Starting phenix.real_space_refine on Thu Jul 2 07:27:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gsi_51549/07_2026/9gsi_51549.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gsi_51549/07_2026/9gsi_51549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gsi_51549/07_2026/9gsi_51549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gsi_51549/07_2026/9gsi_51549.map" model { file = "/net/cci-nas-00/data/ceres_data/9gsi_51549/07_2026/9gsi_51549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gsi_51549/07_2026/9gsi_51549.cif" } resolution = 3.39 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= 0.003 sd= 0.089 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 6 5.49 5 Mg 1 5.21 5 S 46 5.16 5 C 4671 2.51 5 N 1224 2.21 5 O 1367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 7316 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7244 Classifications: {'peptide': 933} Link IDs: {'PTRANS': 45, 'TRANS': 887} Chain breaks: 3 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1, 'ANP': 1, 'KXP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'KXP:plan-1': 1, 'KXP:plan-3': 1, 'KXP:plan-4': 1, 'KXP:plan-5': 1, 'KXP:plan-6': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 1.52, per 1000 atoms: 0.21 Number of scatterers: 7316 At special positions: 0 Unit cell: (101.01, 75.53, 140.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 46 16.00 P 6 15.00 Mg 1 11.99 O 1367 8.00 N 1224 7.00 C 4671 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 325.8 milliseconds 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 53.3% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.742A pdb=" N MET A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 49 removed outlier: 3.504A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.730A pdb=" N ILE A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 150 through 183 removed outlier: 4.529A pdb=" N GLY A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 167 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 177 " --> pdb=" O TRP A 173 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN A 183 " --> pdb=" O PHE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 281 through 288 removed outlier: 4.228A pdb=" N ILE A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 376 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 387 through 410 removed outlier: 3.779A pdb=" N ILE A 401 " --> pdb=" O LYS A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 471 through 474 Processing helix chain 'A' and resid 489 through 501 Processing helix chain 'A' and resid 522 through 535 Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.573A pdb=" N MET A 546 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 3.645A pdb=" N LYS A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 622 removed outlier: 4.534A pdb=" N GLU A 617 " --> pdb=" O LYS A 613 " (cutoff:3.500A) Proline residue: A 618 - end of helix Processing helix chain 'A' and resid 667 through 678 Processing helix chain 'A' and resid 689 through 701 Processing helix chain 'A' and resid 714 through 722 Processing helix chain 'A' and resid 729 through 737 removed outlier: 4.147A pdb=" N LYS A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 786 Processing helix chain 'A' and resid 797 through 803 removed outlier: 3.619A pdb=" N ALA A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 854 removed outlier: 3.898A pdb=" N VAL A 817 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 818 " --> pdb=" O SER A 814 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR A 839 " --> pdb=" O GLN A 835 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 842 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 873 Processing helix chain 'A' and resid 873 through 881 removed outlier: 3.784A pdb=" N SER A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 removed outlier: 4.045A pdb=" N ARG A 892 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 933 removed outlier: 6.005A pdb=" N GLU A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS A 930 " --> pdb=" O PHE A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 968 Processing helix chain 'A' and resid 986 through 1004 Processing helix chain 'A' and resid 1015 through 1037 removed outlier: 3.860A pdb=" N LEU A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 216 removed outlier: 6.488A pdb=" N LYS A 235 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP