Starting phenix.real_space_refine on Wed Sep 25 18:58:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/09_2024/7r8b_24314.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/09_2024/7r8b_24314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/09_2024/7r8b_24314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/09_2024/7r8b_24314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/09_2024/7r8b_24314.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/09_2024/7r8b_24314.cif" } resolution = 3.1 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= 0.004 sd= 0.059 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 67 5.16 5 C 7027 2.51 5 N 1838 2.21 5 O 1936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10868 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4626 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 22, 'TRANS': 565} Chain breaks: 3 Chain: "B" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4482 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 539} Chain breaks: 3 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.98, per 1000 atoms: 0.64 Number of scatterers: 10868 At special positions: 0 Unit cell: (114.121, 105.791, 122.451, 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 67 16.00 O 1936 8.00 N 1838 7.00 C 7027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " 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: 2.67 Conformation dependent library (CDL) restraints added in 1.5 seconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 52.9% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 160 through 175 removed outlier: 4.178A pdb=" N PHE A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.604A pdb=" N ALA A 181 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 224 through 240 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 311 through 332 Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.873A pdb=" N HIS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 removed outlier: 3.604A pdb=" N LYS A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 405 removed outlier: 5.299A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 454 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix removed outlier: 4.196A pdb=" N GLN A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 491 Proline residue: A 473 - end of helix removed outlier: 4.877A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 524 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 526 through 545 Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 566 through 580 removed outlier: 4.272A pdb=" N TYR A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 614 through 618 removed outlier: 4.428A pdb=" N THR A 617 " --> pdb=" O PRO A 614 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 618 " --> pdb=" O GLY A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 618' Processing helix chain 'A' and resid 619 through 646 removed outlier: 4.481A pdb=" N ILE A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Proline residue: A 632 - end of helix Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.560A pdb=" N CYS B 200 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 201 " --> pdb=" O ARG B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 197 through 201' Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 244 through 261 Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.600A pdb=" N ARG B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 306 removed outlier: 3.560A pdb=" N ALA B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 325 removed outlier: 3.750A pdb=" N THR B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 353 removed outlier: 4.046A pdb=" N LEU B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 Processing helix chain 'B' and resid 413 through 435 Processing helix chain 'B' and resid 444 through 458 Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 490 through 513 removed outlier: 4.013A pdb=" N PHE B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Proline residue: B 502 - end of helix Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 525 through 553 Processing helix chain 'B' and resid 555 through 573 Processing helix chain 'B' and resid 585 through 593 Processing helix chain 'B' and resid 594 through 608 Processing helix chain 'B' and resid 627 through 633 removed outlier: 3.618A pdb=" N MET B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 665 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.907A pdb=" N LEU D 103 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 77 