT: A 477 LEU cc_start: 0.9076 (tt) cc_final: 0.8755 (mt) REVERT: A 488 TRP cc_start: 0.5467 (p90) cc_final: 0.3408 (t60) outliers start: 19 outliers final: 11 residues processed: 61 average time/residue: 0.1964 time to fit residues: 14.6135 Evaluate side-chains 61 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.6937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4136 Z= 0.274 Angle : 0.911 28.531 5611 Z= 0.471 Chirality : 0.050 0.323 604 Planarity : 0.005 0.040 738 Dihedral : 5.691 23.549 579 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 3.88 % Allowed : 18.95 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.36), residues: 505 helix: -0.30 (0.72), residues: 57 sheet: -2.25 (0.33), residues: 213 loop : -1.83 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 482 HIS 0.007 0.001 HIS A 285 PHE 0.016 0.002 PHE A 156 TYR 0.014 0.002 TYR A 166 ARG 0.003 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 46 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 23 TYR cc_start: 0.7784 (p90) cc_final: 0.7310 (p90) REVERT: A 45 GLU cc_start: 0.7809 (tt0) cc_final: 0.7456 (tm-30) REVERT: A 163 GLN cc_start: 0.7332 (pt0) cc_final: 0.7037 (tm-30) REVERT: A 169 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7408 (p0) REVERT: A 217 SER cc_start: 0.8977 (t) cc_final: 0.8748 (p) REVERT: A 293 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6720 (mp10) REVERT: A 343 GLU cc_start: 0.8976 (tp30) cc_final: 0.8634 (tp30) REVERT: A 372 ARG cc_start: 0.7824 (ppt170) cc_final: 0.7411 (ppt170) REVERT: A 464 MET cc_start: 0.7309 (tpp) cc_final: 0.6530 (tpp) REVERT: A 477 LEU cc_start: 0.9102 (tt) cc_final: 0.8773 (mt) REVERT: A 488 TRP cc_start: 0.5632 (p90) cc_final: 0.3667 (t60) REVERT: A 490 ASP cc_start: 0.3369 (OUTLIER) cc_final: 0.2773 (t0) outliers start: 17 outliers final: 11 residues processed: 60 average time/residue: 0.1886 time to fit residues: 14.0035 Evaluate side-chains 56 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 490 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.7503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 4136 Z= 0.468 Angle : 1.112 30.808 5611 Z= 0.584 Chirality : 0.057 0.477 604 Planarity : 0.007 0.077 738 Dihedral : 6.706 27.327 579 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 25.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 5.02 % Allowed : 18.26 % Favored : 76.71 % 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: -3.72 (0.35), residues: 505 helix: -0.95 (0.65), residues: 65 sheet: -3.01 (0.32), residues: 203 loop : -2.25 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 482 HIS 0.011 0.002 HIS A 285 PHE 0.025 0.003 PHE A 518 TYR 0.032 0.003 TYR A 166 ARG 0.005 0.001 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7582 (mtm) cc_final: 0.7053 (ttp) REVERT: A 163 GLN cc_start: 0.7552 (pt0) cc_final: 0.7283 (tm-30) REVERT: A 293 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.6742 (mp10) REVERT: A 343 GLU cc_start: 0.8991 (tp30) cc_final: 0.8692 (tp30) REVERT: A 464 MET cc_start: 0.7386 (tpp) cc_final: 0.6588 (tpp) REVERT: A 477 LEU cc_start: 0.9109 (tt) cc_final: 0.8819 (mt) REVERT: A 488 TRP cc_start: 0.5912 (p90) cc_final: 0.3691 (t60) REVERT: A 490 ASP cc_start: 0.3738 (OUTLIER) cc_final: 0.2629 (t0) outliers start: 22 outliers final: 16 residues processed: 66 average time/residue: 0.1708 time to fit residues: 14.3724 Evaluate side-chains 61 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 43 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 516 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 40 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.7422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4136 Z= 0.258 Angle : 0.948 27.544 5611 Z= 0.481 Chirality : 0.054 0.443 604 Planarity : 0.004 0.039 738 Dihedral : 5.871 21.619 579 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.20 % Allowed : 21.00 % Favored : 75.80 % 