Starting phenix.real_space_refine on Sat Aug 23 17:10:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ho8_34922/08_2025/8ho8_34922_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ho8_34922/08_2025/8ho8_34922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ho8_34922/08_2025/8ho8_34922_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ho8_34922/08_2025/8ho8_34922_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ho8_34922/08_2025/8ho8_34922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ho8_34922/08_2025/8ho8_34922.map" } resolution = 2.24 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= -0.000 sd= 1.000 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 52 5.16 5 C 8418 2.51 5 N 2184 2.21 5 O 2800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13454 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6550 Classifications: {'peptide': 809} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 779} Chain: "B" Number of atoms: 6549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6549 Classifications: {'peptide': 809} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 779} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 158 Classifications: {'water': 158} Link IDs: {None: 157} Chain: "B" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 151 Classifications: {'water': 151} Link IDs: {None: 150} Time building chain proxies: 2.61, per 1000 atoms: 0.19 Number of scatterers: 13454 At special positions: 0 Unit cell: (145.25, 92.13, 97.11, 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 52 16.00 O 2800 8.00 N 2184 7.00 C 8418 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 Links applied BETA1-4 " BGC C 1 " - " BGC C 2 " " BGC D 1 " - " BGC D 2 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 594.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 26 sheets defined 33.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 222 through 228 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.867A pdb=" N PHE A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 313 Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 330 through 343 Processing helix chain 'A' and resid 359 through 370 removed outlier: 3.685A pdb=" N LEU A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 387 removed outlier: 3.721A pdb=" N THR A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.914A pdb=" N TRP A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 421 " --> pdb=" O PRO A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 removed outlier: 4.012A pdb=" N ILE A 436 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.707A pdb=" N VAL A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.954A pdb=" N LYS A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 Processing helix chain 'A' and resid 585 through 594 Processing helix chain 'A' and resid 601 through 614 Processing helix chain 'A' and resid 636 through 640 removed outlier: 3.823A pdb=" N TYR A 640 " --> pdb=" O ILE A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 removed outlier: 3.837A pdb=" N ALA A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TRP A 657 " --> pdb=" O HIS A 653 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 679 removed outlier: 4.082A pdb=" N ILE A 678 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 719 through 730 Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 222 through 228 Processing helix chain 'B' and resid 268 through 271 Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.853A pdb=" N PHE B 291 " --> pdb=" O MET B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 312 Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 359 through 370 removed outlier: 3.760A pdb=" N LEU B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 387 removed outlier: 3.730A pdb=" N THR B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.922A pdb=" N TRP B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 421 " --> pdb=" O PRO B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.998A pdb=" N ILE B 436 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 465 removed outlier: 4.033A pdb=" N VAL B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 468 No H-bonds generated for 'chain 'B' and resid 466 through 468' Processing helix chain 'B' and resid 512 through 532 removed outlier: 3.921A pdb=" N LYS B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP B 524 " --> pdb=" O PHE B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 585 through 594 Processing helix chain 'B' and resid 601 through 614 Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.828A pdb=" N TYR B 640 " --> pdb=" O ILE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 665 removed outlier: 3.733A pdb=" N ALA B 656 " --> pdb=" O CYS B 652 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TRP B 657 " --> pdb=" O HIS B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 677 Processing helix chain 'B' and resid 679 through 684 Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 719 through 730 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.677A pdb=" N SER A 94 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 56 removed outlier: 5.628A pdb=" N ILE A 55 " --> pdb=" O CYS A 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 56 removed outlier: 5.628A pdb=" N ILE A 55 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS A 