Starting phenix.real_space_refine on Thu Jul 2 08:53:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d43_27173/07_2026/8d43_27173.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d43_27173/07_2026/8d43_27173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d43_27173/07_2026/8d43_27173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d43_27173/07_2026/8d43_27173.map" model { file = "/net/cci-nas-00/data/ceres_data/8d43_27173/07_2026/8d43_27173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d43_27173/07_2026/8d43_27173.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d43_27173/07_2026/8d43_27173.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d43_27173/07_2026/8d43_27173.cif" } resolution = 2.88 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= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 35 5.16 5 C 4926 2.51 5 N 1346 2.21 5 O 1454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7763 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6952 Classifications: {'peptide': 862} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 801} Chain breaks: 2 Chain: "B" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 758 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.89, per 1000 atoms: 0.24 Number of scatterers: 7763 At special positions: 0 Unit cell: (70.62, 88.81, 116.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 35 16.00 O 1454 8.00 N 1346 7.00 C 4926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 99 " distance=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN A 97 " Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 482.6 milliseconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 22.3% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 371 through 383 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.624A pdb=" N VAL A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 453 through 459 removed outlier: 3.799A pdb=" N LYS A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 484 Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.517A pdb=" N GLY A 565 " --> pdb=" O HIS A 562 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 566 " --> pdb=" O TYR A 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 566' Processing helix chain 'A' and resid 571 through 592 removed outlier: 4.340A pdb=" N GLY A 576 " --> pdb=" O HIS A 572 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.689A pdb=" N ARG A 610 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 611 " --> pdb=" O SER A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 611' Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 628 through 639 removed outlier: 3.875A pdb=" N VAL A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 668 Processing helix chain 'A' and resid 685 through 689 removed outlier: 3.912A pdb=" N LEU A 689 " --> pdb=" O PRO A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.597A pdb=" N ILE A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 697 " --> pdb=" O HIS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 721 Processing helix chain 'A' and resid 728 through 733 removed outlier: 4.203A pdb=" N GLN A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 removed outlier: 4.113A pdb=" N ASN A 741 " --> pdb=" O THR A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 Processing helix chain 'A' and resid 852 through 857 removed outlier: 3.812A pdb=" N THR A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.390A pdb=" N HIS B 29 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 removed outlier: 3.830A pdb=" N MET A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS A 255 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 133 removed outlier: 5.579A pdb=" N VAL A 130 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR A 141 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR A 147 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 167 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 133 removed outlier: 5.579A pdb=" N VAL A 130 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR A 141 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR A 147 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 167 " --> pdb=" O PRO A 251 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 321 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA6, first strand: chain 'A' and resid 644 through 645 removed outlier: 6.870A pdb=" N VAL A 614 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 599 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TRP