Starting phenix.real_space_refine on Thu Dec 7 21:51:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/12_2023/7pag_13269.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/12_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_13269/12_2023/7pag_13269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/12_2023/7pag_13269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/12_2023/7pag_13269.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pag_13269/12_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-1.21rc1-5172/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: 2.68, per 1000 atoms: 0.66 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 695.5 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: 0.40 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: 1.11 Time building geometry restraints manager: 1.70 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: 1.010 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: 3.030 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.920 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- 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 : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2149 time to fit residues: 23.9569 Evaluate side-chains 47 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5800 ------------------------------------------------------------------------------- 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: 0.6200 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4136 Z= 0.294 Angle : 0.740 8.368 5611 Z= 0.389 Chirality : 0.047 0.150 604 Planarity : 0.006 0.059 738 Dihedral : 5.360 22.010 579 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.83 % Allowed : 9.82 % Favored : 88.36 % 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: -2.04 (0.35), residues: 505 helix: 0.07 (0.72), residues: 53 sheet: -0.84 (0.32), residues: 213 loop : -2.15 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 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 0.007 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 71 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.518 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 70 average time/residue: 0.1747 time to fit residues: 15.1991 Evaluate side-chains 47 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.453 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0410 time to fit residues: 0.8718 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.6346 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4136 Z= 0.281 Angle : 0.727 9.922 5611 Z= 0.382 Chirality : 0.047 0.158 604 Planarity : 0.005 0.050 738 Dihedral : 5.396 17.866 579 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.97 % Allowed : 12.79 % Favored : 84.25 % 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: -2.46 (0.35), residues: 505 helix: -0.25 (0.69), residues: 59 sheet: -1.29 (0.35), residues: 191 loop : -2.24 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 482 HIS 0.006 0.002 HIS A 513 PHE 0.017 0.002 PHE A 156 TYR 0.013 0.002 TYR A 275 ARG 0.004 0.001 ARG A 360 *********************** 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 70 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 62 average time/residue: 0.2084 time to fit residues: 15.6876 Evaluate side-chains 48 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0472 time to fit residues: 1.1547 ------------------------------------------------------------------------------- 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: 7.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 4136 Z= 0.302 Angle : 0.775 10.600 5611 Z= 0.412 Chirality : 0.050 0.355 604 Planarity : 0.005 0.059 738 Dihedral : 5.588 22.236 579 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.97 % Allowed : 16.67 % Favored : 80.37 % 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: -2.70 (0.36), residues: 505 helix: -0.28 (0.69), residues: 59 sheet: -1.80 (0.34), residues: 208 loop : -2.08 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 482 HIS 0.006 0.002 HIS A 285 PHE 0.019 0.002 PHE A 168 TYR 0.016 0.002 TYR A 275 ARG 0.004 0.001 ARG A 372 *********************** 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 62 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 59 average time/residue: 0.1941 time to fit residues: 14.1062 Evaluate side-chains 49 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0395 time to fit residues: 1.1089 ------------------------------------------------------------------------------- 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: 8.9990 chunk 20 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.6920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 4136 Z= 0.444 Angle : 0.977 16.353 5611 Z= 0.527 Chirality : 0.052 0.218 604 Planarity : 0.006 0.064 738 Dihedral : 6.650 27.914 579 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 24.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 2.97 % Allowed : 16.44 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.35), residues: 505 helix: -0.70 (0.68), residues: 63 sheet: -2.69 (0.32), residues: 208 loop : -2.16 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 482 HIS 0.013 0.002 HIS A 285 PHE 0.037 0.003 PHE A 168 TYR 0.027 0.002 TYR A 166 ARG 0.006 0.001 ARG A 370 *********************** 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 56 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 53 average time/residue: 0.1587 time to fit residues: 10.8650 Evaluate side-chains 48 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0375 time to fit residues: 1.1425 ------------------------------------------------------------------------------- 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: 10.0000 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6569 moved from start: 0.7274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 4136 Z= 0.407 Angle : 0.983 20.409 5611 Z= 0.526 Chirality : 0.056 0.478 604 Planarity : 0.006 0.061 738 Dihedral : 6.569 29.154 579 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 2.28 % Allowed : 20.09 % Favored : 77.63 % Cbeta Deviations : 0.21 % 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: -3.64 (0.35), residues: 505 helix: -0.94 (0.66), residues: 63 sheet: -2.86 (0.32), residues: 199 loop : -2.30 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 482 HIS 0.009 0.002 HIS A 285 PHE 0.033 0.003 PHE A 168 TYR 0.023 0.002 TYR A 166 ARG 0.004 0.001 ARG A 360 *********************** 