Starting phenix.real_space_refine on Sat Jul 4 09:09:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lyc_23592/07_2026/7lyc_23592.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lyc_23592/07_2026/7lyc_23592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lyc_23592/07_2026/7lyc_23592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lyc_23592/07_2026/7lyc_23592.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lyc_23592/07_2026/7lyc_23592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lyc_23592/07_2026/7lyc_23592.map" } resolution = 2.94 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= 0.001 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. 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 P 293 5.49 5 S 29 5.16 5 C 8834 2.51 5 N 2874 2.21 5 O 3445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 15475 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "H" Number of atoms: 737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 735 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 639 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "N" Number of atoms: 2683 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 335, 2663 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 335, 2663 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain breaks: 1 bond proxies already assigned to first conformer: 2702 Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU K 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.45 residue: pdb=" N ASER N 452 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER N 452 " occ=0.50 Time building chain proxies: 3.87, per 1000 atoms: 0.25 Number of scatterers: 15475 At special positions: 0 Unit cell: (108.926, 117.146, 118.174, 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) S 29 16.00 P 293 15.00 O 3445 8.00 N 2874 7.00 C 8834 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 TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 603.4 milliseconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 61.7% alpha, 5.8% beta 140 base pairs and 263 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.677A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.520A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.661A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.505A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 56 through 60 Processing helix chain 'N' and resid 430 through 439 Processing helix chain 'N' and resid 440 through 450 Processing helix chain 'N' and resid 463 through 472 Processing helix chain 'N' and resid 473 through 483 Processing helix chain 'N' and resid 491 through 495 Processing helix chain 'N' and resid 496 through 505 Processing helix chain 'N' and resid 506 through 516 Processing helix chain 'N' and resid 529 through 534 Processing helix chain 'N' and resid 536 through 544 Processing helix chain 'N' and resid 578 through 593 Processing helix chain 'N' and resid 617 through 626 Processing helix chain 'N' and resid 633 through 643 removed outlier: 3.554A pdb=" N LYS N 637 " --> pdb=" O PHE N 633 " (cutoff:3.500A) Processing helix chain 'N' and resid 648 through 652 removed outlier: 3.804A pdb=" N GLU N 652 " --> pdb=" O GLU N 649 " (cutoff:3.500A) Processing helix chain 'N' and resid 656 through 666 removed outlier: 3.915A pdb=" N SER N 660 " --> pdb=" O GLY N 656 " (cutoff:3.500A) Processing helix chain 'N' and resid 687 through 698 Processing helix chain 'N' and resid 711 through 716 Processing helix chain 'N' and resid 760 through 770 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.527A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.943A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.369A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.085A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.951A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.399A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.104A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'K' and resid 12 through 17 removed outlier: 9.097A pdb=" N LEU K 67 " --> pdb=" O GLN K 2 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE K 4 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU K 69 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS K 6 " --> pdb=" O LEU K 69 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N LEU K 71 " --> pdb=" O LYS K 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 595 through 597 removed outlier: 4.380A