removed outlier: 5.875A pdb=" N LYS A 70 " --> pdb=" O TYR A 45 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TYR A 45 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU A 74 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU A 41 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL A 76 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLY A 39 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE A 40 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR A 114 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS A 42 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLU A 112 " --> pdb=" O HIS A 42 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL A 113 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.931A pdb=" N VAL A 245 " --> pdb=" O GLN A 80 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 273 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER A 267 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 96 removed outlier: 7.485A pdb=" N PHE B 93 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG B 50 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL B 95 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU B 48 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.390A pdb=" N LEU B 101 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N MET B 100 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU B 284 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 102 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N MET B 286 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 104 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 293 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR B 287 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 81 removed outlier: 6.698A pdb=" N TRP C 55 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL C 69 " --> pdb=" O MET C 53 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET C 53 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 24 through 27 Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.561A pdb=" N LEU D 31 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLN D 57 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ARG D 66 " --> pdb=" O GLN D 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.561A pdb=" N LEU D 31 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR D 117 " --> pdb=" O GLN D 110 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1749 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: 3.43 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3453 1.34 - 1.46: 2633 1.46 - 1.58: 4913 1.58 - 1.70: 0 1.70 - 1.82: 107 Bond restraints: 11106 Sorted by residual: bond pdb=" C PHE A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.51e-02 4.39e+03 4.49e+00 bond pdb=" CA LYS B 126 " pdb=" CB LYS B 126 " ideal model delta sigma weight residual 1.526 1.545 -0.020 1.68e-02 3.54e+03 1.37e+00 bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.25e+00 bond pdb=" C3 CLR A 701 " pdb=" O1 CLR A 701 " ideal model delta sigma weight residual 1.413 1.391 0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" CA THR A 430 " pdb=" C THR A 430 " ideal model delta sigma weight residual 1.520 1.533 -0.013 1.23e-02 6.61e+03 1.08e+00 ... (remaining 11101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 14648 1.41 - 2.82: 306 2.82 - 4.24: 59 4.24 - 5.65: 19 5.65 - 7.06: 9 Bond angle restraints: 15041 Sorted by residual: angle pdb=" C PRO A 556 " pdb=" N ILE A 557 " pdb=" CA ILE A 557 " ideal model delta sigma weight residual 120.33 123.55 -3.22 8.00e-01 1.56e+00 1.62e+01 angle pdb=" C VAL A 404 " pdb=" N LEU A 405 " pdb=" CA LEU A 405 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C ALA D 70 " pdb=" N ALA D 71 " pdb=" CA ALA D 71 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" N VAL B 205 " pdb=" CA VAL B 205 " pdb=" C VAL B 205 " ideal model delta sigma weight residual 111.91 109.05 2.86 8.90e-01 1.26e+00 1.04e+01 angle pdb=" N ILE B 292 " pdb=" CA ILE B 292 " pdb=" C ILE B 292 " ideal model delta sigma weight residual 111.90 109.40 2.50 8.10e-01 1.52e+00 9.53e+00 ... (remaining 15036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 6087 17.40 - 34.81: 494 34.81 - 52.21: 95 52.21 - 69.61: 29 69.61 - 87.02: 7 Dihedral angle restraints: 6712 sinusoidal: 2754 harmonic: 3958 Sorted by residual: dihedral pdb=" CB ARG A 198 " pdb=" CG ARG A 198 " pdb=" CD ARG A 198 " pdb=" NE ARG A 198 " ideal model delta sinusoidal sigma weight residual 60.00 119.50 -59.50 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG A 122 " pdb=" CA ARG