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 51 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 0.1687 time to fit residues: 10.4174 Evaluate side-chains 43 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.497 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0513 time to fit residues: 1.0653 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 0.0010 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4136 Z= 0.289 Angle : 0.938 24.720 5611 Z= 0.487 Chirality : 0.055 0.487 604 Planarity : 0.005 0.062 738 Dihedral : 5.960 23.093 579 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 1.60 % Allowed : 21.00 % Favored : 77.40 % 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: -3.38 (0.35), residues: 505 helix: -0.94 (0.66), residues: 63 sheet: -2.56 (0.32), residues: 208 loop : -2.15 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 482 HIS 0.006 0.001 HIS A 150 PHE 0.023 0.002 PHE A 518 TYR 0.016 0.002 TYR A 166 ARG 0.004 0.000 ARG A 360 *********************** 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: 7 poor density : 43 time to evaluate : 0.474 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.1874 time to fit residues: 11.5922 Evaluate side-chains 44 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.446 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0422 time to fit residues: 1.0678 ------------------------------------------------------------------------------- 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: 0.0470 chunk 4 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 35 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- 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: 0.6447 moved from start: 0.7426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4136 Z= 0.250 Angle : 0.898 25.853 5611 Z= 0.463 Chirality : 0.053 0.443 604 Planarity : 0.005 0.058 738 Dihedral : 5.602 21.406 579 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.46 % Allowed : 21.23 % Favored : 78.31 % 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: -3.08 (0.35), residues: 505 helix: -0.58 (0.70), residues: 57 sheet: -2.30 (0.33), residues: 206 loop : -2.05 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 482 HIS 0.006 0.001 HIS A 189 PHE 0.017 0.002 PHE A 156 TYR 0.011 0.002 TYR A 162 ARG 0.004 0.000 ARG A 360 *********************** 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 43 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.474 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 43 average time/residue: 0.2001 time to fit residues: 10.7538 Evaluate side-chains 36 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.471 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0405 time to fit residues: 0.8090 ------------------------------------------------------------------------------- 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: 4.9990 chunk 43 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.6580 moved from start: 0.7896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 4136 Z= 0.387 Angle : 1.010 27.044 5611 Z= 0.529 Chirality : 0.056 0.462 604 Planarity : 0.006 0.057 738 Dihedral : 6.516 27.547 579 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 1.37 % Allowed : 22.15 % Favored : 76.48 % 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 (0.34), residues: 505 helix: -1.45 (0.63), residues: 64 sheet: -2.81 (0.32), residues: 203 loop : -2.29 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 482 HIS 0.010 0.002 HIS A 285 PHE 0.035 0.003 PHE A 168 TYR 0.020 0.002 TYR A 166 ARG 0.006 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 50 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.491 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 48 average time/residue: 0.2040 time to fit residues: 12.1457 Evaluate side-chains 43 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.466 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0436 time to fit residues: 1.0105 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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: 0.6491 moved from start: 0.7880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4136 Z= 0.267 Angle : 0.973 29.093 5611 Z= 0.497 Chirality : 0.053 0.435 604 Planarity : 0.005 0.054 738 Dihedral : 5.903 22.676 579 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 0.00 % Allowed : 23.29 % 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: -3.46 (0.35), residues: 505 helix: -1.42 (0.65), residues: 63 sheet: -2.54 (0.32), residues: 206 loop : -2.16 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 482 HIS 0.005 0.001 HIS A 189 PHE 0.020 0.002 PHE A 156 TYR 0.015 0.002 TYR A 162 ARG 0.006 0.001 ARG A 213 ********************** 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 45 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.464 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1974 time to fit residues: 10.9633 Evaluate side-chains 37 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4743 ------------------------------------------------------------------------------- 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: 1.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 = 0.5377 r_free = 0.5377 target = 0.350006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.211142 restraints weight = 4380.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5226 r_free = 0.5226 target = 0.172395 restraints weight = 5101.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5213 r_free = 0.5213 target = 0.166267 restraints weight = 5897.659| |-----------------------------------------------------------------------------| r_work (final): 0.4976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.8200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 4136 Z= 0.351 Angle : 1.047 28.497 5611 Z= 0.538 Chirality : 0.055 0.435 604 Planarity : 0.006 0.051 738 Dihedral : 6.410 25.708 579 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 0.91 % Allowed : 22.83 % Favored : 76.26 % 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: -3.67 (0.35), residues: 505 helix: -1.52 (0.65), residues: 63 sheet: -2.83 (0.31), residues: 208 loop : -2.12 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 482 HIS 0.008 0.001 HIS A 189 PHE 0.030 0.003 PHE A 168 TYR 0.018 0.002 TYR A 166 ARG 0.006 0.001 ARG A 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1090.60 seconds wall clock time: 20 minutes 36.16 seconds (1236.16 seconds total)