A 615 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 601 " --> pdb=" O TRP A 615 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 600 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 463 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N TRP A 540 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA A 465 " --> pdb=" O TRP A 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AA8, first strand: chain 'A' and resid 726 through 727 removed outlier: 3.941A pdb=" N LEU A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 764 through 769 Processing sheet with id=AB1, first strand: chain 'A' and resid 808 through 812 removed outlier: 6.129A pdb=" N ILE A 828 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 891 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP A 888 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY A 932 " --> pdb=" O TRP A 888 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU A 890 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A 916 " --> pdb=" O ARG A 929 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 840 through 846 removed outlier: 3.596A pdb=" N TRP A 939 " --> pdb=" O SER A 874 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AB4, first strand: chain 'B' and resid 74 through 77 273 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2400 1.33 - 1.46: 1518 1.46 - 1.58: 4014 1.58 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 7985 Sorted by residual: bond pdb=" CA SER A 506 " pdb=" C SER A 506 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.22e-02 6.72e+03 7.99e+00 bond pdb=" CA ASP B 101 " pdb=" C ASP B 101 " ideal model delta sigma weight residual 1.525 1.493 0.031 1.28e-02 6.10e+03 5.99e+00 bond pdb=" C CYS B 70 " pdb=" O CYS B 70 " ideal model delta sigma weight residual 1.240 1.214 0.025 1.16e-02 7.43e+03 4.68e+00 bond pdb=" CA ILE B 46 " pdb=" C ILE B 46 " ideal model delta sigma weight residual 1.522 1.506 0.016 8.30e-03 1.45e+04 3.58e+00 bond pdb=" C ARG A 110 " pdb=" N PRO A 111 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.32e-02 5.74e+03 3.57e+00 ... (remaining 7980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 10547 2.19 - 4.38: 281 4.38 - 6.58: 31 6.58 - 8.77: 11 8.77 - 10.96: 3 Bond angle restraints: 10873 Sorted by residual: angle pdb=" N SER A 506 " pdb=" CA SER A 506 " pdb=" C SER A 506 " ideal model delta sigma weight residual 108.96 98.00 10.96 1.59e+00 3.96e-01 4.75e+01 angle pdb=" C ARG A 110 " pdb=" N PRO A 111 " pdb=" CA PRO A 111 " ideal model delta sigma weight residual 119.76 113.52 6.24 1.00e+00 1.00e+00 3.89e+01 angle pdb=" N ASP B 101 " pdb=" CA ASP B 101 " pdb=" C ASP B 101 " ideal model delta sigma weight residual 108.20 97.58 10.62 1.71e+00 3.42e-01 3.86e+01 angle pdb=" N GLY B 61 " pdb=" CA GLY B 61 " pdb=" C GLY B 61 " ideal model delta sigma weight residual 115.64 108.38 7.26 1.46e+00 4.69e-01 2.48e+01 angle pdb=" N TRP A 503 " pdb=" CA TRP A 503 " pdb=" CB TRP A 503 " ideal model delta sigma weight residual 110.39 117.49 -7.10 1.61e+00 3.86e-01 1.94e+01 ... (remaining 10868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3963 18.00 - 36.00: 525 36.00 - 54.01: 155 54.01 - 72.01: 34 72.01 - 90.01: 12 Dihedral angle restraints: 4689 sinusoidal: 1915 harmonic: 2774 Sorted by residual: dihedral pdb=" N TRP A 503 " pdb=" C TRP A 503 " pdb=" CA TRP A 503 " pdb=" CB TRP A 503 " ideal model delta harmonic sigma weight residual 122.80 136.80 -14.00 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" C TRP A 503 " pdb=" N TRP A 503 " pdb=" CA TRP A 503 " pdb=" CB TRP A 503 " ideal model delta harmonic sigma weight residual -122.60 -133.76 11.16 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" CA ASN A 97 " pdb=" C ASN A 97 " pdb=" N MET A 98 " pdb=" CA MET A 98 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 4686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1067 0.102 - 0.205: 80 0.205 - 0.307: 6 0.307 - 0.410: 1 0.410 - 0.512: 1 Chirality restraints: 1155 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.32e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.22e+01 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.33 0.07 2.00e-02 2.50e+03 1.14e+01 ... (remaining 1152 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.143 2.00e-02 2.50e+03 1.19e-01 1.76e+02 pdb=" C7 NAG C 1 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.191 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 503 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO A 