A 122 " pdb=" CB ARG A 122 " pdb=" CG ARG A 122 " ideal model delta sinusoidal sigma weight residual -60.00 -118.56 58.56 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB MET B 558 " pdb=" CG MET B 558 " pdb=" SD MET B 558 " pdb=" CE MET B 558 " ideal model delta sinusoidal sigma weight residual -60.00 -2.80 -57.20 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 6709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1597 0.072 - 0.143: 112 0.143 - 0.215: 2 0.215 - 0.286: 3 0.286 - 0.358: 2 Chirality restraints: 1716 Sorted by residual: chirality pdb=" C14 CLR B 801 " pdb=" C13 CLR B 801 " pdb=" C15 CLR B 801 " pdb=" C8 CLR B 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C14 CLR A 701 " pdb=" C13 CLR A 701 " pdb=" C15 CLR A 701 " pdb=" C8 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C9 CLR B 801 " pdb=" C10 CLR B 801 " pdb=" C11 CLR B 801 " pdb=" C8 CLR B 801 " both_signs ideal model delta sigma weight residual False -2.45 -2.69 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1713 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 490 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO B 491 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 276 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 277 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 126 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C LYS B 126 " 0.020 2.00e-02 2.50e+03 pdb=" O LYS B 126 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE B 127 " -0.007 2.00e-02 2.50e+03 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 154 2.66 - 3.22: 9864 3.22 - 3.78: 16807 3.78 - 4.34: 22984 4.34 - 4.90: 38658 Nonbonded interactions: 88467 Sorted by model distance: nonbonded pdb=" OG SER D 27 " pdb=" OG1 THR D 42 " model vdw 2.103 3.040 nonbonded pdb=" O VAL A 542 " pdb=" OG SER A 546 " model vdw 2.204 3.040 nonbonded pdb=" OG SER D 83 " pdb=" OG1 THR D 94 " model vdw 2.258 3.040 nonbonded pdb=" O ASN A 410 " pdb=" OG1 THR A 586 " model vdw 2.267 3.040 nonbonded pdb=" NE ARG A 550 " pdb=" O LEU B 434 " model vdw 2.290 3.120 ... (remaining 88462 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: 3.860 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.130 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.002 0.032 11106 Z= 0.132 Angle : 0.553 7.058 15041 Z= 0.314 Chirality : 0.040 0.358 1716 Planarity : 0.003 0.035 1884 Dihedral : 13.495 87.019 4163 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.94 % Allowed : 18.92 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.73 (0.21), residues: 1351 helix: 0.06 (0.18), residues: 702 sheet: -1.48 (0.35), residues: 182 loop : -2.85 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 584 HIS 0.003 0.000 HIS B 531 PHE 0.006 0.001 PHE A 502 TYR 0.007 0.001 TYR C 115 ARG 0.003 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 1.129 Fit side-chains REVERT: A 118 ARG cc_start: 0.7989 (mpt180) cc_final: 0.7713 (mmt90) REVERT: A 134 GLN cc_start: 0.7281 (tt0) cc_final: 0.6876 (tm-30) REVERT: A 313 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 437 ASN cc_start: 0.7595 (m-40) cc_final: 0.7357 (m110) REVERT: A 523 ILE cc_start: 0.7575 (tp) cc_final: 0.7314 (tp) REVERT: A 553 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8218 (mm110) REVERT: B 446 MET cc_start: 0.7227 (mmt) cc_final: 0.7018 (mmt) REVERT: C 86 LYS cc_start: 0.8507 (tttp) cc_final: 0.8245 (ttmt) REVERT: C 101 TYR cc_start: 0.8674 (m-80) cc_final: 0.8163 (m-80) REVERT: D 90 ASP cc_start: 0.7779 (m-30) cc_final: 0.7572 (m-30) REVERT: D 99 GLU cc_start: 0.8270 (mp0) cc_final: 0.7320 (mp0) outliers start: 23 outliers final: 11 residues processed: 227 average time/residue: 0.2600 time to fit residues: 80.0206 Evaluate side-chains 154 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 179 HIS A 206 GLN A 230 GLN A 347 HIS A 454 GLN A 462 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN A 597 ASN A 604 GLN A 607 GLN B 43 GLN B 99 GLN B 135 ASN B 153 GLN B 172 GLN B 250 ASN B 262 ASN B 271 GLN B 438 HIS B 526 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN C 75 ASN D 58 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11106 Z= 0.249 Angle : 0.576 9.668 15041 Z= 0.288 Chirality : 0.042 0.242 1716 Planarity : 0.004 0.036 1884 Dihedral : 5.322 47.636 1646 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.63 % Allowed : 18.16 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1351 helix: 1.15 (0.19), residues: 707 sheet: -0.98 (0.36), residues: 190 loop : -2.26 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 584 HIS 0.005 