Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 18:41:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/08_2023/7pag_13269.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/08_2023/7pag_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_13269/08_2023/7pag_13269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/08_2023/7pag_13269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/08_2023/7pag_13269.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/08_2023/7pag_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-1.21rc1-5044/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 chiralities: 1 Time building chain proxies: 2.61, per 1000 atoms: 0.65 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: 1.58 Conformation dependent library (CDL) restraints added in 605.9 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: 0.34 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: 0.99 Time building geometry restraints manager: 1.73 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: 2228 17.11 - 34.22: 200 34.22 - 51.33: 45 51.33 - 68.44: 7 68.44 - 85.55: 7 Dihedral angle restraints: 2487 sinusoidal: 1009 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 2484 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 3.160 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 14.920 Find NCS groups from input model: 0.100 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.740 ------------------------------------------------------------------------------- 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 : 13.856 85.555 1504 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 % 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 *********************** 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 : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2191 time to fit residues: 24.2898 Evaluate side-chains 47 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6583 ------------------------------------------------------------------------------- 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: 4.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.0030 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 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: 0.6197 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 0.055 4136 Z= 0.295 Angle : 0.742 8.699 5611 Z= 0.390 Chirality : 0.047 0.152 604 Planarity : 0.006 0.059 738 Dihedral : 5.351 21.793 558 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 1.83 % 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: -2.05 (0.35), residues: 505 helix: 0.03 (0.72), residues: 53 sheet: -0.78 (0.33), residues: 204 loop : -2.20 (0.38), residues: 248 *********************** 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: 8 poor density : 64 time to evaluate : 0.470 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 71 average time/residue: 0.1816 time to fit residues: 15.9136 Evaluate side-chains 46 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0405 time to fit residues: 0.8757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6444 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 4136 Z= 0.352 Angle : 0.800 10.341 5611 Z= 0.426 Chirality : 0.049 0.184 604 Planarity : 0.006 0.049 738 Dihedral : 6.012 20.335 558 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer Outliers : 4.11 % 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: -2.82 (0.35), residues: 505 helix: -0.39 (0.68), residues: 59 sheet: -1.78 (0.34), residues: 201 loop : -2.27 (0.37), residues: 245 *********************** 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 72 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 64 average time/residue: 0.1979 time to fit residues: 15.5350 Evaluate side-chains 50 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0446 time to fit residues: 1.4242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.6494 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 4136 Z= 0.308 Angle : 0.794 10.687 5611 Z= 0.421 Chirality : 0.049 0.291 604 Planarity : 0.005 0.057 738 Dihedral : 5.817 23.119 558 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer Outliers : 2.05 % 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: -2.95 (0.36), residues: 505 helix: -0.32 (0.70), residues: 59 sheet: -2.12 (0.34), residues: 199 loop : -2.15 (0.38), residues: 247 *********************** 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 59 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 57 average time/residue: 0.2048 time to fit residues: 14.5819 Evaluate side-chains 47 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.477 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0407 time to fit residues: 1.0898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 0.0060 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.6260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 4136 Z= 0.184 Angle : 0.714 10.551 5611 Z= 0.363 Chirality : 0.048 0.351 604 Planarity : 0.004 0.063 738 Dihedral : 4.677 17.544 558 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.68 % 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: -2.35 (0.36), residues: 505 helix: -0.41 (0.71), residues: 59 sheet: -1.25 (0.37), residues: 197 loop : -2.07 (0.37), residues: 249 *********************** 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 51 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 50 average time/residue: 0.1692 time to fit residues: 10.7847 Evaluate side-chains 43 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.431 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.7226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.082 4136 Z= 0.468 Angle : 1.030 21.155 5611 Z= 0.555 Chirality : 0.053 0.306 604 Planarity : 0.007 0.061 738 Dihedral : 6.605 26.632 558 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 25.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.87 % Favored : 87.13 % Rotamer Outliers : 3.88 % 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: -3.36 (0.35), residues: 505 helix: -0.80 (0.68), residues: 64 sheet: -2.63 (0.32), residues: 208 loop : -2.10 (0.39), residues: 233 *********************** 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 62 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 45 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 58 average time/residue: 0.1716 time to fit residues: 12.8441 Evaluate side-chains 50 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0433 time to fit residues: 1.4707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 49 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.6455 moved from start: 0.7197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 4136 Z= 0.260 Angle : 0.861 22.936 5611 Z= 0.449 Chirality : 0.053 0.427 604 Planarity : 0.005 0.062 738 Dihedral : 5.923 21.316 558 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer Outliers : 1.37 % 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: -0.92 (0.66), residues: 64 sheet: -2.13 (0.34), residues: 201 loop : -2.03 (0.39), residues: 240 *********************** 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 50 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.1977 time to fit residues: 11.8566 Evaluate side-chains 43 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0538 time to fit residues: 0.9678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.6506 moved from start: 0.7576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 4136 Z= 0.312 Angle : 0.935 26.068 5611 Z= 0.481 Chirality : 0.054 0.465 604 Planarity : 0.005 0.059 738 Dihedral : 6.139 23.129 558 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.36), residues: 505 helix: -1.10 (0.64), residues: 64 sheet: -2.31 (0.35), residues: 203 loop : -2.04 (0.39), residues: 238 *********************** 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 50 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.2044 time to fit residues: 12.0939 Evaluate side-chains 42 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0419 time to fit residues: 0.7947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.7870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 4136 Z= 0.355 Angle : 1.021 30.147 5611 Z= 0.529 Chirality : 0.055 0.446 604 Planarity : 0.006 0.059 738 Dihedral : 6.490 25.251 558 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer Outliers : 0.68 % 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: -3.34 (0.36), residues: 505 helix: -1.07 (0.66), residues: 64 sheet: -2.58 (0.33), residues: 204 loop : -2.05 (0.39), residues: 237 *********************** 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 47 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.2029 time to fit residues: 11.7539 Evaluate side-chains 45 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.511 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0422 time to fit residues: 0.9048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 0.0980 chunk 40 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.6496 moved from start: 0.7930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 4136 Z= 0.277 Angle : 0.973 28.487 5611 Z= 0.494 Chirality : 0.054 0.435 604 Planarity : 0.005 0.057 738 Dihedral : 6.051 22.640 558 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer Outliers : 0.46 % 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: -3.28 (0.36), residues: 505 helix: -0.84 (0.69), residues: 57 sheet: -2.59 (0.32), residues: 215 loop : -1.94 (0.41), residues: 233 ********************** 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 49 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.514 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 48 average time/residue: 0.2266 time to fit residues: 13.2350 Evaluate side-chains 45 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0442 time to fit residues: 0.8165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5394 r_free = 0.5394 target = 0.354978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5317 r_free = 0.5317 target = 0.216758 restraints weight = 4339.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5268 r_free = 0.5268 target = 0.174138 restraints weight = 5204.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.166905 restraints weight = 4856.316| |-----------------------------------------------------------------------------| r_work (final): 0.4985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.8140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 4136 Z= 0.275 Angle : 0.972 27.614 5611 Z= 0.495 Chirality : 0.053 0.414 604 Planarity : 0.005 0.054 738 Dihedral : 5.995 21.399 558 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer Outliers : 0.46 % 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: -3.28 (0.36), residues: 505 helix: -1.20 (0.67), residues: 57 sheet: -2.49 (0.32), residues: 211 loop : -1.97 (0.40), residues: 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1162.95 seconds wall clock time: 21 minutes 36.10 seconds (1296.10 seconds total)