Starting phenix.real_space_refine on Wed Mar 12 18:46:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsk_30835/03_2025/7dsk_30835_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsk_30835/03_2025/7dsk_30835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dsk_30835/03_2025/7dsk_30835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsk_30835/03_2025/7dsk_30835.map" model { file = "/net/cci-nas-00/data/ceres_data/7dsk_30835/03_2025/7dsk_30835_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsk_30835/03_2025/7dsk_30835_neut.cif" } resolution = 2.9 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 27 5.16 5 C 4936 2.51 5 N 1191 2.21 5 O 1369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7524 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3670 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 22, 'TRANS': 448} Chain: "B" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3586 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 24, 'TRANS': 439} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 108 Unusual residues: {'HNX': 1, 'Y01': 2} Classifications: {'undetermined': 3, 'water': 12} Link IDs: {None: 14} Time building chain proxies: 5.04, per 1000 atoms: 0.67 Number of scatterers: 7524 At special positions: 0 Unit cell: (83.699, 82.612, 125.005, 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) S 27 16.00 P 1 15.00 O 1369 8.00 N 1191 7.00 C 4936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 969.8 milliseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 57.4% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 178 through 206 Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.590A pdb=" N THR A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.893A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.546A pdb=" N LYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.848A pdb=" N VAL A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 357 through 372 removed outlier: 3.860A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.871A pdb=" N THR A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.565A pdb=" N SER A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.557A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.604A pdb=" N LEU A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN A 530 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 71 through 80 Processing helix chain 'B' and resid 81 through 110 Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.701A pdb=" N VAL B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 139 through 157 removed outlier: 3.671A pdb=" N SER B 143 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 189 Processing helix chain 'B' and resid 189 through 220 removed outlier: 3.715A pdb=" N ALA B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 243 through 253 removed outlier: 4.074A pdb=" N ALA B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 274 through 298 Proline residue: B 283 - end of helix removed outlier: 3.503A pdb=" N THR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 325 through 356 removed outlier: 3.716A pdb=" N GLY B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 387 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 396 through 422 removed outlier: 3.505A pdb=" N PHE B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N PHE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 451 Processing helix chain 'B' and resid 454 through 466 removed outlier: 4.269A pdb=" N CYS B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 473 removed outlier: 4.171A pdb=" N VAL B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 501 removed outlier: 4.045A pdb=" N GLN B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY B 488 " --> pdb=" O TRP B 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.482A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLY A 380 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 348 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 removed outlier: 3.676A pdb=" N LYS A 267 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.766A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA5, first strand: chain 'B' and resid 365 through 366 376 hydrogen bonds defined for protein. 