504 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 504 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 504 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 826 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO A 827 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 827 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 827 " 0.032 5.00e-02 4.00e+02 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 1 2.08 - 2.78: 1750 2.78 - 3.49: 10223 3.49 - 4.19: 20876 4.19 - 4.90: 35979 Nonbonded interactions: 68829 Sorted by model distance: nonbonded pdb=" OD2 ASP B 57 " pdb="CA CA B 602 " model vdw 1.371 2.510 nonbonded pdb=" OE2 GLU B 105 " pdb="CA CA B 601 " model vdw 2.091 2.510 nonbonded pdb=" OD1 ASP B 94 " pdb="CA CA B 601 " model vdw 2.112 2.510 nonbonded pdb=" OD1 ASP B 53 " pdb="CA CA B 602 " model vdw 2.177 2.510 nonbonded pdb=" O VAL B 96 " pdb="CA CA B 601 " model vdw 2.194 2.510 ... (remaining 68824 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: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.390 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:9.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0242 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 : 0.004 0.042 7993 Z= 0.243 Angle : 0.847 10.960 10893 Z= 0.483 Chirality : 0.057 0.512 1155 Planarity : 0.007 0.119 1426 Dihedral : 18.271 90.009 2901 Min Nonbonded Distance : 1.371 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.48 % Allowed : 26.82 % Favored : 67.70 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 5.97 % 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 are not related in a simple way. whole: -1.48 (0.26), residues: 954 helix: -1.16 (0.40), residues: 160 sheet: -0.25 (0.33), residues: 223 loop : -1.24 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 720 TYR 0.011 0.001 TYR A 287 PHE 0.016 0.002 PHE A 101 TRP 0.026 0.002 TRP A 503 HIS 0.008 0.001 HIS A 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.24 ( 7985) covalent geometry : angle 0.84162 / 0.48 (10873) SS BOND : bond 0.00690 / 0.28 ( 4) SS BOND : angle 1.12741 / 0.62 ( 8) hydrogen bonds : bond 0.19066 / 12.94 ( 254) hydrogen bonds : angle 7.79637 / 5.33 ( 714) link_ALPHA1-3 : bond 0.00181 / 0.10 ( 1) link_ALPHA1-3 : angle 0.40572 / 0.23 ( 3) link_BETA1-4 : bond 0.00130 / 0.06 ( 2) link_BETA1-4 : angle 0.99119 / 0.55 ( 6) link_NAG-ASN : bond 0.00735 / 0.39 ( 1) link_NAG-ASN : angle 5.81755 / 3.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 65 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.2636 (ttp80) cc_final: 0.2126 (tpm170) REVERT: A 310 ASP cc_start: 0.0472 (OUTLIER) cc_final: 0.0268 (m-30) REVERT: A 446 PHE cc_start: -0.0472 (m-80) cc_final: -0.1925 (m-80) REVERT: A 635 SER cc_start: -0.0488 (OUTLIER) cc_final: -0.0979 (t) REVERT: A 708 LEU cc_start: -0.1898 (OUTLIER) cc_final: -0.2332 (mp) REVERT: A 781 SER cc_start: -0.2229 (OUTLIER) cc_final: -0.3649 (t) REVERT: A 814 MET cc_start: 0.1757 (mmt) cc_final: -0.0771 (tpp) outliers start: 46 outliers final: 13 residues processed: 110 average time/residue: 0.4203 time to fit residues: 50.2225 Evaluate side-chains 53 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 935 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 HIS A 732 GLN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 HIS A 934 ASN A 942 HIS B 27 ASN B 28 HIS B 29 HIS B 93 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.197227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176141 restraints weight = 8861.357| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.70 r_work: 0.3933 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3825 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0264 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7993 Z= 0.167 Angle : 0.716 10.521 10893 Z= 0.358 Chirality : 0.047 0.173 1155 Planarity : 0.007 0.062 1426 Dihedral : 7.590 78.926 1090 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 6.44 % Allowed : 23.96 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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 are not related in a simple way. whole: -1.27 (0.27), residues: 954 helix: -0.68 (0.36), residues: 168 sheet: -0.29 (0.33), residues: 229 loop : -1.12 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 493 TYR 0.018 0.002 TYR A 509 PHE 0.016 0.002 PHE A 860 TRP 0.027 0.003 TRP A 520 HIS 0.009 0.002 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 7985) covalent geometry : angle 0.71256 / 0.36 (10873) SS BOND : bond 0.00175 / 0.09 ( 4) SS BOND : angle 0.81577 / 0.45 ( 8) hydrogen bonds : bond 0.04155 / 2.77 ( 254) hydrogen bonds : angle 5.68136 / 3.94 ( 714) link_ALPHA1-3 : bond 0.01109 / 0.58 ( 1) link_ALPHA1-3 : angle 2.10323 / 1.07 ( 3) link_BETA1-4 : bond 0.00295 / 0.14 ( 2) link_BETA1-4 : angle 1.18528 / 0.57 ( 6) link_NAG-ASN : bond 0.01208 / 0.64 ( 1) link_NAG-ASN : angle 3.27531 / 1.