pdb=" N GLY N 574 " --> pdb=" O TYR N 597 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL N 571 " --> pdb=" O HIS N 606 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL N 608 " --> pdb=" O VAL N 571 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE N 573 " --> pdb=" O VAL N 608 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 701 through 702 removed outlier: 6.455A pdb=" N TYR N 676 " --> pdb=" O TYR N 736 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE N 738 " --> pdb=" O TYR N 676 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR N 678 " --> pdb=" O ILE N 738 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN N 735 " --> pdb=" O TRP N 756 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA N 758 " --> pdb=" O GLN N 735 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE N 737 " --> pdb=" O ALA N 758 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1559 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 358 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 263 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1965 1.32 - 1.44: 5712 1.44 - 1.56: 8057 1.56 - 1.69: 584 1.69 - 1.81: 45 Bond restraints: 16363 Sorted by residual: bond pdb=" C3' DC I -4 " pdb=" O3' DC I -4 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.08e+01 bond pdb=" C3' DA J 72 " pdb=" C2' DA J 72 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C GLU E 50 " pdb=" O GLU E 50 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" C3' DG I -7 " pdb=" O3' DG I -7 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 1.00e+01 bond pdb=" C ARG E 116 " pdb=" O ARG E 116 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.28e-02 6.10e+03 9.86e+00 ... (remaining 16358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 20800 1.20 - 2.39: 2124 2.39 - 3.59: 395 3.59 - 4.78: 30 4.78 - 5.98: 11 Bond angle restraints: 23360 Sorted by residual: angle pdb=" N3 DT I 1 " pdb=" C4 DT I 1 " pdb=" O4 DT I 1 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT J 33 " pdb=" C4 DT J 33 " pdb=" O4 DT J 33 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 38 " pdb=" C4 DT I 38 " pdb=" O4 DT I 38 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" O5' DG I 47 " pdb=" C5' DG I 47 " pdb=" C4' DG I 47 " ideal model delta sigma weight residual 109.40 112.85 -3.45 8.00e-01 1.56e+00 1.86e+01 angle pdb=" N3 DT J -17 " pdb=" C4 DT J -17 " pdb=" O4 DT J -17 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 ... (remaining 23355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.16: 7531 33.16 - 66.31: 1554 66.31 - 99.47: 38 99.47 - 132.62: 0 132.62 - 165.78: 2 Dihedral angle restraints: 9125 sinusoidal: 5671 harmonic: 3454 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual -180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 54.22 165.78 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 66.57 153.43 1 3.50e+01 8.16e-04 1.48e+01 ... (remaining 9122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2122 0.062 - 0.123: 493 0.123 - 0.185: 29 0.185 - 0.247: 0 0.247 - 0.308: 1 Chirality restraints: 2645 Sorted by residual: chirality pdb=" CA GLN A 76 " pdb=" N GLN A 76 " pdb=" C GLN A 76 " pdb=" CB GLN A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" C3' DC I 7 " pdb=" C4' DC I 7 " pdb=" O3' DC I 7 " pdb=" C2' DC I 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.15e-01 ... (remaining 2642 not shown) Planarity restraints: 1950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -52 " 0.011 2.00e-02 2.50e+03 1.36e-02 5.57e+00 pdb=" N9 DG I -52 " -0.001 2.00e-02 2.50e+03 pdb=" C8 DG I -52 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I -52 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I -52 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DG I -52 " -0.016 2.00e-02 2.50e+03 pdb=" O6 DG I -52 " 0.018 2.00e-02 2.50e+03 pdb=" N1 DG I -52 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DG I -52 " -0.033 2.00e-02 2.50e+03 pdb=" N2 DG I -52 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DG I -52 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DG I -52 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO D 103 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 496 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO N 497 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO N 497 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO N 497 " 0.028 5.00e-02 4.00e+02 ... (remaining 1947 