A 233 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY A 269 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY A 231 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N MET A 271 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 229 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 234 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 216 removed outlier: 6.488A pdb=" N LYS A 235 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP A 233 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY A 269 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY A 231 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N MET A 271 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 229 " --> pdb=" O MET A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 434 through 436 removed outlier: 6.200A pdb=" N GLY A 789 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU A 808 " --> pdb=" O GLY A 789 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA A 791 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 770 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N PHE A 790 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL A 772 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N MET A 792 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA A 450 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N THR A 773 " --> pdb=" O ALA A 450 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N CYS A 452 " --> pdb=" O THR A 773 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 451 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL A 685 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER A 453 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG A 741 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU A 710 " --> pdb=" O ARG A 741 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A 743 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 712 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 465 through 469 removed outlier: 5.665A pdb=" N VAL A 466 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU A 661 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 468 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N CYS A 654 " --> pdb=" O TYR A 631 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR A 631 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS A 656 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A 575 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 553 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 469 removed outlier: 5.665A pdb=" N VAL A 466 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU A 661 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 468 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N CYS A 656 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 507 through 508 366 hydrogen bonds defined for protein. 1059 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: 1.06 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1206 1.28 - 1.41: 1661 1.41 - 1.55: 4485 1.55 - 1.68: 20 1.68 - 1.81: 75 Bond restraints: 7447 Sorted by residual: bond pdb=" C3 KXP A1304 " pdb=" C6 KXP A1304 " ideal model delta sigma weight residual 1.523 1.225 0.298 2.00e-02 2.50e+03 2.23e+02 bond pdb=" C49 KXP A1304 " pdb=" O50 KXP A1304 " ideal model delta sigma weight residual 1.204 1.459 -0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" N3B ANP A1301 " pdb=" PG ANP A1301 " ideal model delta sigma weight residual 1.795 1.628 0.167 2.00e-02 2.50e+03 6.97e+01 bond pdb=" C21 KXP A1304 " pdb=" C22 KXP A1304 " ideal model delta sigma weight residual 1.506 1.650 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" O45 KXP A1304 " pdb=" P42 KXP A1304 " ideal model delta sigma weight residual 1.527 1.387 0.140 2.00e-02 2.50e+03 4.89e+01 ... (remaining 7442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.40: 10104 13.40 - 26.80: 2 26.80 - 40.20: 0 40.20 - 53.60: 0 53.60 - 67.00: 2 Bond angle restraints: 10108 Sorted by residual: angle pdb=" C5 KXP A1304 " pdb=" C3 KXP A1304 " pdb=" C6 KXP A1304 " ideal model delta sigma weight residual 112.30 179.30 -67.00 3.00e+00 1.11e-01 4.99e+02 angle pdb=" O48 KXP A1304 " pdb=" C49 KXP A1304 " pdb=" O50 KXP A1304 " ideal model delta sigma weight residual 123.72 179.83 -56.11 3.00e+00 1.11e-01 3.50e+02 angle pdb=" O26 KXP A1304 " pdb=" P25 KXP A1304 " pdb=" O27 KXP A1304 " ideal model delta