Starting phenix.real_space_refine on Sun Apr 27 18:45:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrk_34976/04_2025/8hrk_34976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrk_34976/04_2025/8hrk_34976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hrk_34976/04_2025/8hrk_34976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrk_34976/04_2025/8hrk_34976.map" model { file = "/net/cci-nas-00/data/ceres_data/8hrk_34976/04_2025/8hrk_34976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrk_34976/04_2025/8hrk_34976.cif" } resolution = 3.3 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= -0.001 sd= 0.157 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4101 2.51 5 N 1066 2.21 5 O 1208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1542 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 183} Time building chain proxies: 4.49, per 1000 atoms: 0.70 Number of scatterers: 6412 At special positions: 0 Unit cell: (71.38, 88.58, 126.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1208 8.00 N 1066 7.00 C 4101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 992.4 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 48.2% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.720A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.592A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.823A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.740A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.669A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 removed outlier: 3.577A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.549A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.881A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.560A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 4.248A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 removed outlier: 4.247A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 330' Processing helix chain 'A' and resid 365 through 383 removed outlier: 3.633A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.543A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.733A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.525A pdb=" N LYS A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.168A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.547A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.747A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.078A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.749A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.767A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 370' Processing helix chain 'E' and resid 385 through 389 removed outlier: 3.977A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 385 through 389' Processing helix chain 'E' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.451A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 352 removed outlier: 3.938A pdb=" N TRP A 349 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.537A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR E 396 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 511 " --> pdb=" O ILE E 434 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 434 " --> pdb=" O VAL E 511 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.767A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 597 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: 1.72 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1286 1.33 - 1.45: 1729 1.45 - 1.57: 3516 1.57 - 1.69: 3 1.69 - 1.81: 58 Bond restraints: 6592 Sorted by residual: bond pdb=" CG PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 1.503 1.208 0.295 3.40e-02 8.65e+02 7.55e+01 bond pdb=" N PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" CB PRO A 235 " pdb=" CG PRO A 235 " ideal model delta sigma weight residual 1.492 1.654 -0.162 5.00e-02 4.00e+02 1.05e+01 bond pdb=" CB PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.59e+00 bond pdb=" CG PRO A 235 " pdb=" CD PRO A 235 " ideal model delta sigma weight residual 1.503 1.416 0.087 3.40e-02 8.65e+02 6.52e+00 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 8926 3.56 - 7.12: 25 7.12 - 10.68: 3 10.68 - 14.24: 2 14.24 - 17.80: 2 Bond angle restraints: 8958 Sorted by residual: angle pdb=" CA PRO A 235 " pdb=" N PRO A 235 " pdb=" CD PRO A 235 " ideal model delta sigma weight residual 112.00 94.20 17.80 