1083 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: 2.01 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1170 1.31 - 1.43: 2057 1.43 - 1.56: 4410 1.56 - 1.68: 23 1.68 - 1.81: 41 Bond restraints: 7701 Sorted by residual: bond pdb=" CAI Y01 B 603 " pdb=" CAZ Y01 B 603 " ideal model delta sigma weight residual 1.332 1.557 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" CAI Y01 B 602 " pdb=" CAZ Y01 B 602 " ideal model delta sigma weight residual 1.332 1.548 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C02 HNX B 601 " pdb=" C07 HNX B 601 " ideal model delta sigma weight residual 1.507 1.707 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C09 HNX B 601 " pdb=" C10 HNX B 601 " ideal model delta sigma weight residual 1.523 1.323 0.200 2.00e-02 2.50e+03 9.97e+01 bond pdb=" C18 HNX B 601 " pdb=" C19 HNX B 601 " ideal model delta sigma weight residual 1.411 1.564 -0.153 2.00e-02 2.50e+03 5.87e+01 ... (remaining 7696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 10211 2.95 - 5.91: 216 5.91 - 8.86: 49 8.86 - 11.82: 8 11.82 - 14.77: 4 Bond angle restraints: 10488 Sorted by residual: angle pdb=" C PRO A 209 " pdb=" N ARG A 210 " pdb=" CA ARG A 210 " ideal model delta sigma weight residual 121.54 133.29 -11.75 1.91e+00 2.74e-01 3.79e+01 angle pdb=" N THR B 71 " pdb=" CA THR B 71 " pdb=" C THR B 71 " ideal model delta sigma weight residual 109.81 121.90 -12.09 2.21e+00 2.05e-01 2.99e+01 angle pdb=" C08 HNX B 601 " pdb=" C09 HNX B 601 " pdb=" C10 HNX B 601 " ideal model delta sigma weight residual 111.98 126.75 -14.77 3.00e+00 1.11e-01 2.42e+01 angle pdb=" N THR B 299 " pdb=" CA THR B 299 " pdb=" C THR B 299 " ideal model delta sigma weight residual 114.62 109.03 5.59 1.14e+00 7.69e-01 2.40e+01 angle pdb=" C VAL B 322 " pdb=" N MET B 323 " pdb=" CA MET B 323 " ideal model delta sigma weight residual 122.74 129.75 -7.01 1.44e+00 4.82e-01 2.37e+01 ... (remaining 10483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 4514 33.93 - 67.86: 141 67.86 - 101.79: 34 101.79 - 135.72: 33 135.72 - 169.66: 11 Dihedral angle restraints: 4733 sinusoidal: 2053 harmonic: 2680 Sorted by residual: dihedral pdb=" CA LEU B 137 " pdb=" C LEU B 137 " pdb=" N LEU B 138 " pdb=" CA LEU B 138 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PRO A 209 " pdb=" C PRO A 209 " pdb=" N ARG A 210 " pdb=" CA ARG A 210 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CAD Y01 B 603 " pdb=" CAZ Y01 B 603 " pdb=" CBH Y01 B 603 " pdb=" CAV Y01 B 603 " ideal model delta sinusoidal sigma weight residual 288.69 119.03 169.66 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.191: 1223 1.191 - 2.381: 0 2.381 - 3.572: 0 3.572 - 4.763: 0 4.763 - 5.954: 10 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CBI Y01 B 602 " pdb=" CAU Y01 B 602 " pdb=" CBE Y01 B 602 " pdb=" CBG Y01 B 602 " both_signs ideal model delta sigma weight residual False 2.94 -3.02 5.95 2.00e-01 2.50e+01 8.86e+02 chirality pdb=" CBI Y01 B 603 " pdb=" CAU Y01 B 603 " pdb=" CBE Y01 B 603 " pdb=" CBG Y01 B 603 " both_signs ideal model delta sigma weight residual False 2.94 -2.96 5.90 2.00e-01 2.50e+01 8.71e+02 chirality pdb=" CBH Y01 B 602 " pdb=" CAT Y01 B 602 " pdb=" CAZ Y01 B 602 " pdb=" CBF Y01 B 602 " both_signs ideal model delta sigma weight residual False -2.85 2.64 -5.49 2.00e-01 2.50e+01 7.55e+02 ... (remaining 1230 not shown) Planarity restraints: 1285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 137 " 0.020 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" C LEU B 137 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU B 137 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU B 138 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 282 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO B 283 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 283 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 283 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 469 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO B 470 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.034 5.00e-02 4.00e+02 ... (remaining 1282 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 57 2.56 - 3.14: 5470 3.14 - 3.73: 11392 3.73 - 4.31: 15995 4.31 - 4.90: 26576 Nonbonded interactions: 59490 Sorted by model distance: nonbonded pdb=" OE1 GLU B 506 " pdb=" N THR B 507 " model vdw 1.969 3.120 nonbonded pdb=" O GLY B 67 " pdb=" OG1 THR B 71 " model vdw 2.279 3.040 nonbonded