sigma weight residual 119.47 101.77 17.70 3.00e+00 1.11e-01 3.48e+01 angle pdb=" O24 KXP A1304 " pdb=" P25 KXP A1304 " pdb=" O28 KXP A1304 " ideal model delta sigma weight residual 90.95 108.61 -17.66 3.00e+00 1.11e-01 3.47e+01 angle pdb=" O41 KXP A1304 " pdb=" P42 KXP A1304 " pdb=" O43 KXP A1304 " ideal model delta sigma weight residual 101.82 114.09 -12.27 3.00e+00 1.11e-01 1.67e+01 ... (remaining 10103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 4419 35.77 - 71.54: 140 71.54 - 107.31: 12 107.31 - 143.08: 4 143.08 - 178.85: 1 Dihedral angle restraints: 4576 sinusoidal: 1890 harmonic: 2686 Sorted by residual: dihedral pdb=" CA VAL A 273 " pdb=" C VAL A 273 " pdb=" N THR A 274 " pdb=" CA THR A 274 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" C2 KXP A1304 " pdb=" C1 KXP A1304 " pdb=" C18 KXP A1304 " pdb=" O1 KXP A1304 " ideal model delta sinusoidal sigma weight residual -21.13 157.72 -178.85 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O20 KXP A1304 " pdb=" C21 KXP A1304 " pdb=" C22 KXP A1304 " pdb=" O48 KXP A1304 " ideal model delta sinusoidal sigma weight residual 51.71 -166.42 -141.87 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 4573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 929 0.051 - 0.102: 236 0.102 - 0.153: 30 0.153 - 0.204: 1 0.204 - 0.255: 3 Chirality restraints: 1199 Sorted by residual: chirality pdb=" C3' ANP A1301 " pdb=" C2' ANP A1301 " pdb=" C4' ANP A1301 " pdb=" O3' ANP A1301 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C22 KXP A1304 " pdb=" C21 KXP A1304 " pdb=" C23 KXP A1304 " pdb=" O48 KXP A1304 " both_signs ideal model delta sigma weight residual False -2.41 -2.63 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C29 KXP A1304 " pdb=" C30 KXP A1304 " pdb=" C34 KXP A1304 " pdb=" O28 KXP A1304 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1196 not shown) Planarity restraints: 1267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 203 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO A 204 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 829 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C SER A 829 " 0.029 2.00e-02 2.50e+03 pdb=" O SER A 829 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 830 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 827 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C TYR A 827 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR A 827 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 828 " 0.010 2.00e-02 2.50e+03 ... (remaining 1264 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 255 2.72 - 3.27: 7634 3.27 - 3.81: 11414 3.81 - 4.36: 13612 4.36 - 4.90: 22922 Nonbonded interactions: 55837 Sorted by model distance: nonbonded pdb=" OD2 ASP A 873 " pdb="CA CA A1302 " model vdw 2.181 3.250 nonbonded pdb=" O VAL A 410 " pdb="CA CA A1302 " model vdw 2.228 3.250 nonbonded pdb=" O VAL A 407 " pdb="CA CA A1302 " model vdw 2.448 3.250 nonbonded pdb=" O GLU A 207 " pdb=" O ILE A 208 " model vdw 2.488 3.040 nonbonded pdb=" O SER A 579 " pdb=" OG SER A 579 " model vdw 2.511 3.040 ... (remaining 55832 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.730 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.060 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 0.298 7447 Z= 0.369 Angle : 1.197 66.997 10108 Z= 0.504 Chirality : 0.044 0.255 1199 Planarity : 0.004 0.050 1267 Dihedral : 17.392 178.851 2838 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.54 % Favored : 95.24 % Rotamer: Outliers : 0.74 % Allowed : 16.09 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.28), residues: 925 helix: 0.60 (0.25), residues: 444 sheet: -1.13 (0.48), residues: 93 loop : -0.99 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 463 TYR 0.008 0.001 TYR A 631 PHE 0.008 0.001 PHE A1024 TRP 0.008 0.001 TRP A 737 HIS 0.005 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.37 ( 7447) covalent geometry : angle 1.19698 / 0.50 (10108) hydrogen bonds : bond 0.17081 / 11.02 ( 357) hydrogen bonds : angle 7.77170 / 5.51 ( 1059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.6426 (pmm) cc_final: 0.5785 (ppp) REVERT: A 124 TYR cc_start: 0.5868 (t80) cc_final: 0.5654 (t80) REVERT: A 257 MET cc_start: 0.1763 (mpp) cc_final: 0.0443 (mtp) REVERT: A 370 TYR cc_start: 0.7369 (t80) cc_final: 0.6975 (t80) REVERT: A 393 GLN cc_start: 0.8212 (mm110) cc_final: 0.7595 (mt0) REVERT: A 538 ASP cc_start: 0.8106 (t0) cc_final: 0.7840 (t0) REVERT: A 601 ARG cc_start: 0.6610 (ptp90) cc_final: 0.6238 (ptp90) REVERT: A 617 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7773 (mp0) REVERT: A 662 ASP cc_start: 0.8532 (p0) cc_final: 0.7937 (p0) REVERT: A 727 GLU cc_start: 0.7476 (pm20) cc_final: 0.7216 (pm20) REVERT: A 873 ASP cc_start: 0.8610 (m-30) cc_final: 0.8139 (m-30) REVERT: A 929 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: A 931 MET cc_start: 0.7928 (mtp) cc_final: 0.7712 (mtt) outliers start: 6 outliers final: 4 residues processed: 85 average time/residue: 0.0833 time to fit residues: 9.6262 Evaluate side-chains 81 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 929 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.0770 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 393 GLN A 644 ASN A 909 ASN A 943 HIS ** A 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.215961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.163139 restraints weight = 7766.802| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.93 r_work: 0.3106 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7447 Z= 0.127 Angle : 0.562 7.289 10108 Z= 0.292 Chirality : 0.043 0.272 1199 Planarity : 0.004 0.057 1267 Dihedral : 14.176 173.845 1092 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.08 % Favored : 94.70 % Rotamer: Outliers : 2.85 % Allowed : 13.86 % Favored : 83.29 % 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: 0.31 (0.29), residues: 925 helix: 1.41 (0.25), residues: 454 sheet: -0.95 (0.48), residues: 93 loop : -0.95 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 975 TYR 0.009 0.001 TYR A 394 PHE 0.007 0.001 PHE A 123 TRP 0.009 0.001 TRP A 737 HIS 0.004 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 7447) covalent geometry : angle 0.56177 / 0.29 (10108) hydrogen bonds : bond 0.05632 / 3.74 ( 357) hydrogen bonds : angle 5.34681 / 3.84 ( 1059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.6598 (pmm) cc_final: 0.5958 (ppp) REVERT: A 257 MET cc_start: 0.1726 (mpp) cc_final: 0.0364 (mtp) REVERT: A 370 TYR cc_start: 0.7400 (t80) cc_final: 0.7016 (t80) REVERT: A 393 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7712 (mt0) REVERT: A 412 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7932 (pt0) REVERT: A 537 GLN cc_start: 0.7065 (mm110) cc_final: 0.6575 (mm110) REVERT: A 538 ASP cc_start: 0.8234 (t0) cc_final: 0.7811 (t0) REVERT: A 601 ARG cc_start: 0.6439 (ptp90) cc_final: 0.6192 (ptm-80) REVERT: A 617 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7728 (mp0) REVERT: A 662 ASP cc_start: 0.8576 (p0) cc_final: 0.7869 (p0) REVERT: A 931 MET cc_start: 0.7881 (mtp) cc_final: 0.7671 (mtt) outliers start: 23 outliers final: 11 residues processed: 94 average time/residue: 0.0728 time to fit residues: 9.1763 Evaluate side-chains 87 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 920 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 chunk 20 optimal weight: 0.0770 chunk 30 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.214108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.165618 restraints weight = 7747.673| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 3.43 r_work: 0.3242 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7447 Z= 0.124 Angle : 0.554 7.594 10108 Z= 0.285 Chirality : 0.043 0.248 1199 Planarity : 0.004 0.051 1267 Dihedral : 13.261 162.502 1085 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.41 % Favored : 94.38 % Rotamer: Outliers : 3.59 % Allowed : 13.74 % Favored : 82.67 % 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: 0.37 (0.28), residues: 925 helix: 1.55 (0.25), residues: 461 sheet: -0.95 (0.49), residues: 93 loop : -1.11 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 536 TYR 0.008 0.001 TYR A 631 PHE 0.009 0.001 PHE A 954 TRP 0.009 0.001 TRP A 737 HIS 0.003 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 7447) covalent geometry : angle 0.55372 / 0.28 (10108) hydrogen bonds : bond 0.05220 / 3.49 ( 357) hydrogen bonds : angle 4.85999 / 3.48 ( 1059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.6546 (pmm) cc_final: 0.5962 (ppp) REVERT: A 257 MET cc_start: 0.1598 (mpp) cc_final: 0.0215 (mtp) REVERT: A 370 TYR cc_start: 0.7594 (t80) cc_final: 0.7261 (t80) REVERT: A 393 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7856 (mt0) REVERT: A 518 ARG cc_start: 0.8559 (mtp85) cc_final: 0.8262 (ttm170) REVERT: A 537 GLN cc_start: 