244 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A 207 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER A 243 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE A 205 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 275 removed outlier: 6.856A pdb=" N VAL A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 315 through 318 Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 440 through 443 removed outlier: 5.753A pdb=" N LYS A 449 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 510 through 511 Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AB2, first strand: chain 'A' and resid 615 through 616 Processing sheet with id=AB3, first strand: chain 'A' and resid 650 through 651 removed outlier: 6.442A pdb=" N ALA A 698 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER A 715 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 735 through 738 removed outlier: 3.889A pdb=" N LEU A 742 " --> pdb=" O LEU A 795 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.636A pdb=" N SER B 94 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 25 through 28 Processing sheet with id=AB7, first strand: chain 'B' and resid 54 through 56 removed outlier: 5.622A pdb=" N ILE B 55 " --> pdb=" O CYS B 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 54 through 56 removed outlier: 5.622A pdb=" N ILE B 55 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS B 244 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER B 207 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER B 243 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE B 205 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.850A pdb=" N VAL B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 315 through 318 removed outlier: 4.811A pdb=" N ILE B 783 " --> pdb=" O ILE B 790 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AC3, first strand: chain 'B' and resid 440 through 443 removed outlier: 5.728A pdb=" N LYS B 449 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AC5, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AC6, first strand: chain 'B' and resid 615 through 616 Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 removed outlier: 6.446A pdb=" N ALA B 698 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER B 715 " --> pdb=" O ALA B 698 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 735 through 738 removed outlier: 3.949A pdb=" N LEU B 742 " --> pdb=" O LEU B 795 " (cutoff:3.500A) 591 hydrogen bonds defined for protein. 1650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4238 1.34 - 1.46: 3223 1.46 - 1.58: 5948 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 13491 Sorted by residual: bond pdb=" CB THR B 20 " pdb=" CG2 THR B 20 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.44e+00 bond pdb=" C5 BGC D 1 " pdb=" O5 BGC D 1 " ideal model delta sigma weight residual 1.411 1.434 -0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" C5 BGC D 2 " pdb=" O5 BGC D 2 " ideal model delta sigma weight residual 1.411 1.434 -0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" C5 BGC C 1 " pdb=" O5 BGC C 1 " ideal model delta sigma weight residual 1.411 1.434 -0.023 2.00e-02 2.50e+03 1.35e+00 bond pdb=" C5 BGC C 2 " pdb=" O5 BGC C 2 " ideal model delta sigma weight residual 1.411 1.433 -0.022 2.00e-02 2.50e+03 1.25e+00 ... (remaining 13486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 17482 1.28 - 2.56: 606 2.56 - 3.84: 128 3.84 - 5.11: 26 5.11 - 6.39: 10 Bond angle restraints: 18252 Sorted by residual: angle pdb=" N TRP B 716 " pdb=" CA TRP B 716 " pdb=" CB TRP B 716 " ideal model delta sigma weight residual 114.17 109.82 4.35 1.14e+00 7.69e-01 1.46e+01 angle pdb=" N TRP A 716 " pdb=" CA TRP A 716 " pdb=" CB TRP A 716 " ideal model delta sigma weight residual 114.17 109.82 4.35 1.14e+00 7.69e-01 1.45e+01 angle pdb=" N VAL A 686 " pdb=" CA VAL A 686 " pdb=" C VAL A 686 " ideal model delta sigma weight residual 111.88 107.91 3.97 1.06e+00 8.90e-01 1.40e+01 angle pdb=" N VAL B 686 " pdb=" CA VAL B 686 " pdb=" C VAL B 686 " ideal model delta sigma weight residual 111.88 107.96 3.92 1.06e+00 8.90e-01 1.37e+01 angle pdb=" N GLY A 741 " pdb=" CA GLY A 741 " pdb=" C GLY A 741 " ideal model delta sigma weight residual 110.38 114.95 -4.57 1.28e+00 6.10e-01 1.27e+01 ... (remaining 18247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6947 17.88 - 35.75: 711 35.75 - 53.63: 235 53.63 - 71.50: 48 71.50 - 89.38: 25 Dihedral angle restraints: 7966 sinusoidal: 3270 harmonic: 4696 Sorted by residual: dihedral pdb=" CA PHE B 413 " pdb=" C PHE B 413 " pdb=" N ASN B 414 " pdb=" CA ASN B 414 " ideal model delta harmonic sigma weight residual -180.00 -156.04 -23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA PHE A 413 " pdb=" C PHE A 413 " pdb=" N ASN A 414 " pdb=" CA ASN A 414 " ideal model delta harmonic sigma weight residual 180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ILE A 330 " pdb=" C ILE A 330 " pdb=" N TRP A 331 " pdb=" CA TRP A 331 " ideal model delta harmonic sigma weight residual 180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 7963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 928 0.029 - 0.058: 578 0.058 - 0.087: 220 0.087 - 0.116: 121 0.116 - 0.145: 33 Chirality restraints: 1880 Sorted by residual: chirality pdb=" CA ILE B 262 " pdb=" N ILE B 262 " pdb=" C ILE B 262 " pdb=" CB ILE B 262 