0.001 HIS B 531 PHE 0.016 0.001 PHE B 595 TYR 0.019 0.001 TYR D 111 ARG 0.006 0.001 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 149 time to evaluate : 1.317 Fit side-chains REVERT: B 50 ARG cc_start: 0.7288 (ttp-170) cc_final: 0.7014 (ttm170) REVERT: B 116 ASP cc_start: 0.8097 (m-30) cc_final: 0.7809 (m-30) REVERT: B 319 ASP cc_start: 0.7534 (m-30) cc_final: 0.7263 (m-30) REVERT: C 65 GLU cc_start: 0.8304 (tt0) cc_final: 0.8025 (tt0) REVERT: C 86 LYS cc_start: 0.8602 (tttp) cc_final: 0.8337 (ttmt) REVERT: C 101 TYR cc_start: 0.8785 (m-80) cc_final: 0.8205 (m-80) REVERT: D 75 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: D 99 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.6991 (mp0) outliers start: 43 outliers final: 26 residues processed: 180 average time/residue: 0.2426 time to fit residues: 61.4643 Evaluate side-chains 163 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS A 597 ASN B 150 HIS B 172 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11106 Z= 0.322 Angle : 0.578 8.309 15041 Z= 0.292 Chirality : 0.043 0.173 1716 Planarity : 0.004 0.037 1884 Dihedral : 4.996 46.076 1637 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.65 % Allowed : 16.64 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.23), residues: 1351 helix: 1.43 (0.20), residues: 706 sheet: -0.85 (0.36), residues: 197 loop : -1.95 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 584 HIS 0.003 0.001 HIS B 531 PHE 0.015 0.002 PHE B 461 TYR 0.018 0.002 TYR D 111 ARG 0.004 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 130 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: A 313 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6951 (tm-30) REVERT: A 353 MET cc_start: 0.7008 (pmm) cc_final: 0.6776 (pmm) REVERT: B 116 ASP cc_start: 0.8058 (m-30) cc_final: 0.7785 (m-30) REVERT: B 214 SER cc_start: 0.7419 (OUTLIER) cc_final: 0.7113 (p) REVERT: B 513 MET cc_start: 0.8133 (mtt) cc_final: 0.7870 (mtt) REVERT: C 86 LYS cc_start: 0.8603 (tttp) cc_final: 0.8143 (ttmt) REVERT: C 101 TYR cc_start: 0.8829 (m-80) cc_final: 0.8204 (m-80) REVERT: D 99 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7054 (mp0) outliers start: 55 outliers final: 36 residues processed: 175 average time/residue: 0.2380 time to fit residues: 58.8915 Evaluate side-chains 166 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 128 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.0010 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS A 597 ASN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11106 Z= 0.270 Angle : 0.559 11.390 15041 Z= 0.282 Chirality : 0.042 0.189 1716 Planarity : 0.004 0.035 1884 Dihedral : 4.997 48.275 1637 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.05 % Allowed : 17.31 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1351 helix: 1.73 (0.20), residues: 700 sheet: -0.71 (0.36), residues: 197 loop : -1.79 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.027 0.001 PHE C 89 TYR 0.015 0.001 TYR D 111 ARG 0.003 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 127 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7809 (mmt90) cc_final: 0.7479 (mmt90) REVERT: A 134 GLN cc_start: 0.7748 (tt0) cc_final: 0.7244 (pt0) REVERT: A 313 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6984 (tm-30) REVERT: B 50 ARG cc_start: 0.7156 (ttp-170) cc_final: 0.6804 (ttm110) REVERT: B 116 ASP cc_start: 0.8066 (m-30) cc_final: 0.7798 (m-30) REVERT: B 477 MET cc_start: 0.8500 (ttp) cc_final: 0.8230 (ttp) REVERT: C 86 LYS cc_start: 0.8590 (tttp) cc_final: 0.8155 (ttmt) REVERT: C 101 TYR cc_start: 0.8802 (m-80) cc_final: 0.8139 (m-80) REVERT: D 59 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8576 (mmtm) REVERT: D 99 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7055 (mp0) outliers start: 48 outliers final: 37 residues processed: 167 average time/residue: 0.2454 time to fit residues: 57.2920 Evaluate side-chains 167 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 129 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 0.3980 chunk 117 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 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 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11106 Z= 0.193 Angle : 0.533 12.345 15041 Z= 0.266 Chirality : 0.040 0.165 1716 Planarity : 0.003 0.034 1884 Dihedral : 4.931 51.210 1637 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.89 % Allowed : 17.40 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1351 helix: 1.95 (0.20), residues: 700 sheet: -0.61 (0.36), residues: 197 loop : -1.67 