1.40e+00 5.10e-01 1.62e+02 angle pdb=" N PRO A 415 " pdb=" CD PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 103.20 85.48 17.72 1.50e+00 4.44e-01 1.40e+02 angle pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 112.00 98.48 13.52 1.40e+00 5.10e-01 9.33e+01 angle pdb=" N PRO A 235 " pdb=" CD PRO A 235 " pdb=" CG PRO A 235 " ideal model delta sigma weight residual 103.20 93.98 9.22 1.50e+00 4.44e-01 3.77e+01 angle pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 104.50 92.97 11.53 1.90e+00 2.77e-01 3.68e+01 ... (remaining 8953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3337 18.00 - 36.00: 432 36.00 - 53.99: 97 53.99 - 71.99: 19 71.99 - 89.99: 8 Dihedral angle restraints: 3893 sinusoidal: 1573 harmonic: 2320 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 176.81 -83.81 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 147.88 -54.88 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CB CYS E 336 " pdb=" SG CYS E 336 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual -86.00 -44.04 -41.96 1 1.00e+01 1.00e-02 2.46e+01 ... (remaining 3890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 414 0.024 - 0.049: 319 0.049 - 0.073: 142 0.073 - 0.097: 35 0.097 - 0.121: 24 Chirality restraints: 934 Sorted by residual: chirality pdb=" CA VAL E 511 " pdb=" N VAL E 511 " pdb=" C VAL E 511 " pdb=" CB VAL E 511 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CB PRO A 415 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.22e-01 ... (remaining 931 not shown) Planarity restraints: 1165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.106 5.00e-02 4.00e+02 1.45e-01 3.34e+01 pdb=" N PRO A 235 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " 0.082 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO A 321 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " 0.063 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO A 415 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " 0.047 5.00e-02 4.00e+02 ... (remaining 1162 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1697 2.80 - 3.32: 5341 3.32 - 3.85: 9886 3.85 - 4.37: 11141 4.37 - 4.90: 19953 Nonbonded interactions: 48018 Sorted by model distance: nonbonded pdb=" NH1 ARG E 346 " pdb=" O PHE E 347 " model vdw 2.273 3.120 nonbonded pdb=" OE2 GLU A 489 " pdb=" OH TYR A 613 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR E 351 " pdb=" NH2 ARG E 452 " model vdw 2.273 3.120 nonbonded pdb=" OG SER E 371 " pdb=" OG SER E 373 " model vdw 2.288 3.040 nonbonded pdb=" O LEU A 333 " pdb=" OG1 THR A 362 " model vdw 2.293 3.040 ... (remaining 48013 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 ========== 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 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.370 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 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 0.295 6599 Z= 0.192 Angle : 0.713 17.801 8972 Z= 0.445 Chirality : 0.040 0.121 934 Planarity : 0.008 0.145 1165 Dihedral : 16.730 89.990 2384 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.14 % Allowed : 17.87 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.80 (0.29), residues: 787 helix: -0.48 (0.29), residues: 345 sheet: -2.36 (0.79), residues: 42 loop : -1.69 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 349 HIS 0.001 0.000 HIS A 239 PHE 0.008 0.001 PHE A 369 TYR 0.018 0.001 TYR A 41 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.20776 ( 211) hydrogen bonds : angle 6.46196 ( 597) SS BOND : bond 0.00157 ( 7) SS BOND : angle 1.56305 ( 14) covalent geometry : bond 0.00538 ( 6592) covalent geometry : angle 0.71052 ( 8958) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.6793 (tt0) cc_final: 0.6416 (mt-10) REVERT: A 376 MET cc_start: 0.7200 (ttt) cc_final: 0.6910 (ttt) REVERT: E 335 LEU cc_start: 0.0534 (OUTLIER) cc_final: -0.0132 (mm) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.1934 time to fit residues: 23.7312 Evaluate side-chains 79 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 335 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS A 380 GLN A 432 ASN E 474 GLN E 493 GLN E 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149887 restraints weight = 7769.233| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.16 r_work: 0.3496 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 6599 Z= 0.354 Angle : 