Starting phenix.real_space_refine on Wed Jun 3 21:18:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pkp_71703/06_2026/9pkp_71703_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pkp_71703/06_2026/9pkp_71703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pkp_71703/06_2026/9pkp_71703_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pkp_71703/06_2026/9pkp_71703_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pkp_71703/06_2026/9pkp_71703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pkp_71703/06_2026/9pkp_71703.map" } resolution = 3.05 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= 0.005 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 48 5.16 5 C 5714 2.51 5 N 1276 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8426 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3999 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 3999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3999 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 215 Unusual residues: {' K': 2, 'LMT': 24} Classifications: {'undetermined': 26} Link IDs: {None: 25} Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 963 Unresolved non-hydrogen dihedrals: 1323 Unresolved non-hydrogen chiralities: 240 Chain: "B" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 213 Unusual residues: {'LMT': 24} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 963 Unresolved non-hydrogen dihedrals: 1323 Unresolved non-hydrogen chiralities: 240 Time building chain proxies: 2.25, per 1000 atoms: 0.27 Number of scatterers: 8426 At special positions: 0 Unit cell: (93.451, 101.721, 124.05, 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) K 2 19.00 S 48 16.00 O 1386 8.00 N 1276 7.00 C 5714 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: 0.82 Conformation dependent library (CDL) restraints added in 308.0 milliseconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 80.2% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 121 through 143 removed outlier: 3.910A pdb=" N ALA A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Proline residue: A 131 - end of helix removed outlier: 3.602A pdb=" N VAL A 139 " --> pdb=" O MET A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 185 removed outlier: 3.833A pdb=" N PHE A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 216 removed outlier: 3.542A pdb=" N SER A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 257 Processing helix chain 'A' and resid 267 through 295 removed outlier: 3.612A pdb=" N ARG A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 272 " --> pdb=" O GLN A 268 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 274 " --> pdb=" O GLN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'A' and resid 323 through 351 removed outlier: 3.705A pdb=" N VAL A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 380 Processing helix chain 'A' and resid 384 through 431 removed outlier: 3.517A pdb=" N GLY A 422 " --> pdb=" O PHE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.520A pdb=" N LEU A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 499 Proline residue: A 473 - end of helix removed outlier: 3.603A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 627 through 651 removed outlier: 3.658A pdb=" N HIS A 631 " --> pdb=" O LYS A 627 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 642 " --> pdb=" O LEU A 638 " (cutoff:3.500A) Proline residue: A 643 - end of helix Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 674 through 678 Processing helix chain 'A' and resid 681 through 704 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 111 through 121 Processing helix chain 'B' and resid 121 through 143 removed outlier: 3.910A pdb=" N ALA B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.602A pdb=" N VAL B 139 " --> pdb=" O MET B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 185 removed outlier: 3.833A pdb=" N PHE B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 216 removed outlier: 3.542A pdb=" N SER B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 257 Processing helix chain 'B' and resid 267 through 295 removed outlier: 3.612A pdb=" N ARG B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 272 " --> pdb=" O GLN B 268 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 312 Processing helix chain 'B' and resid 323 through 351 removed outlier: 3.705A pdb=" N VAL B 351 " --> pdb=" O THR B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 380 Processing helix chain 'B' and resid 384 through 431 removed outlier: 3.517A pdb=" N GLY B 422 " --> pdb=" O PHE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.520A pdb=" N LEU B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 499 Proline residue: B 473 - end of helix removed outlier: 3.603A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 626 Processing helix chain 'B' and resid 627 through 651 removed outlier: 3.658A pdb=" N HIS B 631 " --> pdb=" O LYS B 627 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) Proline residue: B 643 - end of helix Processing helix