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 52 2.56 - 3.14: 11255 3.14 - 3.73: 26418 3.73 - 4.31: 38941 4.31 - 4.90: 57149 Nonbonded interactions: 133815 Sorted by model distance: nonbonded pdb=" NH1 ARG N 427 " pdb=" OE1 GLU N 429 " model vdw 1.972 3.120 nonbonded pdb=" O ASN N 626 " pdb=" OD1 ASN N 626 " model vdw 2.086 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.179 2.496 nonbonded pdb=" O ILE N 624 " pdb=" OG SER N 660 " model vdw 2.186 3.040 nonbonded pdb=" ND2 ASN N 524 " pdb=" OH TYR N 533 " model vdw 2.189 3.120 ... (remaining 133810 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 20 through 102) selection = (chain 'F' and (resid 20 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 123)) } 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=0.45 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.140 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.007 0.048 16365 Z= 0.558 Angle : 0.772 5.980 23366 Z= 0.644 Chirality : 0.049 0.308 2645 Planarity : 0.005 0.051 1948 Dihedral : 25.815 165.775 6895 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.10 % Allowed : 0.69 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.23), residues: 1172 helix: 0.47 (0.19), residues: 709 sheet: 0.08 (0.69), residues: 58 loop : -0.73 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 53 TYR 0.016 0.002 TYR H 121 PHE 0.010 0.002 PHE A 78 TRP 0.011 0.001 TRP N 629 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.56 (16363) covalent geometry : angle 0.77138 / 0.64 (23360) hydrogen bonds : bond 0.12087 / 8.43 ( 894) hydrogen bonds : angle 4.85023 / 3.48 ( 2271) link_TRANS : bond 0.01096 / 0.52 ( 2) link_TRANS : angle 1.61988 / 0.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8406 (pp30) cc_final: 0.7784 (pt0) REVERT: A 129 ARG cc_start: 0.7873 (tpt-90) cc_final: 0.7258 (ttp-170) REVERT: B 74 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7442 (mt-10) REVERT: D 85 LYS cc_start: 0.9010 (mttp) cc_final: 0.8765 (mtmm) REVERT: D 99 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.7965 (mtt180) REVERT: H 34 LYS cc_start: 0.8071 (ptmt) cc_final: 0.7119 (mmtm) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.9763 time to fit residues: 152.7862 Evaluate side-chains 111 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN C 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.197511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150565 restraints weight = 26618.156| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.18 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16365 Z= 0.169 Angle : 0.650 6.743 23366 Z= 0.373 Chirality : 0.048 0.259 2645 Planarity : 0.005 0.046 1948 Dihedral : 29.398 168.289 4517 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.89 % Allowed : 7.38 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1172 helix: 1.29 (0.19), residues: 717 sheet: 0.04 (0.72), residues: 53 loop : -0.60 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 529 TYR 0.012 0.002 TYR D 121 PHE 0.008 0.001 PHE N 633 TRP 0.010 0.001 TRP N 629 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (16363) covalent geometry : angle 0.64989 / 0.37 (23360) hydrogen bonds : bond 0.05648 / 3.83 ( 894) hydrogen bonds : angle 3.54071 / 2.56 ( 2271) link_TRANS : bond 0.00246 / 0.12 ( 2) link_TRANS : angle 0.82258 / 0.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8232 (pp30) cc_final: 0.7765 (pt0) REVERT: B 74 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7361 (mt-10) REVERT: D 71 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: D 86 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7988 (mmp80) REVERT: D 93 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: D 99 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7871 (mtt180) REVERT: F 59 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7721 (mtmt) REVERT: H 34 LYS cc_start: 0.7765 (ptmt) cc_final: 0.6551 (mmtm) REVERT: N 649 GLU cc_start: 0.4922 (OUTLIER) cc_final: 0.4700 (mt-10) outliers start: 8 outliers final: 2 residues processed: 121 average time/residue: 0.8712 time to fit residues: 112.7125 Evaluate side-chains 114 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 78 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS E 76 GLN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.195923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.154304 restraints weight = 29042.979| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.84 