Starting phenix.real_space_refine on Wed Sep 17 14:29:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kwi_62611/09_2025/9kwi_62611.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kwi_62611/09_2025/9kwi_62611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kwi_62611/09_2025/9kwi_62611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kwi_62611/09_2025/9kwi_62611.map" model { file = "/net/cci-nas-00/data/ceres_data/9kwi_62611/09_2025/9kwi_62611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kwi_62611/09_2025/9kwi_62611.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.002 sd= 0.068 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 5773 2.51 5 N 1611 2.21 5 O 1702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9127 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4348 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 19, 'TRANS': 554} Chain: "B" Number of atoms: 4715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4715 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 18, 'TRANS': 597} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.32, per 1000 atoms: 0.25 Number of scatterers: 9127 At special positions: 0 Unit cell: (68.224, 89.024, 151.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 6 15.00 Mg 2 11.99 O 1702 8.00 N 1611 7.00 C 5773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.88 Conformation dependent library (CDL) restraints added in 226.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 72.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid -1 through 11 removed outlier: 3.732A pdb=" N TRP A 3 " --> pdb=" O SER A -1 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 4 " --> pdb=" O ASN A 0 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 45 Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 50 through 99 Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.892A pdb=" N PHE A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 119 through 135 removed outlier: 3.814A pdb=" N ILE A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 128 " --> pdb=" O HIS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 154 Processing helix chain 'A' and resid 157 through 203 removed outlier: 4.052A pdb=" N LEU A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Proline residue: A 166 - end of helix Proline residue: A 181 - end of helix removed outlier: 3.868A pdb=" N GLY A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 210 Processing helix chain 'A' and resid 212 through 239 removed outlier: 3.611A pdb=" N TRP A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 266 removed outlier: 3.803A pdb=" N VAL A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 294 removed outlier: 3.889A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 313 removed outlier: 4.443A pdb=" N ARG A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.563A pdb=" N GLY A 396 " --> pdb=" O ARG A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 425 through 434 removed outlier: 3.579A pdb=" N TYR A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 451 through 456 Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.778A pdb=" N ARG A 488 " --> pdb=" O ARG A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'B' and resid 16 through 29 removed outlier: 3.725A pdb=" N SER B 20 " --> pdb=" O ASP B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 72 removed outlier: 3.665A pdb=" N GLY B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Proline residue: B 53 - end of helix removed outlier: 3.778A pdb=" N GLU B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 91 through 99 removed outlier: 3.601A pdb=" N ASP B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 160 Processing helix chain 'B' and resid 161 through 167 removed outlier: 3.868A pdb=" N PHE B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 178 through 213 removed outlier: 5.994A pdb=" N SER B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLN B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 222 through 262 removed outlier: 3.593A pdb=" N ALA B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Proline residue: B 240 - end of helix removed outlier: 3.552A pdb=" N GLY B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 271 through 299 Processing helix chain 'B' and resid 299 through 326 removed outlier: 3.602A pdb=" N ALA B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 372 Proline residue: B 346 - end of helix removed outlier: 4.743A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 438 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 481 through 487 Processing helix chain 'B' and resid 493 through 504 Processing helix chain 'B' and resid 505 through 511 removed outlier: 4.212A pdb=" N PHE B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 544 removed outlier: 3.796A pdb=" N ALA B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 576 removed outlier: 3.734A pdb=" N LEU B 565 " --> pdb=" O ARG B 561 