0.7080 (mm110) cc_final: 0.6657 (mm110) REVERT: A 538 ASP cc_start: 0.8147 (t0) cc_final: 0.7743 (t0) REVERT: A 601 ARG cc_start: 0.6603 (ptp90) cc_final: 0.6345 (ptm-80) REVERT: A 617 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7928 (mp0) REVERT: A 662 ASP cc_start: 0.8646 (p0) cc_final: 0.8153 (p0) REVERT: A 865 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8163 (mtt) REVERT: A 929 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8066 (mt-10) outliers start: 29 outliers final: 14 residues processed: 95 average time/residue: 0.0758 time to fit residues: 9.8878 Evaluate side-chains 87 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 967 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 40 optimal weight: 30.0000 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4308 r_free = 0.4308 target = 0.210445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149609 restraints weight = 7955.568| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.80 r_work: 0.3344 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7447 Z= 0.154 Angle : 0.585 8.180 10108 Z= 0.302 Chirality : 0.045 0.245 1199 Planarity : 0.004 0.051 1267 Dihedral : 12.747 162.598 1085 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.05 % Rotamer: Outliers : 3.22 % Allowed : 15.35 % Favored : 81.44 % 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: 0.23 (0.28), residues: 925 helix: 1.44 (0.24), residues: 463 sheet: -1.01 (0.48), residues: 93 loop : -1.19 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 536 TYR 0.009 0.001 TYR A 916 PHE 0.012 0.001 PHE A 954 TRP 0.009 0.001 TRP A 737 HIS 0.004 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 7447) covalent geometry : angle 0.58484 / 0.30 (10108) hydrogen bonds : bond 0.05886 / 3.94 ( 357) hydrogen bonds : angle 4.74448 / 3.39 ( 1059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.6540 (pmm) cc_final: 0.5918 (ppp) REVERT: A 257 MET cc_start: 0.1703 (mpp) cc_final: 0.0314 (mtp) REVERT: A 370 TYR cc_start: 0.7619 (t80) cc_final: 0.7267 (t80) REVERT: A 393 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7778 (mt0) REVERT: A 518 ARG cc_start: 0.8473 (mtp85) cc_final: 0.8177 (ttm170) REVERT: A 537 GLN cc_start: 0.7158 (mm110) cc_final: 0.6732 (mm110) REVERT: A 538 ASP cc_start: 0.8050 (t0) cc_final: 0.7678 (t0) REVERT: A 601 ARG cc_start: 0.6731 (ptp90) cc_final: 0.6483 (ptm-80) REVERT: A 617 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7856 (mp0) REVERT: A 662 ASP cc_start: 0.8771 (p0) cc_final: 0.8131 (p0) REVERT: A 929 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8117 (mt-10) outliers start: 26 outliers final: 18 residues processed: 91 average time/residue: 0.0806 time to fit residues: 10.0145 Evaluate side-chains 92 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 967 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 13 optimal weight: 10.0000 chunk 89 optimal weight: 0.0670 chunk 40 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.9922 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.210106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.161814 restraints weight = 7823.314| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 4.00 r_work: 0.3157 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7447 Z= 0.150 Angle : 0.579 8.401 10108 Z= 0.299 Chirality : 0.044 0.251 1199 Planarity : 0.004 0.053 1267 Dihedral : 12.064 159.397 1085 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.05 % Rotamer: Outliers : 3.47 % Allowed : 15.35 % Favored : 81.19 % 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: 0.16 (0.28), residues: 925 helix: 1.43 (0.24), residues: 463 sheet: -1.20 (0.48), residues: 93 loop : -1.25 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 536 TYR 0.008 0.001 TYR A 916 PHE 0.010 0.001 PHE A 954 TRP 0.010 0.001 TRP A 737 HIS 0.003 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 7447) covalent geometry : angle 0.57872 / 0.30 (10108) hydrogen bonds : bond 0.05675 / 3.81 ( 357) hydrogen bonds : angle 4.61914 / 3.30 ( 1059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.6531 (pmm) cc_final: 0.5897 (ppp) REVERT: A 203 ILE cc_start: 0.2896 (OUTLIER) cc_final: 0.2689 (mt) REVERT: A 257 MET cc_start: 0.1669 (mpp) cc_final: 0.0303 (mtp) REVERT: A 370 TYR cc_start: 0.7625 (t80) cc_final: 0.7245 (t80) REVERT: A 393 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7712 (mt0) REVERT: A 518 ARG cc_start: 