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 43 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 ILE cc_start: 0.1721 (pt) cc_final: 0.0548 (mt) REVERT: A 591 SER cc_start: -0.2303 (OUTLIER) cc_final: -0.2666 (t) REVERT: A 615 TRP cc_start: 0.0138 (OUTLIER) cc_final: -0.0380 (p90) REVERT: A 635 SER cc_start: 0.0676 (OUTLIER) cc_final: -0.0302 (m) REVERT: A 656 GLU cc_start: -0.0160 (OUTLIER) cc_final: -0.1265 (mt-10) REVERT: A 699 ASP cc_start: -0.0776 (OUTLIER) cc_final: -0.1008 (t70) REVERT: A 814 MET cc_start: 0.2108 (mmt) cc_final: -0.1161 (tpp) outliers start: 54 outliers final: 18 residues processed: 92 average time/residue: 0.4586 time to fit residues: 45.6496 Evaluate side-chains 57 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 34 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 935 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 35 optimal weight: 0.9990 chunk 88 optimal weight: 0.0050 chunk 86 optimal weight: 8.9990 overall best weight: 0.5172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.215907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.195692 restraints weight = 8751.824| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 1.81 r_work: 0.4125 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4015 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0587 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7993 Z= 0.147 Angle : 0.666 13.701 10893 Z= 0.328 Chirality : 0.045 0.206 1155 Planarity : 0.006 0.061 1426 Dihedral : 6.663 82.388 1073 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.05 % Allowed : 26.58 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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 are not related in a simple way. whole: -1.21 (0.26), residues: 954 helix: -0.39 (0.36), residues: 166 sheet: -0.34 (0.32), residues: 231 loop : -1.12 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 309 TYR 0.013 0.002 TYR A 669 PHE 0.015 0.002 PHE A 538 TRP 0.020 0.003 TRP A 687 HIS 0.009 0.002 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 7985) covalent geometry : angle 0.66459 / 0.33 (10873) SS BOND : bond 0.00287 / 0.14 ( 4) SS BOND : angle 0.55608 / 0.29 ( 8) hydrogen bonds : bond 0.03698 / 2.46 ( 254) hydrogen bonds : angle 5.63857 / 3.92 ( 714) link_ALPHA1-3 : bond 0.00971 / 0.51 ( 1) link_ALPHA1-3 : angle 1.75982 / 0.95 ( 3) link_BETA1-4 : bond 0.00919 / 0.47 ( 2) link_BETA1-4 : angle 0.95172 / 0.47 ( 6) link_NAG-ASN : bond 0.00326 / 0.17 ( 1) link_NAG-ASN : angle 2.45910 / 1.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 43 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: -0.0715 (OUTLIER) cc_final: -0.1018 (tp) REVERT: A 242 MET cc_start: -0.1279 (mmm) cc_final: -0.1566 (pmm) REVERT: A 259 ILE cc_start: 0.1904 (OUTLIER) cc_final: 0.0921 (mt) REVERT: A 456 LEU cc_start: -0.0173 (OUTLIER) cc_final: -0.0546 (tp) REVERT: A 615 TRP cc_start: -0.0088 (OUTLIER) cc_final: -0.0372 (p90) REVERT: A 635 SER cc_start: 0.1018 (OUTLIER) cc_final: 0.0162 (m) REVERT: A 656 GLU cc_start: 0.0073 (OUTLIER) cc_final: -0.1661 (tm-30) REVERT: A 812 ARG cc_start: 0.2750 (OUTLIER) cc_final: 0.1915 (mtt180) REVERT: A 814 MET cc_start: 0.1835 (mmt) cc_final: -0.1820 (tpp) outliers start: 34 outliers final: 11 residues processed: 73 average time/residue: 0.4761 time to fit residues: 37.5380 Evaluate side-chains 57 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 812 ARG Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 935 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 0.2980 chunk 89 optimal weight: 0.4980 chunk 90 optimal weight: 0.0970 chunk 68 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 HIS A 670 GLN B 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.226902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.208688 restraints weight = 9041.218| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 1.66 r_work: 0.4265 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4157 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0740 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7993 Z= 0.132 Angle : 0.651 13.917 10893 Z= 0.320 