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA VAL B 441 " pdb=" N VAL B 441 " pdb=" C VAL B 441 " pdb=" CB VAL B 441 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1877 not shown) Planarity restraints: 2369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 493 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 494 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 494 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 494 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 480 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C ASP B 480 " 0.024 2.00e-02 2.50e+03 pdb=" O ASP B 480 " -0.009 2.00e-02 2.50e+03 pdb=" N TRP B 481 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 480 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ASP A 480 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP A 480 " 0.008 2.00e-02 2.50e+03 pdb=" N TRP A 481 " 0.008 2.00e-02 2.50e+03 ... (remaining 2366 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3618 2.80 - 3.33: 12039 3.33 - 3.85: 26208 3.85 - 4.38: 32487 4.38 - 4.90: 50151 Nonbonded interactions: 124503 Sorted by model distance: nonbonded pdb=" OD2 ASP B 321 " pdb=" OH TYR B 682 " model vdw 2.278 3.040 nonbonded pdb=" O MET A 67 " pdb=" O HOH A 901 " model vdw 2.301 3.040 nonbonded pdb=" O MET B 67 " pdb=" O HOH B 901 " model vdw 2.304 3.040 nonbonded pdb=" OE2 GLU B 247 " pdb=" O HOH B 902 " model vdw 2.305 3.040 nonbonded pdb=" OE2 GLU A 247 " pdb=" O HOH A 902 " model vdw 2.307 3.040 ... (remaining 124498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 461 or (resid 462 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ or name OH )) or resid 463 through 810)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 4.640 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.400 Find NCS groups from input model: 0.120 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 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 0.061 13493 Z= 0.161 Angle : 0.598 8.510 18258 Z= 0.334 Chirality : 0.046 0.145 1880 Planarity : 0.004 0.036 2369 Dihedral : 17.233 89.378 4990 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.30 % Allowed : 16.98 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.44 (0.21), residues: 1614 helix: 0.99 (0.24), residues: 477 sheet: 1.02 (0.28), residues: 281 loop : -0.31 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.015 0.002 TYR A 13 PHE 0.017 0.002 PHE B 119 TRP 0.021 0.002 TRP A 331 HIS 0.005 0.001 HIS B 653 Details of bonding type rmsd covalent geometry : bond 0.00345 (13491) covalent geometry : angle 0.59001 (18252) hydrogen bonds : bond 0.12737 ( 589) hydrogen bonds : angle 6.56633 ( 1650) link_BETA1-4 : bond 0.01096 ( 2) link_BETA1-4 : angle 5.46067 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.356 Fit side-chains REVERT: A 355 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7902 (mtt90) REVERT: A 605 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8447 (ttpt) REVERT: B 229 LYS cc_start: 0.8332 (ttmt) cc_final: 0.7907 (tttt) outliers start: 18 outliers final: 14 residues processed: 144 average time/residue: 0.8074 time to fit residues: 123.5720 Evaluate side-chains 141 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN B 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.098294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.086402 restraints weight = 14033.513| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.03 r_work: 0.2823 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.0433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 13493 Z= 0.230 Angle : 0.667 7.046 18258 Z= 0.369 Chirality : 0.051 0.167 1880 Planarity : 0.005 0.044 2369 Dihedral : 7.212 55.424 1894 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.46 % Allowed : 15.39 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.36 (0.21), residues: 1614 helix: 0.90 (0.23), residues: 498 sheet: 1.01 (0.28), residues: 281 loop : -0.39 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 57 TYR 0.020 0.002 TYR A 13 PHE 0.020 0.003 PHE A 369 TRP 0.023 0.003 TRP A 331 HIS 0.007 0.002 HIS B 653 Details of bonding type rmsd covalent geometry : bond 0.00523 (13491) covalent geometry : angle 0.66261 (18252) hydrogen bonds : bond 0.06180 ( 589) hydrogen bonds : angle 6.04379 ( 1650) link_BETA1-4 : bond 0.00732 ( 2) link_BETA1-4 : angle 4.37643 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.579 Fit side-chains REVERT: A 379 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: A 802 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8664 (mtpt) REVERT: A 807 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: B 379 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: B 523 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8476 (ttmm) REVERT: B 599 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8311 (mp0) outliers start: 34 outliers final: 17 residues processed: 148 average time/residue: 0.8360 time to fit residues: 131.9907 Evaluate side-chains 146 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 599 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 77 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 9 optimal weight: 0.0070 chunk 59 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 86 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.091848 restraints weight = 14047.744| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.02 