pdb=" O ASP A 325 " pdb=" OG1 THR A 329 " model vdw 2.291 3.040 nonbonded pdb=" O TYR A 251 " pdb=" OG SER A 254 " model vdw 2.300 3.040 nonbonded pdb=" O ILE B 139 " pdb=" OG SER B 143 " model vdw 2.309 3.040 ... (remaining 59485 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.400 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.011 0.225 7701 Z= 0.663 Angle : 1.122 14.771 10488 Z= 0.580 Chirality : 0.490 5.954 1233 Planarity : 0.007 0.071 1281 Dihedral : 23.271 169.655 3008 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.16 % Favored : 91.30 % Rotamer: Outliers : 0.63 % Allowed : 5.45 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.22), residues: 931 helix: -1.97 (0.18), residues: 485 sheet: -1.34 (0.61), residues: 65 loop : -2.73 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 220 HIS 0.004 0.001 HIS B 367 PHE 0.017 0.002 PHE A 627 TYR 0.014 0.002 TYR B 387 ARG 0.002 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8282 (pttm) cc_final: 0.7927 (mtmt) REVERT: B 77 LYS cc_start: 0.8421 (tppt) cc_final: 0.7895 (mmtm) REVERT: B 81 SER cc_start: 0.8881 (p) cc_final: 0.8660 (p) REVERT: B 238 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5821 (pt) REVERT: B 365 MET cc_start: 0.8943 (mtt) cc_final: 0.8591 (mtt) outliers start: 5 outliers final: 4 residues processed: 122 average time/residue: 1.0052 time to fit residues: 131.3162 Evaluate side-chains 79 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 506 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 47 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 340 GLN A 353 ASN A 539 HIS A 557 HIS A 580 GLN B 273 ASN B 358 HIS ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.082642 restraints weight = 12670.712| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.94 r_work: 0.2878 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7701 Z= 0.185 Angle : 1.229 32.933 10488 Z= 0.483 Chirality : 0.111 1.853 1233 Planarity : 0.005 0.044 1281 Dihedral : 24.284 179.534 1373 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.41 % Favored : 92.16 % Rotamer: Outliers : 1.65 % Allowed : 12.55 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.32 (0.27), residues: 931 helix: 0.22 (0.22), residues: 498 sheet: -1.08 (0.60), residues: 69 loop : -2.40 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.004 0.001 HIS A 620 PHE 0.018 0.001 PHE B 462 TYR 0.012 0.001 TYR A 629 ARG 0.006 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7315 (t70) cc_final: 0.6980 (t0) REVERT: A 575 LEU cc_start: 0.8820 (mp) cc_final: 0.8606 (mt) REVERT: B 77 LYS cc_start: 0.8292 (tppt) cc_final: 0.7975 (ttpp) REVERT: B 218 GLN cc_start: 0.7851 (tp40) cc_final: 0.7498 (tm-30) REVERT: B 451 PHE cc_start: 0.7715 (m-80) cc_final: 0.7457 (m-10) outliers start: 13 outliers final: 7 residues processed: 94 average time/residue: 0.8175 time to fit residues: 84.3570 Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 84 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN ** B 367 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 = 0.3494 r_free = 0.3494 target = 0.113318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.082391 restraints weight = 12786.199| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.93 r_work: 0.2860 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7701 Z= 0.190 Angle : 1.179 31.005 10488 Z= 0.453 Chirality : 0.112 1.875 1233 Planarity : 0.004 0.039 1281 Dihedral : 23.561 179.589 1364 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.52 % Favored : 92.27 % Rotamer: Outliers : 3.30 % Allowed : 12.93 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.28), residues: 931 helix: 1.19 (0.24), residues: 499 sheet: -0.90 (0.60), residues: 69 loop : -2.12 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.003 0.001 HIS B 420 PHE 0.022 0.001 PHE B 462 TYR 0.020 0.001 TYR A 629 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7443 (t70) cc_final: 0.7082 (t0) REVERT: A 499 ASP cc_start: 0.7973 (p0) cc_final: 0.7762 (t0) REVERT: A 562 GLU cc_start: 0.8158 (tp30) cc_final: 0.7851 (tp30) REVERT: B 77 LYS cc_start: 0.8240 (tppt) cc_final: 0.7931 (ttpp) REVERT: B 218 GLN cc_start: 0.7745 (tp40) cc_final: 0.7441 (tm-30) REVERT: B 394 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7067 (m-80) REVERT: B 451 PHE cc_start: 0.7705 (m-80) cc_final: 