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16365 Z= 0.204 Angle : 0.649 6.784 23366 Z= 0.371 Chirality : 0.048 0.299 2645 Planarity : 0.005 0.044 1948 Dihedral : 29.480 167.019 4517 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.48 % Allowed : 9.25 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1172 helix: 1.46 (0.19), residues: 718 sheet: -0.04 (0.71), residues: 53 loop : -0.59 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 49 TYR 0.015 0.002 TYR D 121 PHE 0.007 0.001 PHE G 25 TRP 0.009 0.001 TRP N 629 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (16363) covalent geometry : angle 0.64935 / 0.37 (23360) hydrogen bonds : bond 0.05811 / 3.96 ( 894) hydrogen bonds : angle 3.44078 / 2.48 ( 2271) link_TRANS : bond 0.00306 / 0.16 ( 2) link_TRANS : angle 0.91122 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8452 (pp30) cc_final: 0.7884 (pt0) REVERT: B 74 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7350 (mt-10) REVERT: B 91 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8077 (tttp) REVERT: D 71 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: D 86 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.6802 (mtp85) REVERT: D 93 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: H 34 LYS cc_start: 0.7993 (ptmt) cc_final: 0.6983 (mmtm) outliers start: 14 outliers final: 7 residues processed: 119 average time/residue: 0.8472 time to fit residues: 107.9211 Evaluate side-chains 120 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 60 optimal weight: 10.0000 chunk 66 optimal weight: 50.0000 chunk 120 optimal weight: 8.9990 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.197381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.149373 restraints weight = 24993.650| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.02 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16365 Z= 0.146 Angle : 0.626 7.314 23366 Z= 0.360 Chirality : 0.047 0.271 2645 Planarity : 0.004 0.043 1948 Dihedral : 29.464 167.209 4517 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.38 % Allowed : 11.12 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.24), residues: 1172 helix: 1.64 (0.19), residues: 718 sheet: -0.08 (0.71), residues: 53 loop : -0.52 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 42 TYR 0.012 0.002 TYR B 51 PHE 0.007 0.001 PHE A 67 TRP 0.007 0.001 TRP N 629 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (16363) covalent geometry : angle 0.62635 / 0.36 (23360) hydrogen bonds : bond 0.05225 / 3.55 ( 894) hydrogen bonds : angle 3.38216 / 2.44 ( 2271) link_TRANS : bond 0.00122 / 0.06 ( 2) link_TRANS : angle 0.61391 / 0.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8339 (pp30) cc_final: 0.7762 (pt0) REVERT: B 74 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7500 (mt-10) REVERT: B 91 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8135 (tttp) REVERT: D 71 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: D 85 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.7951 (mtmm) REVERT: D 86 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.6803 (mtp85) REVERT: D 93 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: D 99 ARG cc_start: 0.8173 (mtt-85) cc_final: 0.7850 (mtt180) REVERT: H 34 LYS cc_start: 0.7609 (ptmt) cc_final: 0.6407 (mmtm) REVERT: N 649 GLU cc_start: 0.4852 (OUTLIER) cc_final: 0.4641 (mt-10) outliers start: 13 outliers final: 6 residues processed: 116 average time/residue: 0.8748 time to fit residues: 108.4603 Evaluate side-chains 117 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 79 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 68 optimal weight: 20.0000 chunk 34 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 129 optimal weight: 0.4980 chunk 56 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.197870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.154281 restraints weight = 34895.922| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.09 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16365 Z= 0.144 Angle : 0.614 7.628 23366 Z= 0.353 Chirality : 0.046 0.271 2645 Planarity : 0.004 0.041 1948 Dihedral : 29.451 168.516 4517 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.77 % Allowed : 11.12 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1172 helix: 1.70 (0.19), residues: 718 sheet: -0.06 (0.72), residues: 53 loop : -0.48 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.012 0.001 TYR N 446 PHE 0.007 0.001 PHE E 67 TRP 0.007 0.001 TRP N 756 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (16363) covalent geometry : angle 0.61376 / 0.35 (23360) hydrogen bonds : bond 0.05135 / 3.48 ( 894) hydrogen bonds : angle 3.32039 / 2.39 ( 2271) link_TRANS : bond 0.00158 / 0.08 ( 2) link_TRANS : angle 0.55762 / 0.