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: -3.07 (0.36), residues: 505 helix: -0.39 (0.72), residues: 57 sheet: -2.49 (0.33), residues: 203 loop : -1.91 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 482 HIS 0.006 0.001 HIS A 150 PHE 0.017 0.002 PHE A 156 TYR 0.014 0.002 TYR A 162 ARG 0.007 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 279 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7497 (mp0) REVERT: A 343 GLU cc_start: 0.8980 (tp30) cc_final: 0.8757 (tm-30) REVERT: A 464 MET cc_start: 0.7301 (tpp) cc_final: 0.6540 (tpp) REVERT: A 477 LEU cc_start: 0.9103 (tt) cc_final: 0.8816 (mt) REVERT: A 488 TRP cc_start: 0.5528 (p90) cc_final: 0.3585 (t60) REVERT: A 490 ASP cc_start: 0.3653 (OUTLIER) cc_final: 0.2639 (t0) outliers start: 14 outliers final: 12 residues processed: 57 average time/residue: 0.1732 time to fit residues: 12.3990 Evaluate side-chains 53 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 490 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.7837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 4136 Z= 0.396 Angle : 1.056 27.530 5611 Z= 0.548 Chirality : 0.055 0.418 604 Planarity : 0.006 0.040 738 Dihedral : 6.578 24.941 579 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Rotamer: Outliers : 3.42 % Allowed : 21.69 % Favored : 74.89 % 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: -3.45 (0.36), residues: 505 helix: -0.46 (0.73), residues: 57 sheet: -2.93 (0.32), residues: 208 loop : -1.97 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 482 HIS 0.011 0.002 HIS A 285 PHE 0.025 0.002 PHE A 518 TYR 0.023 0.002 TYR A 166 ARG 0.010 0.001 ARG A 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7218 (mtm) cc_final: 0.6982 (ttp) REVERT: A 119 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: A 169 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.7861 (p0) REVERT: A 293 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6845 (mp10) REVERT: A 464 MET cc_start: 0.7323 (tpp) cc_final: 0.6592 (tpp) REVERT: A 477 LEU cc_start: 0.9148 (tt) cc_final: 0.8878 (mt) REVERT: A 488 TRP cc_start: 0.5768 (p90) cc_final: 0.3689 (t60) REVERT: A 490 ASP cc_start: 0.4034 (OUTLIER) cc_final: 0.2849 (t0) outliers start: 15 outliers final: 11 residues processed: 58 average time/residue: 0.1712 time to fit residues: 12.4370 Evaluate side-chains 56 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 490 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 29 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 1 optimal weight: 0.0670 chunk 32 optimal weight: 4.9990 overall best weight: 1.6524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5428 r_free = 0.5428 target = 0.359767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5370 r_free = 0.5370 target = 0.230725 restraints weight = 4391.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.5340 r_free = 0.5340 target = 0.179073 restraints weight = 4561.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.5336 r_free = 0.5336 target = 0.169867 restraints weight = 4115.278| |-----------------------------------------------------------------------------| r_work (final): 0.5014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.7763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4136 Z= 0.245 Angle : 0.939 26.844 5611 Z= 0.479 Chirality : 0.053 0.411 604 Planarity : 0.005 0.054 738 Dihedral : 5.849 25.331 579 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.97 % Allowed : 22.15 % Favored : 74.89 % 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: -3.22 (0.35), residues: 505 helix: -0.72 (0.69), residues: 63 sheet: -2.48 (0.33), residues: 208 loop : -2.06 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 482 HIS 0.005 0.001 HIS A 189 PHE 0.017 0.002 PHE A 156 TYR 0.012 0.002 TYR A 295 ARG 0.008 0.001 ARG A 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1168.01 seconds wall clock time: 21 minutes 51.35 seconds (1311.35 seconds total)