r_work: 0.2932 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13493 Z= 0.111 Angle : 0.530 6.135 18258 Z= 0.293 Chirality : 0.045 0.145 1880 Planarity : 0.004 0.038 2369 Dihedral : 6.279 53.341 1884 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.38 % Allowed : 15.39 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.57 (0.21), residues: 1614 helix: 1.26 (0.23), residues: 491 sheet: 1.05 (0.29), residues: 280 loop : -0.35 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 189 TYR 0.014 0.001 TYR A 462 PHE 0.021 0.002 PHE A 369 TRP 0.017 0.001 TRP A 331 HIS 0.004 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00223 (13491) covalent geometry : angle 0.52520 (18252) hydrogen bonds : bond 0.04342 ( 589) hydrogen bonds : angle 5.70460 ( 1650) link_BETA1-4 : bond 0.00321 ( 2) link_BETA1-4 : angle 3.91967 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.562 Fit side-chains REVERT: A 376 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7936 (mtp85) REVERT: A 379 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: A 802 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8665 (mtpt) REVERT: B 379 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: B 560 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8011 (mm-30) REVERT: B 599 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8233 (mp0) outliers start: 33 outliers final: 15 residues processed: 147 average time/residue: 0.8002 time to fit residues: 125.8149 Evaluate side-chains 144 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 148 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.100914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.089101 restraints weight = 13958.393| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.02 r_work: 0.2884 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.0565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13493 Z= 0.165 Angle : 0.591 6.772 18258 Z= 0.326 Chirality : 0.047 0.146 1880 Planarity : 0.004 0.038 2369 Dihedral : 6.420 54.226 1882 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.38 % Allowed : 15.32 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.57 (0.21), residues: 1614 helix: 1.20 (0.23), residues: 492 sheet: 1.05 (0.29), residues: 281 loop : -0.30 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 564 TYR 0.018 0.002 TYR A 13 PHE 0.019 0.002 PHE B 369 TRP 0.019 0.002 TRP A 331 HIS 0.006 0.001 HIS B 653 Details of bonding type rmsd covalent geometry : bond 0.00364 (13491) covalent geometry : angle 0.58643 (18252) hydrogen bonds : bond 0.05163 ( 589) hydrogen bonds : angle 5.79670 ( 1650) link_BETA1-4 : bond 0.00490 ( 2) link_BETA1-4 : angle 4.22807 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.331 Fit side-chains REVERT: A 376 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7984 (mtp85) REVERT: A 379 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: A 802 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8663 (mtpt) REVERT: B 379 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: B 599 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8272 (mp0) REVERT: B 670 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8573 (mtt) outliers start: 33 outliers final: 17 residues processed: 146 average time/residue: 0.8305 time to fit residues: 129.1213 Evaluate side-chains 149 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 103 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 153 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.091310 restraints weight = 14023.703| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.02 r_work: 0.2920 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13493 Z= 0.122 Angle : 0.539 6.278 18258 Z= 0.298 Chirality : 0.045 0.143 1880 Planarity : 0.004 0.039 2369 Dihedral : 6.160 52.826 1882 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.17 % Allowed : 15.46 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.60 (0.21), residues: 1614 helix: 1.32 (0.24), residues: 489 sheet: 1.07 (0.29), residues: 280 loop : -0.34 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.014 0.001 TYR A 462 PHE 0.019 0.002 PHE B 369 TRP 0.017 0.002 TRP A 331 HIS 0.005 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00256 (13491) covalent geometry : angle 0.53446 (18252) hydrogen bonds : bond 0.04442 ( 589) hydrogen bonds : angle 5.67285 ( 1650) link_BETA1-4 : bond 0.00332 ( 2) link_BETA1-4 : angle 4.00362 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.498 Fit side-chains REVERT: A 376 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7938 (mtp85) REVERT: A 379 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: A 802 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8676 (mtpt) REVERT: A 809 ILE cc_start: 0.8996 (mm) cc_final: 0.8742 (mm) REVERT: B 379 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: B 560 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8043 (mm-30) REVERT: B 599 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: B 605 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8623 (ttpt) outliers start: 30 outliers final: 17 residues processed: 148 average time/residue: 0.8006 time to fit residues: 126.2679 Evaluate side-chains 149 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 126 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.085736 restraints weight = 