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8311 (pp30) cc_final: 0.7720 (pt0) REVERT: B 74 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7371 (mt-10) REVERT: B 91 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8051 (tttp) REVERT: D 71 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: D 85 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.7960 (mtmm) REVERT: D 86 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.6598 (mtp85) REVERT: D 93 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: D 99 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.7905 (mtt180) REVERT: H 34 LYS cc_start: 0.7956 (ptmt) cc_final: 0.6847 (mmtm) REVERT: N 649 GLU cc_start: 0.4968 (OUTLIER) cc_final: 0.4735 (mt-10) outliers start: 17 outliers final: 5 residues processed: 119 average time/residue: 0.8499 time to fit residues: 108.2566 Evaluate side-chains 116 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 7 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 67 optimal weight: 30.0000 chunk 111 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.194125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.151508 restraints weight = 28685.865| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.90 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 16365 Z= 0.273 Angle : 0.691 8.623 23366 Z= 0.387 Chirality : 0.051 0.333 2645 Planarity : 0.005 0.050 1948 Dihedral : 29.597 166.295 4517 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.77 % Allowed : 12.11 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1172 helix: 1.38 (0.19), residues: 719 sheet: -0.05 (0.71), residues: 53 loop : -0.64 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 71 TYR 0.016 0.002 TYR D 121 PHE 0.013 0.002 PHE A 78 TRP 0.008 0.001 TRP N 629 HIS 0.004 0.001 HIS N 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.27 (16363) covalent geometry : angle 0.69104 / 0.39 (23360) hydrogen bonds : bond 0.06404 / 4.36 ( 894) hydrogen bonds : angle 3.47437 / 2.51 ( 2271) link_TRANS : bond 0.00410 / 0.21 ( 2) link_TRANS : angle 0.85414 / 0.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.461 Fit side-chains REVERT: A 76 GLN cc_start: 0.8487 (pp30) cc_final: 0.7944 (pt0) REVERT: A 90 MET cc_start: 0.8128 (mmp) cc_final: 0.7803 (mmm) REVERT: B 74 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7267 (mt-10) REVERT: B 91 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8087 (tttp) REVERT: D 71 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: D 86 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.6731 (mtp85) REVERT: H 34 LYS cc_start: 0.7977 (ptmt) cc_final: 0.6969 (mmtm) REVERT: N 474 LEU cc_start: 0.7692 (mm) cc_final: 0.7253 (mp) REVERT: N 649 GLU cc_start: 0.4976 (OUTLIER) cc_final: 0.4724 (mt-10) outliers start: 17 outliers final: 7 residues processed: 123 average time/residue: 0.8257 time to fit residues: 109.2024 Evaluate side-chains 123 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 93 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.197611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.151452 restraints weight = 24692.712| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.02 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16365 Z= 0.139 Angle : 0.630 10.204 23366 Z= 0.359 Chirality : 0.047 0.256 2645 Planarity : 0.004 0.045 1948 Dihedral : 29.541 168.461 4517 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.77 % Allowed : 12.80 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1172 helix: 1.69 (0.19), residues: 719 sheet: -0.02 (0.73), residues: 53 loop : -0.50 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 71 TYR 0.013 0.001 TYR N 676 PHE 0.007 0.001 PHE A 67 TRP 0.032 0.002 TRP N 629 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (16363) covalent geometry : angle 0.63033 / 0.36 (23360) hydrogen bonds : bond 0.05092 / 3.45 ( 894) hydrogen bonds : angle 3.32165 / 2.39 ( 2271) link_TRANS : bond 0.00131 / 0.06 ( 2) link_TRANS : angle 0.25067 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.450 Fit side-chains REVERT: A 76 GLN cc_start: 0.8301 (pp30) cc_final: 0.7726 (pt0) REVERT: A 90 MET cc_start: 0.8137 (mmp) cc_final: 