0.7504 (m-10) outliers start: 26 outliers final: 7 residues processed: 101 average time/residue: 1.0566 time to fit residues: 115.9701 Evaluate side-chains 82 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 394 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 51 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 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 = 0.3542 r_free = 0.3542 target = 0.115975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.084990 restraints weight = 12653.313| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.90 r_work: 0.2911 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7701 Z= 0.176 Angle : 1.171 31.027 10488 Z= 0.444 Chirality : 0.110 1.819 1233 Planarity : 0.004 0.039 1281 Dihedral : 23.236 178.330 1364 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.30 % Favored : 92.48 % Rotamer: Outliers : 1.90 % Allowed : 15.21 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.29), residues: 931 helix: 1.67 (0.24), residues: 493 sheet: -0.85 (0.58), residues: 72 loop : -1.96 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 420 PHE 0.009 0.001 PHE B 95 TYR 0.012 0.001 TYR A 629 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.818 Fit side-chains REVERT: A 398 ASP cc_start: 0.7434 (t70) cc_final: 0.7105 (t0) REVERT: A 562 GLU cc_start: 0.8111 (tp30) cc_final: 0.7845 (tp30) REVERT: B 77 LYS cc_start: 0.8323 (tppt) cc_final: 0.8042 (ttpp) REVERT: B 218 GLN cc_start: 0.7703 (tp40) cc_final: 0.7391 (tm-30) REVERT: B 394 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.6945 (m-80) outliers start: 15 outliers final: 7 residues processed: 97 average time/residue: 0.8153 time to fit residues: 86.2616 Evaluate side-chains 83 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** 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 = 0.3522 r_free = 0.3522 target = 0.114294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.083468 restraints weight = 12652.842| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.87 r_work: 0.2873 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7701 Z= 0.229 Angle : 1.189 31.289 10488 Z= 0.456 Chirality : 0.111 1.826 1233 Planarity : 0.004 0.041 1281 Dihedral : 23.043 179.222 1362 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.73 % Favored : 92.16 % Rotamer: Outliers : 2.53 % Allowed : 16.98 % Favored : 80.48 % 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: 0.34 (0.29), residues: 931 helix: 1.89 (0.24), residues: 487 sheet: -0.83 (0.57), residues: 72 loop : -1.92 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 367 PHE 0.022 0.001 PHE B 462 TYR 0.012 0.001 TYR A 554 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.723 Fit side-chains REVERT: A 398 ASP cc_start: 0.7539 (t70) cc_final: 0.7206 (t0) REVERT: A 562 GLU cc_start: 0.8044 (tp30) cc_final: 0.7811 (tp30) REVERT: B 77 LYS cc_start: 0.8324 (tppt) cc_final: 0.8058 (ttpp) REVERT: B 218 GLN cc_start: 0.7791 (tp40) cc_final: 0.7468 (tm-30) REVERT: B 394 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.6910 (m-80) REVERT: B 451 PHE cc_start: 0.7684 (m-10) cc_final: 0.7299 (m-10) outliers start: 20 outliers final: 9 residues processed: 89 average time/residue: 1.0578 time to fit residues: 102.3154 Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 0.0270 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 59 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 HIS ** B 487 GLN ** 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 = 0.3568 r_free = 0.3568 target = 0.117584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.087043 restraints weight = 12635.394| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.88 r_work: 0.2942 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7701 Z= 0.156 Angle : 1.163 30.846 10488 Z= 0.438 Chirality : 0.110 1.835 1233 Planarity : 0.004 0.038 1281 Dihedral : 22.791 179.995 1362 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.09 % Favored : 92.80 % Rotamer: Outliers : 2.41 % Allowed : 16.98 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.29), residues: 931 helix: 2.19 (0.24), residues: 486 sheet: -0.68 (0.58), residues: 72 loop : -1.82 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 405 HIS 0.003 0.001 HIS B 367 PHE 0.009 0.001 PHE A 542 TYR 0.008 0.001 TYR A 226 ARG 0.001 