14050.285| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.03 r_work: 0.2811 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 13493 Z= 0.270 Angle : 0.690 7.164 18258 Z= 0.381 Chirality : 0.053 0.193 1880 Planarity : 0.005 0.055 2369 Dihedral : 6.589 54.892 1878 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.46 % Allowed : 14.96 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.42 (0.21), residues: 1614 helix: 0.96 (0.23), residues: 497 sheet: 1.01 (0.28), residues: 282 loop : -0.35 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 57 TYR 0.022 0.003 TYR A 13 PHE 0.019 0.003 PHE B 119 TRP 0.022 0.003 TRP B 331 HIS 0.007 0.002 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00622 (13491) covalent geometry : angle 0.68457 (18252) hydrogen bonds : bond 0.06209 ( 589) hydrogen bonds : angle 5.95999 ( 1650) link_BETA1-4 : bond 0.00962 ( 2) link_BETA1-4 : angle 4.69777 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.502 Fit side-chains REVERT: A 376 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8033 (mtp85) REVERT: A 379 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: A 802 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8687 (mtpt) REVERT: A 807 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: B 188 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: B 379 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: B 523 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8500 (ttmm) REVERT: B 560 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8038 (mm-30) REVERT: B 599 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: B 605 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8617 (ttpt) outliers start: 34 outliers final: 17 residues processed: 145 average time/residue: 0.7824 time to fit residues: 121.0847 Evaluate side-chains 149 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 75 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.0050 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN A 407 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.101399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.089658 restraints weight = 13869.538| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.02 r_work: 0.2891 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13493 Z= 0.145 Angle : 0.578 6.551 18258 Z= 0.319 Chirality : 0.047 0.144 1880 Planarity : 0.004 0.038 2369 Dihedral : 6.267 55.063 1878 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.67 % Allowed : 14.81 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.55 (0.21), residues: 1614 helix: 1.16 (0.24), residues: 492 sheet: 1.03 (0.29), residues: 281 loop : -0.31 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 360 TYR 0.016 0.002 TYR A 13 PHE 0.019 0.002 PHE A 369 TRP 0.019 0.002 TRP B 331 HIS 0.005 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00314 (13491) covalent geometry : angle 0.57252 (18252) hydrogen bonds : bond 0.04895 ( 589) hydrogen bonds : angle 5.77259 ( 1650) link_BETA1-4 : bond 0.00514 ( 2) link_BETA1-4 : angle 4.25179 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.563 Fit side-chains REVERT: A 376 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7982 (mtp85) REVERT: A 379 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: A 802 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8683 (mtpt) REVERT: B 379 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: B 560 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8020 (mm-30) REVERT: B 599 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: B 605 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8592 (ttpt) REVERT: B 670 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8577 (mtt) outliers start: 37 outliers final: 19 residues processed: 155 average time/residue: 0.7136 time to fit residues: 118.2126 Evaluate side-chains 152 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 47 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 159 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.101028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.089281 restraints weight = 13867.007| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.02 r_work: 0.2886 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13493 Z= 0.161 Angle : 0.591 6.774 18258 Z= 0.327 Chirality : 0.047 0.145 1880 Planarity : 0.004 0.040 2369 Dihedral : 6.288 54.924 1878 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.24 % Allowed : 15.25 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.55 (0.21), residues: 1614 helix: 1.18 (0.24), residues: 491 sheet: 1.03 (0.29), residues: 281 loop : -0.32 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 564 TYR 0.018 0.002 TYR A 13 PHE 0.019 0.002 PHE B 369 TRP 0.019 0.002 TRP B 331 HIS 0.005 0.001 HIS B 653 Details of bonding type rmsd covalent geometry : bond 0.00355 (13491) covalent geometry : angle 0.58641 (18252) hydrogen bonds : bond 0.05097 ( 589) hydrogen bonds : angle 5.78235 ( 1650) link_BETA1-4 : bond 0.00527 ( 2) link_BETA1-4 : angle 4.25646 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.394 Fit side-chains REVERT: A 376 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7975 (mtp85) REVERT: A 379 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: A 802 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8681 (mtpt) REVERT: B 379 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: B 560 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8018 (mm-30) REVERT: B 599 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: B 605 LYS cc_start: 0.8847 (ttpt) cc_final: 0.8584 (ttpt) REVERT: B 670 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8577 (mtt) outliers start: 31 outliers final: 19 residues processed: 144 average time/residue: 0.7849 time to fit residues: 120.8533 Evaluate side-chains 150 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.089311 restraints weight = 13977.338| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.03 r_work: 0.2887 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13493 Z= 0.159 Angle : 0.589 6.770 18258 Z= 0.325 Chirality : 0.047 0.144 1880 Planarity : 0.004 0.040 2369 Dihedral : 6.275 54.751 1878 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.17 % Allowed : 15.32 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.54 (0.21), residues: 1614 helix: 1.16 (0.24), residues: 492 sheet: 1.02 (0.29), residues: 281 loop : -0.31 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 564 TYR 0.017 0.002 TYR A 13 PHE 0.019 0.002 PHE B 369 TRP 0.019 0.002 TRP B 331 HIS 0.005 0.001 HIS B 653 Details of bonding type rmsd covalent geometry : bond 0.00349 (13491) covalent geometry : angle 0.58377 (18252) hydrogen bonds : bond 0.05051 ( 589) hydrogen bonds : angle 5.77748 ( 1650) link_BETA1-4 : bond 0.00537 ( 2) link_BETA1-4 : angle 4.25526 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.556 Fit side-chains REVERT: A 376 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7978 (mtp85) REVERT: A 379 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: A 802 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8682 (mtpt) REVERT: B 379 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: B 560 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8027 (mm-30) REVERT: B 599 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: B 605 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8581 (ttpt) REVERT: B 670 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8572 (mtt) outliers start: 30 outliers final: 19 residues processed: 145 average time/residue: 0.8331 time to fit residues: 129.1152 Evaluate side-chains 150 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 156 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 76 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.102915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.091229 restraints weight = 13898.249| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.01 r_work: 0.2919 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13493 Z= 0.122 Angle : 0.544 6.537 18258 Z= 0.300 Chirality : 0.045 0.143 1880 Planarity : 0.004 0.041 2369 Dihedral : 6.023 53.182 1878 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.88 % Allowed : 15.53 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.58 (0.21), residues: 1614 helix: 1.27 (0.24), residues: 490 sheet: 1.04 (0.29), residues: 280 loop : -0.34 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.014 0.001 TYR A 462 PHE 0.019 0.002 PHE A 369 TRP 0.019 0.002 TRP A 331 HIS 0.005 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00257 (13491) covalent geometry : angle 0.53946 (18252) hydrogen bonds : bond 0.04434 ( 589) hydrogen bonds : angle 5.66508 ( 1650) link_BETA1-4 : bond 0.00384 ( 2) link_BETA1-4 : angle 4.01907 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.541 Fit side-chains REVERT: A 376 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7935 (mtp85) REVERT: A 379 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: A 802 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8694 (mtpt) REVERT: B 379 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: B 560 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8018 (mm-30) REVERT: B 599 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8210 (mp0) REVERT: B 605 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8571 (ttpt) outliers start: 26 outliers final: 19 residues processed: 145 average time/residue: 0.8803 time to fit residues: 136.1323 Evaluate side-chains 149 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 155 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.097969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.085977 restraints weight = 14044.584| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.03 r_work: 0.2816 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 13493 Z= 0.262 Angle : 0.689 7.068 18258 Z= 0.381 Chirality : 0.052 0.185 1880 Planarity : 0.005 0.053 2369 Dihedral : 6.598 55.125 1878 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.17 % Allowed : 15.25 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.40 (0.21), residues: 1614 helix: 0.95 (0.23), residues: 498 sheet: 0.98 (0.28), residues: 282 loop : -0.35 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 57 TYR 0.022 0.003 TYR A 13 PHE 0.019 0.003 PHE B 119 TRP 0.021 0.003 TRP B 331 HIS 0.007 0.002 HIS B 653 Details of bonding type rmsd covalent geometry : bond 0.00603 (13491) covalent geometry : angle 0.68347 (18252) hydrogen bonds : bond 0.06142 ( 589) hydrogen bonds : angle 5.95807 ( 1650) link_BETA1-4 : bond 0.00932 ( 2) link_BETA1-4 : angle 4.68888 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4256.55 seconds wall clock time: 73 minutes 34.76 seconds (4414.76 seconds total)