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU B 572 " --> pdb=" O HIS B 568 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 590 removed outlier: 3.655A pdb=" N ILE B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 Processing helix chain 'B' and resid 616 through 628 removed outlier: 3.893A pdb=" N TRP B 620 " --> pdb=" O HIS B 616 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N HIS B 626 " --> pdb=" O MET B 622 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 627 " --> pdb=" O THR B 623 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 354 removed outlier: 5.391A pdb=" N GLN A 352 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE A 341 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP A 338 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER A 391 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414 removed outlier: 6.757A pdb=" N VAL A 539 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 541 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AA4, first strand: chain 'B' and resid 407 through 414 removed outlier: 6.481A pdb=" N GLU B 408 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER B 397 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU B 410 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE B 393 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B 449 " --> pdb=" O PHE B 393 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS B 395 " --> pdb=" O ARG B 447 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG B 447 " --> pdb=" O HIS B 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 467 through 470 removed outlier: 6.447A pdb=" N ALA B 421 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N MET B 598 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B 423 " --> pdb=" O MET B 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 479 through 480 648 hydrogen bonds defined for protein. 1905 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: 1.57 Time building geometry restraints manager: 1.10 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: 1817 1.33 - 1.45: 2129 1.45 - 1.57: 5266 1.57 - 1.69: 10 1.69 - 1.81: 61 Bond restraints: 9283 Sorted by residual: bond pdb=" CA ALA B 554 " pdb=" CB ALA B 554 " ideal model delta sigma weight residual 1.532 1.467 0.064 1.65e-02 3.67e+03 1.52e+01 bond pdb=" C ALA B 554 " pdb=" O ALA B 554 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.32e-02 5.74e+03 4.90e+00 bond pdb=" C ASP B 552 " pdb=" O ASP B 552 " ideal model delta sigma weight residual 1.233 1.210 0.023 1.26e-02 6.30e+03 3.44e+00 bond pdb=" C ALA B 554 " pdb=" N THR B 555 " ideal model delta sigma weight residual 1.330 1.305 0.026 1.43e-02 4.89e+03 3.19e+00 bond pdb=" C LEU B 551 " pdb=" O LEU B 551 " ideal model delta sigma weight residual 1.234 1.214 0.020 1.20e-02 6.94e+03 2.73e+00 ... (remaining 9278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 12393 1.48 - 2.96: 208 2.96 - 4.43: 27 4.43 - 5.91: 19 5.91 - 7.39: 4 Bond angle restraints: 12651 Sorted by residual: angle pdb=" CA ASP B 552 " pdb=" CB ASP B 552 " pdb=" CG ASP B 552 " ideal model delta sigma weight residual 112.60 116.77 -4.17 1.00e+00 1.00e+00 1.74e+01 angle pdb=" N ALA B 554 " pdb=" CA ALA B 554 " pdb=" C ALA B 554 " ideal model delta sigma weight residual 113.23 108.34 4.89 1.24e+00 6.50e-01 1.56e+01 angle pdb=" C GLN B 553 " pdb=" CA GLN B 553 " pdb=" CB GLN B 553 " ideal model delta sigma weight residual 110.42 117.81 -7.39 1.99e+00 2.53e-01 1.38e+01 angle pdb=" CA ASP B 552 " pdb=" C ASP B 552 " pdb=" O ASP B 552 " ideal model delta sigma weight residual 120.92 117.17 3.75 1.04e+00 9.25e-01 1.30e+01 angle pdb=" N GLN B 553 " pdb=" CA GLN B 553 " pdb=" C GLN B 553 " ideal model delta sigma weight residual 110.80 104.98 5.82 2.13e+00 2.20e-01 7.46e+00 ... (remaining 12646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4790 17.69 - 35.39: 562 35.39 - 53.08: 151 53.08 - 70.77: 30 70.77 - 88.47: 15 Dihedral angle restraints: 5548 sinusoidal: 2148 harmonic: 3400 Sorted by residual: dihedral pdb=" CA ILE A 404 " pdb=" C ILE A 404 " pdb=" N GLU A 405 " pdb=" CA GLU A 405 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASN A 320 " pdb=" C ASN A 320 " pdb=" N PRO A 321 " pdb=" CA PRO A 321 " ideal model delta harmonic sigma weight residual 180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA VAL B 401 " pdb=" C VAL B 401 " pdb=" N PRO B 402 " pdb=" CA PRO B 402 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1129 0.040 - 0.079: 290 0.079 - 0.119: 93 0.119 - 0.158: 7 0.158 - 0.198: 1 Chirality restraints: 1520 Sorted by residual: chirality pdb=" CB VAL B 188 " pdb=" CA VAL B 188 " pdb=" CG1 VAL B 188 " pdb=" CG2 VAL B 188 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CA ILE B 407 " pdb=" N ILE B 407 " pdb=" C ILE B 407 " pdb=" CB ILE B 407 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ALA B 554 " pdb=" N ALA B 554 " pdb=" C ALA B 554 " pdb=" CB ALA B 554 " both_signs ideal model delta sigma weight residual False 2.48 2.61 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1517 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 52 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO B 53 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 53 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 53 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 550 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C VAL B 550 " -0.030 2.00e-02 2.50e+03 pdb=" O VAL B 550 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 551 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 160 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C LEU A 160 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 160 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 161 " -0.010 2.00e-02 2.50e+03 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 64 2.54 - 3.13: 7072 3.13 - 3.72: 15174 3.72 - 4.31: 19713 4.31 - 4.90: 34331 Nonbonded interactions: 76354 Sorted by model distance: nonbonded pdb=" OG SER A 375 " pdb="MG MG A 602 " model vdw 1.952 2.170 nonbonded pdb=" OG1 THR B 431 " pdb="MG MG B 701 " model vdw 1.963 2.170 nonbonded pdb=" OE1 GLN A 416 " pdb="MG MG A 602 " model vdw 2.015 2.170 nonbonded pdb=" OE1 GLN B 472 " pdb="MG MG B 701 " model vdw 2.021 2.170 nonbonded pdb=" O3G ATP A 601 " pdb="MG MG A 602 " model vdw 2.065 2.170 ... (remaining 76349 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: 2.550 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.770 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.003 0.064 9283 Z= 0.138 Angle : 0.518 7.390 12651 Z= 0.287 Chirality : 0.039 0.198 1520 Planarity : 0.003 0.049 1614 Dihedral : 16.984 88.467 3360 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.95 % Favored : 96.88 % Rotamer: Outliers : 2.94 % Allowed : 22.96 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.25), residues: 1186 helix: 2.04 (0.19), residues: 793 sheet: 1.82 (0.80), residues: 47 loop : -0.48 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 417 TYR 0.011 0.001 TYR B 400 PHE 0.013 0.001 PHE A 453 TRP 0.010 0.001 TRP B 246 HIS 0.009 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9283) covalent geometry : angle 0.51820 (12651) hydrogen bonds : bond 0.12354 ( 648) hydrogen bonds : angle 5.12894 ( 1905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 159 TRP cc_start: 0.7998 (p-90) cc_final: 0.7733 (p-90) REVERT: A 315 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8262 (pt0) REVERT: B 208 MET cc_start: 0.9069 (tpp) cc_final: 0.8716 (mmt) REVERT: B 227 SER cc_start: 0.8518 (t) cc_final: 0.8273 (m) REVERT: B 287 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7302 (tt0) outliers start: 28 outliers final: 19 residues processed: 129 average time/residue: 0.0720 time to fit residues: 13.7191 Evaluate side-chains 127 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 553 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.0670 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS A 270 GLN B 186 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.139904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116459 restraints weight = 12985.748| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.24 r_work: 0.3284 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9283 Z= 0.173 Angle : 0.520 5.542 12651 Z= 0.279 Chirality : 0.041 0.149 1520 Planarity : 0.004 0.050 1614 Dihedral : 8.264 78.270 1408 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.12 % Favored : 96.71 % Rotamer: Outliers : 4.61 % Allowed : 20.34 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.25), residues: 1186 helix: 2.05 (0.18), residues: 799 sheet: 1.22 (0.78), residues: 47 loop : -0.45 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 488 TYR 0.012 0.002 TYR B 400 PHE 0.015 0.002 PHE A 453 TRP 0.007 0.001 TRP B 246 HIS 0.006 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 9283) covalent geometry : angle 0.51953 (12651) hydrogen bonds : bond 0.04749 ( 648) hydrogen bonds : angle 4.36418 ( 1905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.338 Fit side-chains REVERT: A 159 TRP cc_start: 0.8045 (p-90) cc_final: 0.7788 (p-90) REVERT: A 256 LEU cc_start: 0.8459 (tp) cc_final: 0.8189 (tt) REVERT: A 315 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8242 (pt0) REVERT: A 427 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: A 515 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7629 (mtp85) REVERT: B 208 MET cc_start: 0.9076 (tpp) cc_final: 0.8488 (mmt) REVERT: B 287 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: B 325 THR cc_start: 0.7881 (m) cc_final: 0.7450 (p) REVERT: B 620 TRP cc_start: 0.8826 (t60) cc_final: 0.8549 (t-100) outliers start: 44 outliers final: 27 residues processed: 160 average time/residue: 0.0824 time to fit residues: 18.8203 Evaluate side-chains 139 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 80 