0.913 11.283 8972 Z= 0.495 Chirality : 0.055 0.231 934 Planarity : 0.008 0.088 1165 Dihedral : 6.440 49.050 863 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.03 % Allowed : 19.45 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.79 (0.26), residues: 787 helix: -1.41 (0.26), residues: 341 sheet: -1.58 (1.52), residues: 12 loop : -2.28 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 473 HIS 0.020 0.003 HIS A 241 PHE 0.029 0.003 PHE A 230 TYR 0.028 0.003 TYR E 351 ARG 0.007 0.001 ARG A 245 Details of bonding type rmsd hydrogen bonds : bond 0.12246 ( 211) hydrogen bonds : angle 6.10338 ( 597) SS BOND : bond 0.00546 ( 7) SS BOND : angle 1.80091 ( 14) covalent geometry : bond 0.00833 ( 6592) covalent geometry : angle 0.91059 ( 8958) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.704 Fit side-chains REVERT: A 35 GLU cc_start: 0.7883 (tt0) cc_final: 0.7382 (mt-10) REVERT: A 167 SER cc_start: 0.8753 (t) cc_final: 0.7460 (m) REVERT: A 171 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.5759 (mp0) REVERT: A 432 ASN cc_start: 0.7675 (m110) cc_final: 0.6407 (t0) REVERT: E 414 GLN cc_start: 0.7085 (mm-40) cc_final: 0.6197 (mp10) REVERT: E 442 ASP cc_start: 0.8018 (m-30) cc_final: 0.7807 (m-30) outliers start: 28 outliers final: 10 residues processed: 109 average time/residue: 0.1878 time to fit residues: 27.5665 Evaluate side-chains 75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 494 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 380 GLN A 401 HIS E 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.189139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.151589 restraints weight = 7829.855| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.47 r_work: 0.3550 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6599 Z= 0.140 Angle : 0.549 5.302 8972 Z= 0.297 Chirality : 0.043 0.192 934 Planarity : 0.005 0.067 1165 Dihedral : 5.079 50.566 863 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.45 % Allowed : 20.46 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.11 (0.28), residues: 787 helix: -0.66 (0.28), residues: 339 sheet: -1.78 (1.34), residues: 12 loop : -2.06 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 473 HIS 0.006 0.001 HIS A 345 PHE 0.016 0.001 PHE A 327 TYR 0.013 0.001 TYR E 495 ARG 0.002 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.06484 ( 211) hydrogen bonds : angle 4.95795 ( 597) SS BOND : bond 0.00189 ( 7) SS BOND : angle 0.70639 ( 14) covalent geometry : bond 0.00301 ( 6592) covalent geometry : angle 0.54864 ( 8958) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 22 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5872 (pt0) REVERT: A 75 GLU cc_start: 0.7129 (tp30) cc_final: 0.6858 (tp30) REVERT: A 123 MET cc_start: 0.8111 (mtt) cc_final: 0.7908 (mtm) REVERT: A 206 ASP cc_start: 0.7354 (t70) cc_final: 0.7144 (t0) outliers start: 17 outliers final: 10 residues processed: 90 average time/residue: 0.1777 time to fit residues: 21.8218 Evaluate side-chains 77 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.185104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147362 restraints weight = 7824.675| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.47 r_work: 0.3500 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6599 Z= 0.150 Angle : 0.543 5.483 8972 Z= 0.291 Chirality : 0.043 0.184 934 Planarity : 0.005 0.056 1165 Dihedral : 4.789 50.156 863 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.75 % Allowed : 20.03 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.90 (0.28), residues: 787 helix: -0.43 (0.28), residues: 340 sheet: -1.48 (0.93), residues: 22 loop : -1.99 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 473 HIS 0.009 0.001 HIS A 241 PHE 0.014 0.002 PHE A 327 TYR 0.016 0.001 TYR E 495 ARG 0.006 0.001 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.06796 ( 211) hydrogen bonds : angle 4.62970 ( 597) SS BOND : bond 0.00214 ( 7) SS BOND : angle 0.63107 ( 14) covalent geometry : bond 0.00334 ( 6592) covalent geometry : angle 0.54247 ( 8958) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 22 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5836 (pt0) REVERT: A 42 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7315 (mm-40) REVERT: A 75 GLU cc_start: 0.7207 (tp30) cc_final: 0.6930 (tp30) REVERT: A 123 MET cc_start: 0.8109 (mtt) cc_final: 