0.8458 (mtp85) cc_final: 0.8187 (ttm170) REVERT: A 537 GLN cc_start: 0.7141 (mm110) cc_final: 0.6701 (mm110) REVERT: A 538 ASP cc_start: 0.8114 (t0) cc_final: 0.7621 (t0) REVERT: A 601 ARG cc_start: 0.6587 (ptp90) cc_final: 0.6229 (ptp90) REVERT: A 617 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7852 (mp0) REVERT: A 661 GLU cc_start: 0.8314 (pp20) cc_final: 0.7883 (pt0) REVERT: A 662 ASP cc_start: 0.8847 (p0) cc_final: 0.8428 (p0) REVERT: A 865 MET cc_start: 0.8426 (mtm) cc_final: 0.8186 (mtt) REVERT: A 929 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8217 (mt-10) outliers start: 28 outliers final: 19 residues processed: 94 average time/residue: 0.0787 time to fit residues: 10.1208 Evaluate side-chains 96 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 967 ASN Chi-restraints excluded: chain A residue 990 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 30.0000 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.0020 chunk 64 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 967 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.213069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 128)---------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143229 restraints weight = 7789.769| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.78 r_work: 0.3131 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7447 Z= 0.119 Angle : 0.553 9.020 10108 Z= 0.282 Chirality : 0.043 0.243 1199 Planarity : 0.004 0.053 1267 Dihedral : 11.218 146.542 1085 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.19 % Favored : 94.59 % Rotamer: Outliers : 3.34 % Allowed : 15.59 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.28), residues: 925 helix: 1.66 (0.24), residues: 462 sheet: -1.33 (0.49), residues: 79 loop : -1.20 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 536 TYR 0.008 0.001 TYR A 631 PHE 0.008 0.001 PHE A 963 TRP 0.011 0.001 TRP A 737 HIS 0.002 0.000 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 7447) covalent geometry : angle 0.55279 / 0.28 (10108) hydrogen bonds : bond 0.04765 / 3.20 ( 357) hydrogen bonds : angle 4.44196 / 3.18 ( 1059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.6533 (pmm) cc_final: 0.5907 (ppp) REVERT: A 109 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7669 (mt) REVERT: A 257 MET cc_start: 0.1753 (mpp) cc_final: 0.0487 (mtp) REVERT: A 393 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7542 (mt0) REVERT: A 518 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8129 (ttm170) REVERT: A 537 GLN cc_start: 0.7084 (mm110) cc_final: 0.6622 (mm110) REVERT: A 538 ASP cc_start: 0.8091 (t0) cc_final: 0.7607 (t0) REVERT: A 601 ARG cc_start: 0.6530 (ptp90) cc_final: 0.6311 (ptm-80) REVERT: A 617 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7790 (mp0) REVERT: A 662 ASP cc_start: 0.8731 (p0) cc_final: 0.8073 (p0) REVERT: A 929 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8099 (mt-10) outliers start: 27 outliers final: 18 residues processed: 90 average time/residue: 0.0739 time to fit residues: 9.1942 Evaluate side-chains 92 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 967 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.213147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.161654 restraints weight = 7840.168| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.97 r_work: 0.3261 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7447 Z= 0.116 Angle : 0.547 9.136 10108 Z= 0.279 Chirality : 0.043 0.227 1199 Planarity : 0.004 0.053 1267 Dihedral : 10.632 134.737 1082 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.30 % Favored : 94.49 % Rotamer: Outliers : 2.85 % Allowed : 16.34 % Favored : 80.82 % 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: 0.44 (0.28), residues: 925 helix: 1.73 (0.24), residues: 462 sheet: -1.26 (0.49), residues: 79 loop : -1.18 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 536 TYR 0.008 0.001 TYR A 631 PHE 0.008 0.001 PHE A 963 TRP 0.010 0.001 TRP A 737 HIS 0.002 0.000 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 7447) covalent geometry : angle 0.54691 / 0.28 (10108) hydrogen bonds : bond 0.04669 / 3.13 ( 357) hydrogen bonds : angle 4.40442 / 3.15 ( 1059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.6579 (pmm) cc_final: 0.5941 (ppp) REVERT: A 109 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7613 (mt) REVERT: A 203 ILE cc_start: 0.2845 (OUTLIER) cc_final: 