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.014 0.001 PHE C 89 TYR 0.011 0.001 TYR D 111 ARG 0.003 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 131 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7787 (mmt90) cc_final: 0.7456 (mmt90) REVERT: A 134 GLN cc_start: 0.7695 (tt0) cc_final: 0.7239 (pt0) REVERT: A 302 MET cc_start: 0.8108 (tpp) cc_final: 0.7873 (mmm) REVERT: A 313 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6897 (tm-30) REVERT: B 50 ARG cc_start: 0.7158 (ttp-170) cc_final: 0.6800 (ttm110) REVERT: B 116 ASP cc_start: 0.8057 (m-30) cc_final: 0.7777 (m-30) REVERT: B 477 MET cc_start: 0.8485 (ttp) cc_final: 0.8211 (ttp) REVERT: C 86 LYS cc_start: 0.8589 (tttp) cc_final: 0.8141 (ttmt) REVERT: C 101 TYR cc_start: 0.8769 (m-80) cc_final: 0.8174 (m-80) REVERT: D 99 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7056 (mp0) outliers start: 46 outliers final: 34 residues processed: 169 average time/residue: 0.2548 time to fit residues: 60.0146 Evaluate side-chains 161 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 10 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11106 Z= 0.182 Angle : 0.539 13.874 15041 Z= 0.267 Chirality : 0.040 0.195 1716 Planarity : 0.003 0.033 1884 Dihedral : 4.892 53.371 1637 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.80 % Allowed : 17.99 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1351 helix: 2.06 (0.20), residues: 700 sheet: -0.52 (0.37), residues: 197 loop : -1.60 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.004 0.000 HIS B 531 PHE 0.027 0.001 PHE C 89 TYR 0.016 0.001 TYR B 571 ARG 0.003 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7719 (mmt90) cc_final: 0.7474 (mmt90) REVERT: A 134 GLN cc_start: 0.7665 (tt0) cc_final: 0.7226 (pt0) REVERT: A 302 MET cc_start: 0.8158 (tpp) cc_final: 0.7925 (mmm) REVERT: A 313 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6895 (tm-30) REVERT: B 50 ARG cc_start: 0.7162 (ttp-170) cc_final: 0.6806 (ttm110) REVERT: B 116 ASP cc_start: 0.8070 (m-30) cc_final: 0.7772 (m-30) REVERT: C 86 LYS cc_start: 0.8566 (tttp) cc_final: 0.8141 (ttmt) REVERT: C 101 TYR cc_start: 0.8758 (m-80) cc_final: 0.8153 (m-80) REVERT: D 99 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7043 (mp0) outliers start: 45 outliers final: 36 residues processed: 162 average time/residue: 0.2605 time to fit residues: 58.8334 Evaluate side-chains 160 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11106 Z= 0.235 Angle : 0.566 13.454 15041 Z= 0.280 Chirality : 0.041 0.194 1716 Planarity : 0.003 0.033 1884 Dihedral : 4.867 54.249 1636 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.22 % Allowed : 17.48 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.24), residues: 1351 helix: 2.05 (0.20), residues: 701 sheet: -0.51 (0.36), residues: 197 loop : -1.55 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.025 0.001 PHE C 89 TYR 0.016 0.001 TYR B 571 ARG 0.004 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 125 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7717 (mmt90) cc_final: 0.7448 (mmt90) REVERT: A 134 GLN cc_start: 0.7725 (tt0) cc_final: 0.7274 (pt0) REVERT: A 302 MET cc_start: 0.8165 (tpp) cc_final: 0.7950 (mmm) REVERT: A 313 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6919 (tm-30) REVERT: B 116 ASP cc_start: 0.8075 (m-30) cc_final: 0.7797 (m-30) REVERT: C 86 LYS cc_start: 0.8558 (tttp) cc_final: 0.8161 (ttmt) REVERT: C 101 TYR cc_start: 0.8757 (m-80) cc_final: 0.8207 (m-80) REVERT: D 37 GLU cc_start: 0.8458 (pm20) cc_final: 0.8228 (pm20) REVERT: D 99 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7072 (mp0) outliers start: 50 outliers final: 42 residues processed: 163 average time/residue: 0.2427 time to fit residues: 55.2790 Evaluate side-chains 167 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11106 Z= 0.217 Angle : 0.558 13.840 15041 Z= 0.276 Chirality : 0.041 0.174 1716 Planarity : 0.003 0.033 1884 Dihedral : 4.862 56.290 1636 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.72 % Allowed : 17.99 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1351 helix: 2.08 (0.20), residues: 700 sheet: -0.47 (0.36), residues: 197 loop : -1.48 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.017 0.001 PHE C 89 TYR 0.015 0.001 TYR B 571 ARG 0.004 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7712 (mmt90) cc_final: 0.7428 (mmt90) REVERT: A 134 GLN cc_start: 0.7712 (tt0) cc_final: 0.7277 (pt0) REVERT: A 302 MET cc_start: 0.8171 (tpp) cc_final: 0.7958 (mmm) REVERT: A 313 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6948 (tm-30) REVERT: B 50 ARG cc_start: 0.7143 (ttp-170) cc_final: 0.6872 (ttm110) REVERT: B 477 MET cc_start: 0.8492 (ttp) cc_final: 0.8217 (ttp) REVERT: C 86 LYS cc_start: 0.8571 (tttp) cc_final: 0.8175 (ttmt) REVERT: C 101 TYR cc_start: 0.8770 (m-80) cc_final: 0.8142 (m-80) REVERT: D 99 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7074 (mp0) outliers start: 44 outliers final: 40 residues processed: 160 average time/residue: 0.2454 time to fit residues: 55.0700 Evaluate side-chains 165 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 124 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 120 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11106 Z= 0.197 Angle : 0.569 14.314 15041 Z= 0.280 Chirality : 0.041 0.173 1716 Planarity : 0.003 0.033 1884 Dihedral : 4.852 58.386 1636 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.97 % Allowed : 17.91 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.24), residues: 1351 helix: 2.12 (0.20), residues: 700 sheet: -0.39 (0.36), residues: 196 loop : -1.44 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.016 0.001 PHE C 89 TYR 0.015 0.001 TYR B 571 ARG 0.004 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 123 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 108 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8255 (p) REVERT: A 118 ARG cc_start: 0.7707 (mmt90) cc_final: 0.7421 (mmt90) REVERT: A 134 GLN cc_start: 0.7699 (tt0) cc_final: 0.7271 (pt0) REVERT: A 313 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6932 (tm-30) REVERT: B 50 ARG cc_start: 0.7152 (ttp-170) cc_final: 0.6884 (ttm110) REVERT: B 477 MET cc_start: 0.8500 (ttp) cc_final: 0.8224 (ttp) REVERT: C 39 LEU cc_start: 0.8867 (mp) cc_final: 0.8414 (mp) REVERT: C 86 LYS cc_start: 0.8515 (tttp) cc_final: 0.8134 (ttmt) REVERT: C 101 TYR cc_start: 0.8726 (m-80) cc_final: 0.8120 (m-80) REVERT: D 99 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7072 (mp0) outliers start: 47 outliers final: 44 residues processed: 160 average time/residue: 0.2498 time to fit residues: 56.1868 Evaluate side-chains 167 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 121 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS B 199 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11106 Z= 0.237 Angle : 0.574 14.764 15041 Z= 0.285 Chirality : 0.041 0.198 1716 Planarity : 0.003 0.033 1884 Dihedral : 4.891 59.329 1636 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.80 % Allowed : 17.99 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1351 helix: 2.08 (0.20), residues: 701 sheet: -0.38 (0.37), residues: 185 loop : -1.48 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.013 0.001 PHE C 89 TYR 0.015 0.001 TYR B 571 ARG 0.004 0.000 ARG B 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 121 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 108 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8234 (p) REVERT: A 118 ARG cc_start: 0.7702 (mmt90) cc_final: 0.7395 (mmt90) REVERT: A 134 GLN cc_start: 0.7728 (tt0) cc_final: 0.7280 (pt0) REVERT: A 313 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6917 (tm-30) REVERT: B 50 ARG cc_start: 0.7167 (ttp-170) cc_final: 0.6899 (ttm110) REVERT: C 86 LYS cc_start: 0.8440 (tttp) cc_final: 0.8038 (ttmt) REVERT: C 101 TYR cc_start: 0.8760 (m-80) cc_final: 0.8160 (m-80) REVERT: C 104 MET cc_start: 0.8737 (mmm) cc_final: 0.8279 (mmm) REVERT: D 99 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7076 (mp0) outliers start: 45 outliers final: 41 residues processed: 158 average time/residue: 0.2417 time to fit residues: 53.3584 Evaluate side-chains 163 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 107 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 0.0040 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.085093 restraints weight = 15518.999| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.20 r_work: 0.2799 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11106 Z= 0.143 Angle : 0.543 14.678 15041 Z= 0.269 Chirality : 0.040 0.205 1716 Planarity : 0.003 0.032 1884 Dihedral : 4.773 55.473 1636 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.29 % Allowed : 18.33 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.07 (0.24), residues: 1351 helix: 2.24 (0.20), residues: 702 sheet: -0.23 (0.37), residues: 179 loop : -1.34 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.026 0.001 PHE C 89 TYR 0.014 0.001 TYR B 571 ARG 0.004 0.000 ARG B 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2546.45 seconds wall clock time: 46 minutes 3.33 seconds (2763.33 seconds total)