0.7835 (mmm) REVERT: B 74 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7408 (mt-10) REVERT: B 91 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8050 (tttp) REVERT: D 71 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: D 85 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8108 (mtmm) REVERT: D 86 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.6696 (mtp85) REVERT: D 93 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: D 99 ARG cc_start: 0.8215 (mtt-85) cc_final: 0.7907 (mtt180) REVERT: H 34 LYS cc_start: 0.7921 (ptmt) cc_final: 0.6753 (mmtm) REVERT: N 474 LEU cc_start: 0.7641 (mm) cc_final: 0.7233 (mp) REVERT: N 584 MET cc_start: 0.3597 (OUTLIER) cc_final: 0.3222 (ppp) REVERT: N 649 GLU cc_start: 0.4951 (OUTLIER) cc_final: 0.4723 (mt-10) outliers start: 17 outliers final: 4 residues processed: 122 average time/residue: 0.8346 time to fit residues: 109.3744 Evaluate side-chains 122 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 584 MET Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 112 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 66 optimal weight: 50.0000 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.197810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.151920 restraints weight = 26390.309| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.21 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16365 Z= 0.159 Angle : 0.605 8.872 23366 Z= 0.348 Chirality : 0.046 0.291 2645 Planarity : 0.004 0.046 1948 Dihedral : 29.452 168.792 4517 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.38 % Allowed : 13.58 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.24), residues: 1172 helix: 1.78 (0.19), residues: 720 sheet: -0.01 (0.74), residues: 53 loop : -0.45 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.013 0.002 TYR N 676 PHE 0.009 0.001 PHE E 67 TRP 0.009 0.001 TRP N 629 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (16363) covalent geometry : angle 0.60506 / 0.35 (23360) hydrogen bonds : bond 0.05122 / 3.48 ( 894) hydrogen bonds : angle 3.26550 / 2.35 ( 2271) link_TRANS : bond 0.00171 / 0.08 ( 2) link_TRANS : angle 0.57686 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.376 Fit side-chains REVERT: A 76 GLN cc_start: 0.8234 (pp30) cc_final: 0.7671 (pt0) REVERT: A 90 MET cc_start: 0.8174 (mmp) cc_final: 0.7947 (mmm) REVERT: B 74 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7305 (mt-10) REVERT: B 91 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8061 (tttp) REVERT: D 71 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: D 86 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.6668 (mtp85) REVERT: D 93 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: D 99 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.7886 (mtt180) REVERT: H 34 LYS cc_start: 0.7933 (ptmt) cc_final: 0.6700 (mmtm) REVERT: N 474 LEU cc_start: 0.7587 (mm) cc_final: 0.7169 (mp) REVERT: N 649 GLU cc_start: 0.4905 (OUTLIER) cc_final: 0.4666 (mt-10) outliers start: 13 outliers final: 7 residues processed: 120 average time/residue: 0.7854 time to fit residues: 101.2390 Evaluate side-chains 120 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN ** N 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.198960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.155448 restraints weight = 32763.176| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.26 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16365 Z= 0.134 Angle : 0.593 9.365 23366 Z= 0.342 Chirality : 0.045 0.273 2645 Planarity : 0.004 0.047 1948 Dihedral : 29.423 170.032 4517 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.67 % Allowed : 13.88 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.24), residues: 1172 helix: 1.91 (0.19), residues: 719 sheet: -0.02 (0.74), residues: 53 loop : -0.38 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.012 0.001 TYR N 446 PHE 0.008 0.001 PHE E 67 TRP 0.012 0.001 TRP N 629 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (16363) covalent geometry : angle 0.59336 / 0.34 (23360) hydrogen bonds : bond 0.04866 / 3.28 ( 894) hydrogen bonds : angle 3.22760 / 2.32 ( 2271) link_TRANS : bond 0.00123 / 0.06 ( 2) link_TRANS : angle 0.44531 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.424 Fit side-chains REVERT: A 76 GLN cc_start: 0.8197 (pp30) cc_final: 0.7468 (pt0) REVERT: A 90 MET cc_start: 0.8103 (mmp) cc_final: 0.7831 (mmm) REVERT: B 74 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7302 (mt-10) REVERT: D 71 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: D 85 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8093 (mtmm) REVERT: D 86 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.6730 (mtp85) REVERT: D 93 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: D 99 ARG cc_start: 0.8192 (mtt-85) cc_final: 0.7893 (mtt180) REVERT: H 34 LYS cc_start: 0.7932 (ptmt) cc_final: 0.6808 (mmtm) REVERT: N 474 LEU cc_start: 0.7599 (mm) cc_final: 0.7163 (mp) REVERT: N 649 GLU cc_start: 0.4930 (OUTLIER) cc_final: 0.4692 (mt-10) outliers start: 16 outliers final: 5 residues processed: 121 average time/residue: 0.8055 time to fit residues: 104.7982 Evaluate side-chains 121 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 59 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 90 optimal weight: 0.0060 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN ** N 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.199436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.156033 restraints weight = 28858.818| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.13 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16365 Z= 0.132 Angle : 0.594 8.552 23366 Z= 0.342 Chirality : 0.044 0.271 2645 Planarity : 0.004 0.045 1948 Dihedral : 29.401 170.226 4517 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.08 % Allowed : 14.67 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.24), residues: 1172 helix: 1.92 (0.19), residues: 722 sheet: -0.03 (0.75), residues: 53 loop : -0.33 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 71 TYR 0.012 0.001 TYR N 446 PHE 0.009 0.001 PHE E 78 TRP 0.011 0.001 TRP N 629 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 (16363) covalent geometry : angle 0.59424 / 0.34 (23360) hydrogen bonds : bond 0.04800 / 3.24 ( 894) hydrogen bonds : angle 3.20673 / 2.30 ( 2271) link_TRANS : bond 0.00099 / 0.05 ( 2) link_TRANS : angle 0.43331 / 0.18 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.391 Fit side-chains REVERT: A 76 GLN cc_start: 0.8165 (pp30) cc_final: 0.7477 (pt0) REVERT: A 90 MET cc_start: 0.8093 (mmp) cc_final: 0.7843 (mmm) REVERT: B 74 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7275 (mt-10) REVERT: D 71 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: D 85 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8035 (mtmm) REVERT: D 86 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.6613 (mtp85) REVERT: D 93 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: D 99 ARG cc_start: 0.8205 (mtt-85) cc_final: 0.7921 (mtt180) REVERT: H 34 LYS cc_start: 0.8025 (ptmt) cc_final: 0.6897 (mmtm) REVERT: N 474 LEU cc_start: 0.7616 (mm) cc_final: 0.7161 (mp) REVERT: N 649 GLU cc_start: 0.5009 (OUTLIER) cc_final: 0.4803 (mt-10) outliers start: 10 outliers final: 4 residues processed: 115 average time/residue: 0.8690 time to fit residues: 107.3310 Evaluate side-chains 120 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 649 GLU Chi-restraints excluded: chain N residue 768 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 134 optimal weight: 0.1980 chunk 53 optimal weight: 40.0000 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 chunk 121 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN ** N 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.198619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.152129 restraints weight = 20707.721| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.45 r_work: 0.3065 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16365 Z= 0.152 Angle : 0.593 10.035 23366 Z= 0.342 Chirality : 0.045 0.289 2645 Planarity : 0.004 0.046 1948 Dihedral : 29.381 170.606 4517 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.28 % Allowed : 14.37 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.24), residues: 1172 helix: 1.92 (0.19), residues: 722 sheet: -0.04 (0.75), residues: 53 loop : -0.35 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 71 TYR 0.013 0.001 TYR H 121 PHE 0.008 0.001 PHE E 67 TRP 0.011 0.001 TRP N 629 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (16363) covalent geometry : angle 0.59308 / 0.34 (23360) hydrogen bonds : bond 0.04965 / 3.37 ( 894) hydrogen bonds : angle 3.20722 / 2.30 ( 2271) link_TRANS : bond 0.00170 / 0.09 ( 2) link_TRANS : angle 0.47331 / 0.19 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3777.50 seconds wall clock time: 65 minutes 13.69 seconds (3913.69 seconds total)