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.900 Fit side-chains REVERT: A 398 ASP cc_start: 0.7497 (t70) cc_final: 0.7152 (t0) REVERT: A 562 GLU cc_start: 0.8063 (tp30) cc_final: 0.7789 (tp30) REVERT: B 77 LYS cc_start: 0.8321 (tppt) cc_final: 0.8097 (ttpp) REVERT: B 218 GLN cc_start: 0.7748 (tp40) cc_final: 0.7454 (tm-30) REVERT: B 305 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7829 (mtm) REVERT: B 394 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: B 451 PHE cc_start: 0.7647 (m-10) cc_final: 0.7287 (m-10) outliers start: 19 outliers final: 9 residues processed: 99 average time/residue: 0.9898 time to fit residues: 106.6968 Evaluate side-chains 86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 16 optimal weight: 0.0370 chunk 72 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** 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 = 0.3539 r_free = 0.3539 target = 0.115515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.084685 restraints weight = 12715.121| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.90 r_work: 0.2907 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7701 Z= 0.199 Angle : 1.176 31.106 10488 Z= 0.445 Chirality : 0.111 1.836 1233 Planarity : 0.004 0.040 1281 Dihedral : 22.704 179.483 1362 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.63 % Favored : 92.27 % Rotamer: Outliers : 2.53 % Allowed : 17.62 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.29), residues: 931 helix: 2.28 (0.24), residues: 485 sheet: -0.71 (0.57), residues: 72 loop : -1.80 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.003 0.001 HIS B 367 PHE 0.018 0.001 PHE B 462 TYR 0.010 0.001 TYR A 554 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8379 (pt) REVERT: A 398 ASP cc_start: 0.7503 (t70) cc_final: 0.7149 (t0) REVERT: A 562 GLU cc_start: 0.8083 (tp30) cc_final: 0.7732 (tp30) REVERT: B 77 LYS cc_start: 0.8451 (tppt) cc_final: 0.8227 (ttpp) REVERT: B 218 GLN cc_start: 0.7744 (tp40) cc_final: 0.7463 (tm-30) REVERT: B 394 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: B 451 PHE cc_start: 0.7709 (m-10) cc_final: 0.7342 (m-10) outliers start: 20 outliers final: 11 residues processed: 90 average time/residue: 0.7341 time to fit residues: 73.1133 Evaluate side-chains 86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.4967 > 50: distance: 48 - 52: 26.351 distance: 52 - 53: 40.351 distance: 53 - 54: 9.161 distance: 53 - 56: 37.208 distance: 54 - 55: 51.672 distance: 54 - 59: 33.903 distance: 56 - 57: 40.306 distance: 56 - 58: 34.743 distance: 59 - 60: 37.505 distance: 60 - 61: 21.182 distance: 60 - 63: 26.777 distance: 61 - 62: 35.894 distance: 61 - 68: 9.806 distance: 63 - 64: 49.843 distance: 64 - 65: 22.222 distance: 65 - 66: 30.058 distance: 65 - 67: 29.484 distance: 68 - 69: 54.726 distance: 68 - 74: 33.848 distance: 69 - 70: 37.542 distance: 69 - 72: 20.870 distance: 70 - 71: 15.059 distance: 70 - 75: 28.518 distance: 72 - 73: 36.825 distance: 73 - 74: 29.438 distance: 75 - 76: 40.708 distance: 76 - 77: 46.963 distance: 77 - 78: 37.423 distance: 77 - 79: 20.691 distance: 79 - 80: 26.274 distance: 80 - 81: 12.105 distance: 80 - 83: 10.711 distance: 81 - 82: 16.233 distance: 81 - 90: 29.798 distance: 83 - 84: 20.854 distance: 84 - 85: 19.747 distance: 85 - 86: 6.767 distance: 86 - 87: 13.396 distance: 87 - 88: 22.921 distance: 87 - 89: 11.891 distance: 90 - 91: 22.347 distance: 91 - 92: 11.328 distance: 91 - 94: 27.171 distance: 92 - 93: 21.972 distance: 92 - 99: 19.767 distance: 94 - 95: 34.086 distance: 95 - 96: 36.928 distance: 96 - 97: 20.073 distance: 96 - 98: 45.436 distance: 99 - 100: 11.636 distance: 100 - 101: 23.043 distance: 100 - 103: 29.927 distance: 101 - 102: 25.573 distance: 101 - 108: 20.212 distance: 103 - 104: 19.997 distance: 104 - 105: 18.793 distance: 105 - 106: 23.311 distance: 105 - 107: 18.351 distance: 108 - 109: 21.415 distance: 109 - 110: 12.528 distance: 110 - 111: 19.068 distance: 110 - 112: 21.281 distance: 112 - 113: 10.729 distance: 113 - 114: 41.528 distance: 113 - 116: 44.488 distance: 114 - 115: 12.878 distance: 114 - 118: 41.023 distance: 116 - 117: 24.654 distance: 118 - 119: 22.581 distance: 118 - 124: 26.689 distance: 119 - 120: 24.772 distance: 119 - 122: 17.526 distance: 120 - 121: 12.242 distance: 120 - 125: 15.116 distance: 122 - 123: 24.267 distance: 123 - 124: 35.011