0.2620 (mt) REVERT: A 257 MET cc_start: 0.1657 (mpp) cc_final: 0.0363 (mtm) REVERT: A 393 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7588 (mt0) REVERT: A 518 ARG cc_start: 0.8451 (mtp85) cc_final: 0.8173 (ttm170) REVERT: A 537 GLN cc_start: 0.7098 (mm110) cc_final: 0.6628 (mm110) REVERT: A 538 ASP cc_start: 0.8078 (t0) cc_final: 0.7594 (t0) REVERT: A 601 ARG cc_start: 0.6531 (ptp90) cc_final: 0.6285 (ptm-80) REVERT: A 617 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7849 (mp0) REVERT: A 662 ASP cc_start: 0.8735 (p0) cc_final: 0.8341 (p0) REVERT: A 929 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8160 (mt-10) outliers start: 23 outliers final: 13 residues processed: 88 average time/residue: 0.0653 time to fit residues: 8.0071 Evaluate side-chains 88 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 929 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 21 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 913 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.209660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.158527 restraints weight = 7858.647| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.48 r_work: 0.3166 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7447 Z= 0.160 Angle : 0.594 9.718 10108 Z= 0.306 Chirality : 0.044 0.172 1199 Planarity : 0.004 0.056 1267 Dihedral : 9.605 117.512 1082 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.05 % Rotamer: Outliers : 3.22 % Allowed : 16.58 % Favored : 80.20 % 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: 0.22 (0.28), residues: 925 helix: 1.54 (0.24), residues: 462 sheet: -1.30 (0.53), residues: 69 loop : -1.30 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 536 TYR 0.009 0.001 TYR A 916 PHE 0.010 0.001 PHE A 833 TRP 0.008 0.001 TRP A 737 HIS 0.004 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 7447) covalent geometry : angle 0.59362 / 0.31 (10108) hydrogen bonds : bond 0.05808 / 3.90 ( 357) hydrogen bonds : angle 4.49069 / 3.22 ( 1059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.6555 (pmm) cc_final: 0.5926 (ppp) REVERT: A 109 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7830 (mt) REVERT: A 203 ILE cc_start: 0.2638 (OUTLIER) cc_final: 0.2417 (mt) REVERT: A 257 MET cc_start: 0.2032 (mpp) cc_final: 0.0566 (mtm) REVERT: A 265 MET cc_start: 0.7107 (tpp) cc_final: 0.6169 (tpp) REVERT: A 370 TYR cc_start: 0.7611 (t80) cc_final: 0.6973 (t80) REVERT: A 393 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7691 (mt0) REVERT: A 518 ARG cc_start: 0.8430 (mtp85) cc_final: 0.8155 (ttm170) REVERT: A 537 GLN cc_start: 0.7153 (mm110) cc_final: 0.6682 (mm110) REVERT: A 538 ASP cc_start: 0.8061 (t0) cc_final: 0.7604 (t0) REVERT: A 601 ARG cc_start: 0.6699 (ptp90) cc_final: 0.6484 (ptm-80) REVERT: A 661 GLU cc_start: 0.8321 (pp20) cc_final: 0.7863 (pt0) REVERT: A 856 GLN cc_start: 0.7675 (pm20) cc_final: 0.7029 (pm20) REVERT: A 929 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8298 (mt-10) outliers start: 26 outliers final: 19 residues processed: 90 average time/residue: 0.0780 time to fit residues: 9.7647 Evaluate side-chains 94 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 967 ASN Chi-restraints excluded: chain A residue 990 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 62 optimal weight: 0.0040 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 0.0570 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 0.0770 chunk 72 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 0.2668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.214713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.162289 restraints weight = 7777.923| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.87 r_work: 0.3313 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7447 Z= 0.109 Angle : 0.526 10.019 10108 Z= 0.272 Chirality : 0.042 0.181 1199 Planarity : 0.004 0.056 1267 Dihedral : 8.973 115.380 1082 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.65 % Favored : 95.14 % Rotamer: Outliers : 1.98 % Allowed : 17.70 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.28), residues: 925 helix: 1.81 (0.24), residues: 462 sheet: -1.25 (0.50), residues: 79 loop : -1.17 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 536 TYR 0.008 0.001 TYR A 631 PHE 0.008 0.001 PHE A 963 TRP 0.012 0.001 TRP A 737 HIS 0.001 0.000 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 7447) covalent geometry : angle 0.52555 / 0.27 (10108) hydrogen bonds : bond 0.04189 / 2.82 ( 357) hydrogen bonds : angle 4.26589 / 3.06 ( 1059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.6582 (pmm) cc_final: 0.5947 (ppp) REVERT: A 203 ILE cc_start: 0.2556 (OUTLIER) cc_final: 0.2341 (mt) REVERT: A 257 MET cc_start: 0.1928 (mpp) cc_final: 0.0808 (mtm) REVERT: A 265 MET cc_start: 0.7064 (tpp) cc_final: 0.6109 (tpp) REVERT: A 393 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7471 (mt0) REVERT: A 518 ARG cc_start: 0.8415 (mtp85) cc_final: 0.8137 (ttm170) REVERT: A 538 ASP cc_start: 0.8059 (t0) cc_final: 0.7585 (t0) REVERT: A 601 ARG cc_start: 0.6625 (ptp90) cc_final: 0.6408 (ptm-80) REVERT: A 661 GLU cc_start: 0.8210 (pp20) cc_final: 0.7712 (pt0) REVERT: A 662 ASP cc_start: 0.8687 (p0) cc_final: 0.8236 (p0) REVERT: A 929 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8172 (mt-10) outliers start: 16 outliers final: 11 residues processed: 85 average time/residue: 0.0682 time to fit residues: 8.0955 Evaluate side-chains 82 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 929 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.212260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.165443 restraints weight = 7899.171| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.10 r_work: 0.3246 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7447 Z= 0.124 Angle : 0.547 10.084 10108 Z= 0.282 Chirality : 0.043 0.175 1199 Planarity : 0.004 0.056 1267 Dihedral : 8.822 115.179 1082 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.41 % Favored : 94.38 % Rotamer: Outliers : 1.73 % Allowed : 17.82 % Favored : 80.45 % 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: 0.48 (0.28), residues: 925 helix: 1.79 (0.24), residues: 462 sheet: -1.23 (0.50), residues: 79 loop : -1.20 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 536 TYR 0.009 0.001 TYR A 631 PHE 0.007 0.001 PHE A 790 TRP 0.008 0.001 TRP A 737 HIS 0.001 0.000 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 7447) covalent geometry : angle 0.54699 / 0.28 (10108) hydrogen bonds : bond 0.04730 / 3.17 ( 357) hydrogen bonds : angle 4.27996 / 3.07 ( 1059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1850 Ramachandran restraints generated. 925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 28 MET cc_start: 0.6529 (pmm) cc_final: 0.5948 (ppp) REVERT: A 203 ILE cc_start: 0.2496 (OUTLIER) cc_final: 0.2278 (mt) REVERT: A 257 MET cc_start: 0.2095 (mpp) cc_final: 0.0904 (mtm) REVERT: A 265 MET cc_start: 0.6995 (tpp) cc_final: 0.6091 (tpp) REVERT: A 393 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7589 (mt0) REVERT: A 518 ARG cc_start: 0.8378 (mtp85) cc_final: 0.8100 (ttm170) REVERT: A 538 ASP cc_start: 0.8038 (t0) cc_final: 0.7573 (t0) REVERT: A 601 ARG cc_start: 0.6675 (ptp90) cc_final: 0.6436 (ptm-80) REVERT: A 661 GLU cc_start: 0.8268 (pp20) cc_final: 0.7768 (pt0) outliers start: 14 outliers final: 11 residues processed: 77 average time/residue: 0.0710 time to fit residues: 7.4977 Evaluate side-chains 81 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 920 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 30.0000 chunk 59 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 967 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.212863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.162793 restraints weight = 7794.535| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.10 r_work: 0.3259 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7447 Z= 0.119 Angle : 0.535 10.194 10108 Z= 0.278 Chirality : 0.042 0.181 1199 Planarity : 0.004 0.060 1267 Dihedral : 8.566 114.471 1082 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.30 % Favored : 94.49 % Rotamer: Outliers : 1.61 % Allowed : 17.57 % Favored : 80.82 % 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: 0.48 (0.28), residues: 925 helix: 1.79 (0.24), residues: 462 sheet: -0.97 (0.55), residues: 69 loop : -1.26 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 536 TYR 0.009 0.001 TYR A 631 PHE 0.007 0.001 PHE A 987 TRP 0.009 0.001 TRP A 737 HIS 0.001 0.000 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7447) covalent geometry : angle 0.53519 / 0.28 (10108) hydrogen bonds : bond 0.04615 / 3.10 ( 357) hydrogen bonds : angle 4.25521 / 3.06 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1691.93 seconds wall clock time: 29 minutes 37.74 seconds (1777.74 seconds total)