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 194 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118545 restraints weight = 12872.620| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.25 r_work: 0.3309 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9283 Z= 0.121 Angle : 0.473 5.537 12651 Z= 0.253 Chirality : 0.039 0.140 1520 Planarity : 0.004 0.051 1614 Dihedral : 7.570 83.513 1390 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.12 % Favored : 96.71 % Rotamer: Outliers : 3.98 % Allowed : 21.07 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.25), residues: 1186 helix: 2.25 (0.18), residues: 796 sheet: 0.96 (0.77), residues: 47 loop : -0.43 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 247 TYR 0.012 0.001 TYR B 339 PHE 0.012 0.001 PHE B 336 TRP 0.007 0.001 TRP B 246 HIS 0.007 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9283) covalent geometry : angle 0.47309 (12651) hydrogen bonds : bond 0.04242 ( 648) hydrogen bonds : angle 4.14512 ( 1905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.342 Fit side-chains REVERT: A 159 TRP cc_start: 0.8067 (p-90) cc_final: 0.7825 (p-90) REVERT: A 256 LEU cc_start: 0.8433 (tp) cc_final: 0.8206 (tt) REVERT: A 427 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: A 515 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7659 (mtp85) REVERT: B 208 MET cc_start: 0.9056 (tpp) cc_final: 0.8723 (mmt) REVERT: B 325 THR cc_start: 0.7948 (m) cc_final: 0.7518 (p) REVERT: B 620 TRP cc_start: 0.8824 (t60) cc_final: 0.8513 (t-100) outliers start: 38 outliers final: 24 residues processed: 154 average time/residue: 0.0766 time to fit residues: 17.0409 Evaluate side-chains 140 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 553 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 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 = 0.3662 r_free = 0.3662 target = 0.136895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114674 restraints weight = 13279.941| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.03 r_work: 0.3237 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9283 Z= 0.197 Angle : 0.543 5.560 12651 Z= 0.289 Chirality : 0.042 0.157 1520 Planarity : 0.004 0.052 1614 Dihedral : 7.547 85.426 1383 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.46 % Favored : 96.46 % Rotamer: Outliers : 4.30 % Allowed : 20.86 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.25), residues: 1186 helix: 2.02 (0.18), residues: 804 sheet: 1.17 (0.85), residues: 36 loop : -0.55 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 366 TYR 0.014 0.002 TYR B 400 PHE 0.017 0.002 PHE B 509 TRP 0.005 0.001 TRP A 408 HIS 0.007 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 9283) covalent geometry : angle 0.54295 (12651) hydrogen bonds : bond 0.04778 ( 648) hydrogen bonds : angle 4.26485 ( 1905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 159 TRP cc_start: 0.8094 (p-90) cc_final: 0.7864 (p-90) REVERT: A 348 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6414 (ptm-80) REVERT: A 427 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: A 515 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7750 (mtp85) REVERT: B 181 VAL cc_start: 0.8538 (t) cc_final: 0.8030 (p) REVERT: B 325 THR cc_start: 0.8146 (m) cc_final: 0.7730 (p) outliers start: 41 outliers final: 33 residues processed: 152 average time/residue: 0.0918 time to fit residues: 19.2773 Evaluate side-chains 143 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 553 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 13 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117519 restraints weight = 13050.247| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.96 r_work: 0.3260 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9283 Z= 0.133 Angle : 0.489 6.910 12651 Z= 0.261 Chirality : 0.040 0.141 1520 Planarity : 0.003 0.050 1614 Dihedral : 7.172 84.310 1383 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 4.09 % Allowed : 20.96 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.25), residues: 1186 helix: 2.21 (0.18), residues: 799 sheet: 1.28 (0.86), residues: 36 loop : -0.54 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 624 TYR 0.010 0.001 TYR B 400 PHE 0.012 0.001 PHE A 453 TRP 0.006 0.001 TRP B 246 HIS 0.007 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9283) covalent geometry : angle 0.48889 (12651) hydrogen bonds : bond 0.04303 ( 648) hydrogen bonds : angle 4.11211 ( 1905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 159 TRP cc_start: 0.8094 (p-90) cc_final: 0.7868 (p-90) REVERT: A 348 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6401 (ptm-80) REVERT: A 427 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: A 515 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7626 (mtp85) REVERT: B 181 VAL cc_start: 0.8543 (t) cc_final: 0.8001 (p) REVERT: B 186 ASN cc_start: 0.7625 (m-40) cc_final: 0.7175 (t0) REVERT: B 325 THR cc_start: 0.8141 (m) cc_final: 0.7733 (p) REVERT: B 620 