0.7903 (mtm) REVERT: A 206 ASP cc_start: 0.7466 (t70) cc_final: 0.7241 (t0) REVERT: A 345 HIS cc_start: 0.2104 (OUTLIER) cc_final: 0.1525 (t70) outliers start: 26 outliers final: 14 residues processed: 98 average time/residue: 0.1837 time to fit residues: 24.6535 Evaluate side-chains 87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 4.9990 chunk 26 optimal weight: 0.0770 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.183836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148913 restraints weight = 7728.654| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.56 r_work: 0.3519 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6599 Z= 0.122 Angle : 0.499 4.997 8972 Z= 0.266 Chirality : 0.042 0.165 934 Planarity : 0.004 0.047 1165 Dihedral : 4.520 48.472 863 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.89 % Allowed : 19.45 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.55 (0.29), residues: 787 helix: -0.15 (0.29), residues: 340 sheet: -1.82 (0.85), residues: 34 loop : -1.73 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.011 0.001 PHE A 327 TYR 0.010 0.001 TYR E 495 ARG 0.006 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.05653 ( 211) hydrogen bonds : angle 4.40346 ( 597) SS BOND : bond 0.00146 ( 7) SS BOND : angle 0.43976 ( 14) covalent geometry : bond 0.00261 ( 6592) covalent geometry : angle 0.49873 ( 8958) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 22 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5702 (pt0) REVERT: A 75 GLU cc_start: 0.7287 (tp30) cc_final: 0.7012 (tp30) REVERT: A 206 ASP cc_start: 0.7618 (t70) cc_final: 0.7329 (t0) REVERT: A 345 HIS cc_start: 0.1703 (OUTLIER) cc_final: 0.1207 (t70) REVERT: A 531 GLN cc_start: 0.7232 (tp-100) cc_final: 0.6314 (tt0) REVERT: A 548 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6876 (m) outliers start: 27 outliers final: 19 residues processed: 98 average time/residue: 0.1686 time to fit residues: 22.6961 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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: 55.6582 > 50: distance: 19 - 32: 3.079 distance: 71 - 76: 9.716 distance: 76 - 77: 5.720 distance: 77 - 78: 14.327 distance: 77 - 80: 8.724 distance: 78 - 79: 8.237 distance: 78 - 81: 7.171 distance: 81 - 82: 9.414 distance: 82 - 83: 20.935 distance: 82 - 85: 7.581 distance: 83 - 84: 19.317 distance: 83 - 95: 17.760 distance: 85 - 86: 11.856 distance: 86 - 87: 7.950 distance: 86 - 88: 3.896 distance: 87 - 89: 8.168 distance: 88 - 90: 8.796 distance: 88 - 91: 5.878 distance: 89 - 90: 10.031 distance: 90 - 92: 6.815 distance: 91 - 93: 7.019 distance: 92 - 94: 7.060 distance: 93 - 94: 6.442 distance: 95 - 96: 7.956 distance: 96 - 97: 6.839 distance: 96 - 99: 4.878 distance: 97 - 98: 10.038 distance: 97 - 103: 7.478 distance: 99 - 100: 7.350 distance: 100 - 101: 6.615 distance: 100 - 102: 7.397 distance: 103 - 104: 6.352 distance: 103 - 131: 25.336 distance: 104 - 105: 16.681 distance: 104 - 107: 8.992 distance: 105 - 106: 16.797 distance: 105 - 111: 11.784 distance: 107 - 108: 6.883 distance: 108 - 109: 26.392 distance: 108 - 110: 13.640 distance: 111 - 112: 16.535 distance: 112 - 113: 26.148 distance: 113 - 114: 24.936 distance: 113 - 115: 24.340 distance: 115 - 116: 26.815 distance: 116 - 117: 21.570 distance: 116 - 119: 19.664 distance: 117 - 118: 38.738 distance: 117 - 124: 17.169 distance: 119 - 120: 12.137 distance: 120 - 121: 21.285 distance: 121 - 122: 23.428 distance: 122 - 123: 25.513 distance: 124 - 125: 3.380 distance: 125 - 126: 23.685 distance: 126 - 127: 34.404 distance: 126 - 128: 24.470 distance: 128 - 129: 6.919 distance: 129 - 130: 8.537 distance: 129 - 132: 6.586 distance: 130 - 136: 29.051 distance: 132 - 133: 6.080 distance: 133 - 134: 20.180 distance: 133 - 135: 22.726 distance: 136 - 137: 25.391 distance: 137 - 138: 4.743 distance: 137 - 140: 12.092 distance: 138 - 139: 9.785 distance: 138 - 147: 5.914 distance: 140 - 141: 13.446 distance: 141 - 142: 10.014 distance: 141 - 143: 12.264 distance: 142 - 144: 4.760 distance: 143 - 145: 6.960 distance: 144 - 146: 17.427 distance: 145 - 146: 8.954 distance: 147 - 148: 4.775 distance: 148 - 149: 4.612 distance: 148 - 151: 9.384 distance: 149 - 158: 6.120 distance: 151 - 152: 7.262 distance: 152 - 153: 8.355 distance: 153 - 154: 7.021 distance: 154 - 155: 9.934 distance: 155 - 156: 10.256