Chirality : 0.045 0.170 1155 Planarity : 0.006 0.055 1426 Dihedral : 6.450 86.272 1072 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.44 % Rotamer: Outliers : 4.77 % Allowed : 25.86 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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 are not related in a simple way. whole: -1.20 (0.27), residues: 954 helix: -0.38 (0.37), residues: 166 sheet: -0.33 (0.34), residues: 226 loop : -1.11 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 173 TYR 0.016 0.002 TYR A 746 PHE 0.014 0.002 PHE A 538 TRP 0.021 0.002 TRP A 730 HIS 0.006 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 7985) covalent geometry : angle 0.64935 / 0.32 (10873) SS BOND : bond 0.00363 / 0.19 ( 4) SS BOND : angle 0.29627 / 0.14 ( 8) hydrogen bonds : bond 0.03353 / 2.23 ( 254) hydrogen bonds : angle 5.47000 / 3.76 ( 714) link_ALPHA1-3 : bond 0.00758 / 0.40 ( 1) link_ALPHA1-3 : angle 1.60523 / 0.84 ( 3) link_BETA1-4 : bond 0.00561 / 0.29 ( 2) link_BETA1-4 : angle 1.04363 / 0.52 ( 6) link_NAG-ASN : bond 0.00495 / 0.26 ( 1) link_NAG-ASN : angle 2.22751 / 1.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 38 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.1204 (mpp) cc_final: -0.0667 (tpp) REVERT: A 259 ILE cc_start: 0.2242 (OUTLIER) cc_final: 0.1646 (mp) REVERT: A 615 TRP cc_start: -0.0249 (OUTLIER) cc_final: -0.0662 (p90) REVERT: A 635 SER cc_start: 0.0946 (OUTLIER) cc_final: 0.0007 (t) REVERT: A 656 GLU cc_start: 0.0652 (OUTLIER) cc_final: -0.1040 (tm-30) REVERT: A 712 TYR cc_start: 0.0393 (OUTLIER) cc_final: -0.0046 (t80) REVERT: A 814 MET cc_start: 0.1958 (mmt) cc_final: -0.2074 (tpp) outliers start: 40 outliers final: 18 residues processed: 74 average time/residue: 0.3914 time to fit residues: 31.9103 Evaluate side-chains 58 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 540 TRP Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 86 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 88 optimal weight: 0.0060 chunk 94 optimal weight: 0.0670 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 882 HIS A 919 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.238047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.221675 restraints weight = 8937.937| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 1.54 r_work: 0.4379 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4276 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1051 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7993 Z= 0.133 Angle : 0.658 15.554 10893 Z= 0.320 Chirality : 0.044 0.136 1155 Planarity : 0.006 0.065 1426 Dihedral : 6.447 89.694 1072 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.97 % Favored : 93.92 % Rotamer: Outliers : 3.93 % Allowed : 26.94 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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 are not related in a simple way. whole: -1.18 (0.27), residues: 954 helix: -0.53 (0.36), residues: 167 sheet: -0.10 (0.34), residues: 232 loop : -1.16 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 698 TYR 0.013 0.002 TYR A 669 PHE 0.015 0.002 PHE A 845 TRP 0.023 0.002 TRP A 687 HIS 0.008 0.001 HIS A 678 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 7985) covalent geometry : angle 0.65637 / 0.32 (10873) SS BOND : bond 0.00296 / 0.15 ( 4) SS BOND : angle 0.53961 / 0.30 ( 8) hydrogen bonds : bond 0.03381 / 2.27 ( 254) hydrogen bonds : angle 5.62644 / 3.88 ( 714) link_ALPHA1-3 : bond 0.00896 / 0.47 ( 1) link_ALPHA1-3 : angle 1.58587 / 0.84 ( 3) link_BETA1-4 : bond 0.00714 / 0.37 ( 2) link_BETA1-4 : angle 0.97244 / 0.48 ( 6) link_NAG-ASN : bond 0.00418 / 0.22 ( 1) link_NAG-ASN : angle 2.31718 / 1.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 44 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.2197 (OUTLIER) cc_final: 0.1906 (tt) REVERT: A 142 MET cc_start: 0.1803 (mpp) cc_final: -0.0199 (tpp) REVERT: A 347 GLU cc_start: 0.4478 (mm-30) cc_final: 0.3943 (pt0) REVERT: A 615 TRP cc_start: -0.0062 (OUTLIER) cc_final: -0.0607 (p90) REVERT: A 712 TYR cc_start: 0.0755 (OUTLIER) cc_final: 0.0120 (t80) outliers start: 33 outliers final: 13 residues processed: 74 average time/residue: 0.4092 time to fit residues: 33.0557 Evaluate side-chains 55 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 935 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 0.0070 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 47 optimal weight: 0.