TRP cc_start: 0.8809 (t60) cc_final: 0.8556 (t60) outliers start: 39 outliers final: 30 residues processed: 158 average time/residue: 0.0849 time to fit residues: 18.8585 Evaluate side-chains 144 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 553 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 98 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 80 GLN ** B 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS ** B 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117439 restraints weight = 13100.035| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.96 r_work: 0.3254 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9283 Z= 0.142 Angle : 0.504 8.981 12651 Z= 0.264 Chirality : 0.040 0.148 1520 Planarity : 0.003 0.048 1614 Dihedral : 7.050 83.519 1382 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 3.56 % Allowed : 22.12 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.25), residues: 1186 helix: 2.25 (0.18), residues: 795 sheet: 0.45 (0.75), residues: 48 loop : -0.40 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 624 TYR 0.011 0.001 TYR B 400 PHE 0.013 0.001 PHE A 453 TRP 0.004 0.001 TRP B 233 HIS 0.008 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9283) covalent geometry : angle 0.50411 (12651) hydrogen bonds : bond 0.04250 ( 648) hydrogen bonds : angle 4.05923 ( 1905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 TRP cc_start: 0.8089 (p-90) cc_final: 0.7874 (p-90) REVERT: A 286 MET cc_start: 0.6953 (tmt) cc_final: 0.6752 (tmt) REVERT: A 348 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.6578 (ptm-80) REVERT: A 427 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: A 515 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7770 (mtp85) REVERT: B 325 THR cc_start: 0.8142 (m) cc_final: 0.7721 (p) outliers start: 34 outliers final: 27 residues processed: 149 average time/residue: 0.0903 time to fit residues: 18.6308 Evaluate side-chains 145 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 179 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.140511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118488 restraints weight = 13119.793| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.02 r_work: 0.3270 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9283 Z= 0.125 Angle : 0.484 6.734 12651 Z= 0.256 Chirality : 0.039 0.141 1520 Planarity : 0.004 0.049 1614 Dihedral : 6.614 85.200 1375 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.46 % Favored : 96.46 % Rotamer: Outliers : 3.46 % Allowed : 22.43 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.25), residues: 1186 helix: 2.27 (0.18), residues: 801 sheet: 1.17 (0.85), residues: 37 loop : -0.51 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 366 TYR 0.010 0.001 TYR B 400 PHE 0.012 0.001 PHE B 509 TRP 0.005 0.001 TRP B 233 HIS 0.008 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9283) covalent geometry : angle 0.48395 (12651) hydrogen bonds : bond 0.04112 ( 648) hydrogen bonds : angle 3.99260 ( 1905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 TRP cc_start: 0.8083 (p-90) cc_final: 0.7862 (p-90) REVERT: A 286 MET cc_start: 0.7007 (tmt) cc_final: 0.6760 (tmt) REVERT: A 348 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6978 (ptt-90) REVERT: A 427 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: A 515 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7802 (mtp85) REVERT: B 208 MET cc_start: 0.9078 (tpp) cc_final: 0.8868 (mmt) REVERT: B 325 THR cc_start: 0.8127 (m) cc_final: 0.7727 (p) outliers start: 33 outliers final: 26 residues processed: 148 average time/residue: 0.0853 time to fit residues: 17.8748 Evaluate side-chains 147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 56 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118991 restraints weight = 13081.351| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.00 r_work: 0.3275 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9283 Z= 0.119 Angle : 0.484 6.776 12651 Z= 0.254 Chirality : 0.039 0.142 1520 Planarity : 0.003 0.048 1614 Dihedral : 6.518 87.915 1375 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.46 % Favored : 96.46 % Rotamer: Outliers : 3.25 % Allowed : 22.96 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.25), residues: 1186 helix: 2.32 (0.18), residues: 800 sheet: 0.43 (0.73), residues: 47 loop : -0.53 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 417 TYR 0.010 0.001 TYR B 400 PHE 0.011 0.001 PHE A 453 TRP 0.005 0.001 TRP B 229 HIS 0.009 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9283) covalent geometry : angle 0.48423 (12651) hydrogen bonds : bond 0.04011 ( 648) hydrogen bonds : angle 3.95049 ( 1905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 TRP cc_start: 0.8060 (p-90) cc_final: 0.7853 (p-90) REVERT: A 348 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6834 (ptt-90) REVERT: A 427 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: A 515 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7698 (mtp85) REVERT: B 208 MET cc_start: 0.9011 (tpp) cc_final: 0.8479 (mmt) REVERT: B 325 THR cc_start: 0.8080 (m) cc_final: 0.7691 (p) outliers start: 31 outliers final: 25 residues processed: 149 average time/residue: 0.0794 time to fit residues: 16.8977 Evaluate side-chains 148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.140966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119179 restraints weight = 13101.244| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.99 r_work: 0.3305 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9283 Z= 0.120 Angle : 0.486 6.801 12651 Z= 0.255 Chirality : 0.039 0.142 1520 Planarity : 0.003 0.048 1614 Dihedral : 6.506 89.109 1375 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 3.56 % Allowed : 23.17 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.25), residues: 1186 helix: 2.35 (0.18), residues: 800 sheet: 1.00 (0.83), residues: 37 loop : -0.56 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 417 TYR 0.009 0.001 TYR B 400 PHE 0.011 0.001 PHE B 509 TRP 0.004 0.001 TRP B 229 HIS 0.009 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9283) covalent geometry : angle 0.48633 (12651) hydrogen bonds : bond 0.03970 ( 648) hydrogen bonds : angle 3.93577 ( 1905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 TRP cc_start: 0.8062 (p-90) cc_final: 0.7844 (p-90) REVERT: A 190 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 286 MET cc_start: 0.7035 (tmt) cc_final: 0.6817 (tmt) REVERT: A 348 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6987 (ptt-90) REVERT: A 427 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: A 515 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7791 (mtp85) REVERT: B 208 MET cc_start: 0.9085 (tpp) cc_final: 0.8572 (mmt) REVERT: B 325 THR cc_start: 0.8123 (m) cc_final: 0.7732 (p) outliers start: 34 outliers final: 27 residues processed: 151 average time/residue: 0.0806 time to fit residues: 17.3310 Evaluate side-chains 147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119366 restraints weight = 13130.891| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.97 r_work: 0.3279 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9283 Z= 0.121 Angle : 0.486 6.718 12651 Z= 0.255 Chirality : 0.039 0.142 1520 Planarity : 0.003 0.048 1614 Dihedral : 6.486 89.560 1375 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.29 % Favored : 96.63 % Rotamer: Outliers : 3.56 % Allowed : 23.38 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.25), residues: 1186 helix: 2.35 (0.18), residues: 800 sheet: 1.01 (0.83), residues: 37 loop : -0.55 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 417 TYR 0.009 0.001 TYR B 400 PHE 0.011 0.001 PHE B 336 TRP 0.004 0.001 TRP B 229 HIS 0.009 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9283) covalent geometry : angle 0.48579 (12651) hydrogen bonds : bond 0.03965 ( 648) hydrogen bonds : angle 3.92626 ( 1905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 159 TRP cc_start: 0.8064 (p-90) cc_final: 0.7841 (p-90) REVERT: A 286 MET cc_start: 0.6983 (tmt) cc_final: 0.6766 (tmt) REVERT: A 348 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6990 (ptt-90) REVERT: A 427 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: A 515 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7776 (mtp85) REVERT: B 208 MET cc_start: 0.9086 (tpp) cc_final: 0.8611 (mmt) REVERT: B 325 THR cc_start: 0.8107 (m) cc_final: 0.7710 (p) outliers start: 34 outliers final: 28 residues processed: 147 average time/residue: 0.0888 time to fit residues: 18.0753 Evaluate side-chains 148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 625 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 78 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 95 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 56 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS A 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121373 restraints weight = 12911.149| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.94 r_work: 0.3308 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9283 Z= 0.108 Angle : 0.480 8.528 12651 Z= 0.251 Chirality : 0.039 0.137 1520 Planarity : 0.003 0.048 1614 Dihedral : 6.336 88.362 1375 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.20 % Favored : 96.71 % Rotamer: Outliers : 2.94 % Allowed : 23.90 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.25), residues: 1186 helix: 2.44 (0.18), residues: 800 sheet: 1.03 (0.83), residues: 37 loop : -0.56 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 417 TYR 0.008 0.001 TYR B 400 PHE 0.009 0.001 PHE B 336 TRP 0.005 0.001 TRP B 233 HIS 0.009 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9283) covalent geometry : angle 0.47958 (12651) hydrogen bonds : bond 0.03784 ( 648) hydrogen bonds : angle 3.86370 ( 1905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.47 seconds wall clock time: 34 minutes 21.44 seconds (2061.44 seconds total)