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.247519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.230605 restraints weight = 9122.026| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 1.62 r_work: 0.4462 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4361 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1266 moved from start: 0.6532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7993 Z= 0.144 Angle : 0.650 10.745 10893 Z= 0.326 Chirality : 0.045 0.148 1155 Planarity : 0.006 0.068 1426 Dihedral : 6.302 85.174 1071 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.44 % Rotamer: Outliers : 3.34 % Allowed : 28.01 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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 are not related in a simple way. whole: -1.23 (0.27), residues: 954 helix: -0.48 (0.36), residues: 169 sheet: -0.16 (0.34), residues: 230 loop : -1.21 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 698 TYR 0.027 0.002 TYR B 86 PHE 0.013 0.002 PHE A 538 TRP 0.026 0.002 TRP A 730 HIS 0.006 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7985) covalent geometry : angle 0.64873 / 0.33 (10873) SS BOND : bond 0.00294 / 0.15 ( 4) SS BOND : angle 0.52825 / 0.28 ( 8) hydrogen bonds : bond 0.03202 / 2.13 ( 254) hydrogen bonds : angle 5.42588 / 3.73 ( 714) link_ALPHA1-3 : bond 0.00759 / 0.40 ( 1) link_ALPHA1-3 : angle 1.65090 / 0.87 ( 3) link_BETA1-4 : bond 0.01378 / 0.70 ( 2) link_BETA1-4 : angle 1.14954 / 0.57 ( 6) link_NAG-ASN : bond 0.00526 / 0.28 ( 1) link_NAG-ASN : angle 2.02621 / 1.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 41 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.2228 (OUTLIER) cc_final: 0.1617 (tt) REVERT: A 142 MET cc_start: 0.2212 (mpp) cc_final: 0.0190 (tpp) REVERT: A 615 TRP cc_start: -0.0240 (OUTLIER) cc_final: -0.0701 (p90) REVERT: A 697 ILE cc_start: 0.1120 (OUTLIER) cc_final: 0.0510 (mt) REVERT: A 712 TYR cc_start: 0.0633 (OUTLIER) cc_final: 0.0048 (t80) REVERT: A 715 LEU cc_start: -0.2095 (OUTLIER) cc_final: -0.2299 (mm) outliers start: 28 outliers final: 16 residues processed: 67 average time/residue: 0.3857 time to fit residues: 28.4667 Evaluate side-chains 57 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.0770 chunk 63 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.253090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.235175 restraints weight = 9270.179| |-----------------------------------------------------------------------------| r_work (start): 0.4567 rms_B_bonded: 1.78 r_work: 0.4482 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4383 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1599 moved from start: 0.7475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7993 Z= 0.148 Angle : 0.716 12.591 10893 Z= 0.347 Chirality : 0.045 0.170 1155 Planarity : 0.006 0.055 1426 Dihedral : 6.196 78.876 1071 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.10 % Allowed : 28.37 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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 are not related in a simple way. whole: -1.27 (0.26), residues: 954 helix: -0.70 (0.36), residues: 168 sheet: 0.03 (0.34), residues: 232 loop : -1.28 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 518 TYR 0.022 0.002 TYR B 86 PHE 0.012 0.002 PHE A 845 TRP 0.025 0.002 TRP A 521 HIS 0.005 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 7985) covalent geometry : angle 0.71501 / 0.35 (10873) SS BOND : bond 0.00323 / 0.17 ( 4) SS BOND : angle 0.73896 / 0.40 ( 8) hydrogen bonds : bond 0.03300 / 2.16 ( 254) hydrogen bonds : angle 5.62005 / 3.85 ( 714) link_ALPHA1-3 : bond 0.00251 / 0.13 ( 1) link_ALPHA1-3 : angle 1.28379 / 0.68 ( 3) link_BETA1-4 : bond 0.00666 / 0.33 ( 2) link_BETA1-4 : angle 1.06105 / 0.53 ( 6) link_NAG-ASN : bond 0.00337 / 0.18 ( 1) link_NAG-ASN : angle 2.10120 / 1.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 41 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.2451 (mpp) cc_final: 0.0449 (tpt) REVERT: A 242 MET cc_start: 0.0169 (mmp) cc_final: -0.1991 (pmm) REVERT: A 615 TRP cc_start: -0.0584 (OUTLIER) cc_final: -0.0987 (p90) REVERT: A 712 TYR cc_start: 0.0697 (OUTLIER) cc_final: 0.0036 (t80) REVERT: A 823 MET cc_start: 0.3977 (tmt) cc_final: 0.3704 (tmt) outliers start: 26 outliers final: 14 residues processed: 65 average time/residue: 0.3854 time to fit residues: 27.7483 Evaluate side-chains 55 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 34 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 HIS A 573 ASN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 841 GLN ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5005 r_free = 0.5005 target = 0.286284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.271392 restraints weight = 9657.562| |-----------------------------------------------------------------------------| r_work (start): 0.4871 rms_B_bonded: 1.72 r_work: 0.4814 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4730 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2869 moved from start: 1.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 7993 Z= 0.268 Angle : 1.017 12.120 10893 Z= 0.521 Chirality : 0.058 0.577 1155 Planarity : 0.008 0.066 1426 Dihedral : 7.442 53.888 1069 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.64 % Favored : 90.25 % Rotamer: Outliers : 3.34 % Allowed : 27.89 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 are not related in a simple way. whole: -2.18 (0.26), residues: 954 helix: -2.11 (0.30), residues: 183 sheet: -0.17 (0.36), residues: 197 loop : -1.73 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.002 ARG B 91 TYR 0.049 0.004 TYR A 403 PHE 0.031 0.004 PHE A 439 TRP 0.033 0.004 TRP A 521 HIS 0.011 0.003 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.27 ( 7985) covalent geometry : angle 1.01487 / 0.52 (10873) SS BOND : bond 0.00602 / 0.31 ( 4) SS BOND : angle 1.86197 / 0.93 ( 8) hydrogen bonds : bond 0.05210 / 3.37 ( 254) hydrogen bonds : angle 7.20414 / 4.96 ( 714) link_ALPHA1-3 : bond 0.00464 / 0.24 ( 1) link_ALPHA1-3 : angle 1.56544 / 0.84 ( 3) link_BETA1-4 : bond 0.00890 / 0.45 ( 2) link_BETA1-4 : angle 1.20845 / 0.62 ( 6) link_NAG-ASN : bond 0.00057 / 0.03 ( 1) link_NAG-ASN : angle 3.00358 / 1.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.5106 (mm-30) cc_final: 0.4903 (tt0) REVERT: A 142 MET cc_start: 0.3650 (OUTLIER) cc_final: 0.1272 (tpp) REVERT: A 403 TYR cc_start: 0.1665 (m-80) cc_final: 0.1436 (m-80) REVERT: A 517 MET cc_start: 0.2858 (OUTLIER) cc_final: 0.0162 (pp-130) REVERT: A 543 MET cc_start: 0.2786 (mtt) cc_final: 0.1424 (tpp) REVERT: A 712 TYR cc_start: 0.1470 (OUTLIER) cc_final: 0.0623 (t80) REVERT: A 813 TRP cc_start: 0.1134 (OUTLIER) cc_final: 0.0275 (m-10) outliers start: 28 outliers final: 9 residues processed: 83 average time/residue: 0.3976 time to fit residues: 36.1955 Evaluate side-chains 67 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN A 719 HIS A 783 GLN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.282395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.267754 restraints weight = 9761.826| |-----------------------------------------------------------------------------| r_work (start): 0.4868 rms_B_bonded: 1.70 r_work: 0.4783 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4685 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2925 moved from start: 1.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 7993 Z= 0.156 Angle : 0.773 12.477 10893 Z= 0.383 Chirality : 0.048 0.291 1155 Planarity : 0.006 0.062 1426 Dihedral : 6.219 51.292 1066 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.31 % Allowed : 29.80 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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 are not related in a simple way. whole: -1.95 (0.26), residues: 954 helix: -1.64 (0.33), residues: 178 sheet: -0.36 (0.35), residues: 203 loop : -1.57 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 484 TYR 0.038 0.003 TYR A 509 PHE 0.049 0.002 PHE A 611 TRP 0.021 0.002 TRP A 813 HIS 0.011 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 7985) covalent geometry : angle 0.77065 / 0.38 (10873) SS BOND : bond 0.00383 / 0.19 ( 4) SS BOND : angle 1.66909 / 0.82 ( 8) hydrogen bonds : bond 0.03864 / 2.46 ( 254) hydrogen bonds : angle 6.46659 / 4.43 ( 714) link_ALPHA1-3 : bond 0.00660 / 0.35 ( 1) link_ALPHA1-3 : angle 1.55774 / 0.84 ( 3) link_BETA1-4 : bond 0.00684 / 0.35 ( 2) link_BETA1-4 : angle 0.82159 / 0.42 ( 6) link_NAG-ASN : bond 0.00511 / 0.27 ( 1) link_NAG-ASN : angle 1.99794 / 1.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.3613 (OUTLIER) cc_final: 0.1231 (tpp) REVERT: A 269 LYS cc_start: 0.6960 (tppt) cc_final: 0.6585 (ttmt) REVERT: A 310 ASP cc_start: 0.3914 (OUTLIER) cc_final: 0.3283 (m-30) REVERT: A 517 MET cc_start: 0.3124 (mtm) cc_final: 0.0450 (pp-130) REVERT: A 543 MET cc_start: 0.2242 (mtt) cc_final: 0.1266 (tpp) REVERT: A 712 TYR cc_start: 0.1356 (OUTLIER) cc_final: 0.0655 (t80) REVERT: A 823 MET cc_start: 0.4003 (tmt) cc_final: 0.3712 (tmt) outliers start: 11 outliers final: 3 residues processed: 70 average time/residue: 0.4360 time to fit residues: 33.3373 Evaluate side-chains 53 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 779 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS A 741 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.290712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.275046 restraints weight = 9541.032| |-----------------------------------------------------------------------------| r_work (start): 0.4929 rms_B_bonded: 1.59 r_work: 0.4868 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4787 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3944 moved from start: 1.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 7993 Z= 0.268 Angle : 1.048 15.224 10893 Z= 0.527 Chirality : 0.060 0.518 1155 Planarity : 0.008 0.073 1426 Dihedral : 6.982 45.286 1066 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 2.03 % Allowed : 29.80 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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 are not related in a simple way. whole: -2.44 (0.25), residues: 954 helix: -1.72 (0.34), residues: 174 sheet: -0.68 (0.35), residues: 209 loop : -2.03 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 596 TYR 0.031 0.003 TYR A 669 PHE 0.021 0.003 PHE A 38 TRP 0.039 0.004 TRP A 322 HIS 0.019 0.003 HIS A 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.27 ( 7985) covalent geometry : angle 1.03975 / 0.53 (10873) SS BOND : bond 0.00273 / 0.13 ( 4) SS BOND : angle 2.24073 / 1.10 ( 8) hydrogen bonds : bond 0.05040 / 3.32 ( 254) hydrogen bonds : angle 6.92206 / 4.76 ( 714) link_ALPHA1-3 : bond 0.00766 / 0.40 ( 1) link_ALPHA1-3 : angle 2.29567 / 1.17 ( 3) link_BETA1-4 : bond 0.01191 / 0.60 ( 2) link_BETA1-4 : angle 3.49552 / 1.81 ( 6) link_NAG-ASN : bond 0.01119 / 0.59 ( 1) link_NAG-ASN : angle 4.96249 / 2.92 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.5462 (mmm) cc_final: 0.4711 (mmm) REVERT: A 310 ASP cc_start: 0.4979 (OUTLIER) cc_final: 0.4571 (m-30) REVERT: A 517 MET cc_start: 0.2798 (mtm) cc_final: 0.0579 (pp-130) REVERT: A 543 MET cc_start: 0.2645 (mtt) cc_final: 0.1442 (tpp) REVERT: A 549 PHE cc_start: 0.6381 (t80) cc_final: 0.5670 (p90) REVERT: A 632 MET cc_start: 0.2789 (ttt) cc_final: 0.0747 (mpt) REVERT: A 813 TRP cc_start: 0.0918 (OUTLIER) cc_final: 0.0503 (m-10) outliers start: 17 outliers final: 4 residues processed: 90 average time/residue: 0.4276 time to fit residues: 41.8236 Evaluate side-chains 64 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 615 TRP Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain B residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN A 480 HIS A 693 HIS A 772 GLN ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 GLN A 855 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.291247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.274195 restraints weight = 9496.766| |-----------------------------------------------------------------------------| r_work (start): 0.4870 rms_B_bonded: 1.63 r_work: 0.4787 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4701 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4340 moved from start: 1.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 7993 Z= 0.207 Angle : 0.877 11.312 10893 Z= 0.435 Chirality : 0.052 0.262 1155 Planarity : 0.007 0.088 1426 Dihedral : 6.131 22.017 1064 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.39 % Favored : 93.50 % Rotamer: Outliers : 1.67 % Allowed : 32.06 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % 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 are not related in a simple way. whole: -2.23 (0.26), residues: 954 helix: -1.79 (0.33), residues: 178 sheet: -0.58 (0.36), residues: 200 loop : -1.76 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 569 TYR 0.023 0.003 TYR A 147 PHE 0.026 0.003 PHE A 852 TRP 0.039 0.003 TRP A 322 HIS 0.014 0.002 HIS A 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 ( 7985) covalent geometry : angle 0.87364 / 0.43 (10873) SS BOND : bond 0.00424 / 0.21 ( 4) SS BOND : angle 2.37445 / 1.16 ( 8) hydrogen bonds : bond 0.04335 / 2.84 ( 254) hydrogen bonds : angle 6.47890 / 4.46 ( 714) link_ALPHA1-3 : bond 0.00401 / 0.21 ( 1) link_ALPHA1-3 : angle 1.32991 / 0.67 ( 3) link_BETA1-4 : bond 0.00568 / 0.27 ( 2) link_BETA1-4 : angle 1.11532 / 0.61 ( 6) link_NAG-ASN : bond 0.00217 / 0.11 ( 1) link_NAG-ASN : angle 2.41412 / 1.33 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2617.21 seconds wall clock time: 45 minutes 40.02 seconds (2740.02 seconds total)