chain 'B' and resid 657 through 662 Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 681 through 704 Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 155 removed outlier: 4.598A pdb=" N LYS A 146 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 154 through 155 removed outlier: 4.598A pdb=" N LYS B 146 " --> pdb=" O VAL B 155 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1824 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: 1.28 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2408 1.34 - 1.46: 1816 1.46 - 1.58: 4268 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 8576 Sorted by residual: bond pdb=" N PRO A 679 " pdb=" CA PRO A 679 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.97e-01 bond pdb=" N PRO B 679 " pdb=" CA PRO B 679 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.77e-01 bond pdb=" CA PRO A 262 " pdb=" C PRO A 262 " ideal model delta sigma weight residual 1.527 1.520 0.007 1.07e-02 8.73e+03 4.54e-01 bond pdb=" CA PRO B 262 " pdb=" C PRO B 262 " ideal model delta sigma weight residual 1.527 1.520 0.007 1.07e-02 8.73e+03 4.22e-01 bond pdb=" CB PRO A 223 " pdb=" CG PRO A 223 " ideal model delta sigma weight residual 1.492 1.522 -0.030 5.00e-02 4.00e+02 3.55e-01 ... (remaining 8571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 11193 1.01 - 2.03: 195 2.03 - 3.04: 52 3.04 - 4.06: 10 4.06 - 5.07: 10 Bond angle restraints: 11460 Sorted by residual: angle pdb=" C ASP A 296 " pdb=" N ASP A 297 " pdb=" CA ASP A 297 " ideal model delta sigma weight residual 122.08 124.82 -2.74 1.47e+00 4.63e-01 3.47e+00 angle pdb=" C ASP B 296 " pdb=" N ASP B 297 " pdb=" CA ASP B 297 " ideal model delta sigma weight residual 122.08 124.81 -2.73 1.47e+00 4.63e-01 3.46e+00 angle pdb=" CA PRO A 262 " pdb=" C PRO A 262 " pdb=" O PRO A 262 " ideal model delta sigma weight residual 123.16 120.75 2.41 1.49e+00 4.50e-01 2.62e+00 angle pdb=" CA PRO B 262 " pdb=" C PRO B 262 " pdb=" O PRO B 262 " ideal model delta sigma weight residual 123.16 120.75 2.41 1.49e+00 4.50e-01 2.62e+00 angle pdb=" CA PRO B 679 " pdb=" C PRO B 679 " pdb=" O PRO B 679 " ideal model delta sigma weight residual 120.60 123.24 -2.64 1.82e+00 3.02e-01 2.10e+00 ... (remaining 11455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4968 17.98 - 35.95: 138 35.95 - 53.93: 12 53.93 - 71.90: 4 71.90 - 89.88: 2 Dihedral angle restraints: 5124 sinusoidal: 2170 harmonic: 2954 Sorted by residual: dihedral pdb=" CA LEU B 680 " pdb=" C LEU B 680 " pdb=" N LYS B 681 " pdb=" CA LYS B 681 " ideal model delta harmonic sigma weight residual 180.00 158.09 21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LEU A 680 " pdb=" C LEU A 680 " pdb=" N LYS A 681 " pdb=" CA LYS A 681 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CB MET A 291 " pdb=" CG MET A 291 " pdb=" SD MET A 291 " pdb=" CE MET A 291 " ideal model delta sinusoidal sigma weight residual 60.00 105.86 -45.86 3 1.50e+01 4.44e-03 8.24e+00 ... (remaining 5121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 847 0.029 - 0.059: 330 0.059 - 0.088: 83 0.088 - 0.118: 28 0.118 - 0.147: 6 Chirality restraints: 1294 Sorted by residual: chirality pdb=" CA ILE B 158 " pdb=" N ILE B 158 " pdb=" C ILE B 158 " pdb=" CB ILE B 158 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE A 158 " pdb=" N ILE A 158 " pdb=" C ILE A 158 " pdb=" CB ILE A 158 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA VAL A 155 " pdb=" N VAL A 155 " pdb=" C VAL A 155 " pdb=" CB VAL A 155 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 1291 not shown) Planarity restraints: 1350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 130 " -0.014 5.00e-02 4.00e+02 2.10e-02 7.06e-01 pdb=" N PRO B 131 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO B 131 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 131 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 130 " 0.014 5.00e-02 4.00e+02 2.08e-02 6.92e-01 pdb=" N PRO A 131 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 226 " -0.013 5.00e-02 4.00e+02 2.04e-02 6.69e-01 pdb=" N PRO B 227 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " -0.011 5.00e-02 4.00e+02 ... (remaining 1347 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.08: 5868 3.08 - 3.59: 9975 3.59 - 4.11: 13749 4.11 - 4.62: 22546 4.62 - 5.14: 28152 Nonbonded interactions: 80290 Sorted by model distance: nonbonded pdb=" O THR B 313 " pdb=" K K A 901 " model vdw 2.564 2.850 nonbonded pdb=" O THR A 313 " pdb=" K K A 901 " model vdw 2.565 2.850 nonbonded pdb=" N LEU A 266 " pdb=" O LEU A 266 " model vdw 2.651 2.496 nonbonded pdb=" N LEU B 266 " pdb=" O LEU B 266 " model vdw 2.651 2.496 nonbonded pdb=" N ASP B 267 " pdb=" O ASP B 267 " model vdw 2.654 2.496 ... (remaining 80285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 82 through 706 or resid 903 or (resid 904 and (name C1 or \ name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 905 and (name C \ 1 or name C2 or name C3 or name C4 )) or resid 907 or (resid 908 and (name C10 o \ r name C7 or name C8 or name C9 )) or resid 909 or (resid 910 through 911 and (n \ ame C10 or name C11 or name C4 or name C5 or name C6 or name C7 or name C8 or na \ me C9 )) or resid 912 or (resid 913 and (name C10 or name C11 or name C12 or nam \ e C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C \ 9 )) or (resid 914 and (name C2 or name C3 or name C4 or name C5 or name C6 or n \ ame C7 )) or resid 915 or (resid 916 and (name C2 or name C3 or name C4 or name \ C5 or name C6 or name C7 )) or resid 917 or (resid 918 through 919 and (name C4 \ or name C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 920 and (nam \ e C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C \ 9 )) or (resid 921 and (name C3 or name C4 or name C5 or name C6 or name C7 or n \ ame C8 or name C9 )) or resid 922 or (resid 923 and (name C3 or name C4 or name \ C5 or name C6 or name C7 or name C8 )) or (resid 924 and (name C3 or name C4 or \ name C5 or name C6 or name C7 )))) selection = (chain 'B' and (resid 82 through 706 or resid 803 through 805 or resid 807 or (r \ esid 808 and (name C10 or name C7 or name C8 or name C9 )) or (resid 809 and (na \ me C10 or name C11 or name C12 or name C7 or name C8 or name C9 )) or (resid 810 \ through 811 and (name C10 or name C11 or name C4 or name C5 or name C6 or name \ C7 or name C8 or name C9 )) or resid 812 through 813 or (resid 814 and (name C2 \ or name C3 or name C4 or name C5 or name C6 or name C7 )) or resid 815 or (resid \ 816 and (name C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or ( \ resid 817 and (name C10 or name C2 or name C3 or name C4 or name C5 or name C6 o \ r name C7 or name C8 or name C9 )) or (resid 818 through 819 and (name C4 or nam \ e C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 820 and (name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r (resid 821 and (name C3 or name C4 or name C5 or name C6 or name C7 or name C8 \ or name C9 )) or (resid 822 and (name C10 or name C3 or name C4 or name C5 or n \ ame C6 or name C7 or name C8 or name C9 )) or resid 823 or (resid 824 and (name \ C3 or name C4 or name C5 or name C6 or name C7 )))) } 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.120 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8576 Z= 0.076 Angle : 0.390 5.074 11460 Z= 0.202 Chirality : 0.035 0.147 1294 Planarity : 0.003 0.026 1350 Dihedral : 8.587 89.879 3216 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.25 (0.24), residues: 1002 helix: 0.48 (0.17), residues: 760 sheet: None (None), residues: 0 loop : -0.49 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.005 0.001 TYR B 255 PHE 0.005 0.001 PHE A 264 TRP 0.004 0.001 TRP A 467 HIS 0.001 0.000 HIS B 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00156 / 0.08 ( 8576) covalent geometry : angle 0.39010 / 0.20 (11460) hydrogen bonds : bond 0.20061 / 12.93 ( 612) hydrogen bonds : angle 6.44963 / 4.60 ( 1824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6063 (mpp) cc_final: 0.5364 (tpp) REVERT: A 268 GLN cc_start: 0.8654 (tp40) cc_final: 0.7902 (tp40) REVERT: A 269 ARG cc_start: 0.8392 (mtt90) cc_final: 0.7928 (mmm160) REVERT: A 270 GLN cc_start: 0.8608 (mt0) cc_final: 0.8278 (mt0) REVERT: A 392 MET cc_start: 0.8676 (mmm) cc_final: 0.8436 (tpp) REVERT: A 696 MET cc_start: 0.9195 (mtt) cc_final: 0.8904 (mtm) REVERT: B 83 MET cc_start: 0.6078 (mpp) cc_final: 0.5390 (tpp) REVERT: B 268 GLN cc_start: 0.8617 (tp40) cc_final: 0.7794 (tp40) REVERT: B 269 ARG cc_start: 0.8347 (mtt90) cc_final: 0.7896 (mmm160) REVERT: B 270 GLN cc_start: 0.8579 (mt0) cc_final: 0.8275 (mt0) REVERT: B 275 LEU cc_start: 0.8920 (mt) cc_final: 0.8501 (tp) REVERT: B 392 MET cc_start: 0.8673 (mmm) cc_final: 0.8433 (tpp) REVERT: B 696 MET cc_start: 0.9223 (mtt) cc_final: 0.8945 (mtm) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1005 time to fit residues: 17.9613 Evaluate side-chains 88 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.090551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.072414 restraints weight = 22625.606| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.15 r_work: 0.2944 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8576 Z= 0.133 Angle : 0.519 6.210 11460 Z= 0.264 Chirality : 0.039 0.179 1294 Planarity : 0.004 0.029 1350 Dihedral : 5.999 58.119 1364 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.59 % Allowed : 5.24 % Favored : 93.17 % 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: 2.45 (0.27), residues: 1002 helix: 2.14 (0.18), residues: 782 sheet: None (None), residues: 0 loop : -0.25 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 699 TYR 0.014 0.001 TYR A 255 PHE 0.013 0.001 PHE B 264 TRP 0.009 0.001 TRP B 115 HIS 0.001 0.000 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 8576) covalent geometry : angle 0.51852 / 0.26 (11460) hydrogen bonds : bond 0.04986 / 3.38 ( 612) hydrogen bonds : angle 3.85600 / 2.77 ( 1824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.287 Fit side-chains REVERT: A 83 MET cc_start: 0.6117 (mpp) cc_final: 0.5338 (tpp) REVERT: A 268 GLN cc_start: 0.8706 (tp40) cc_final: 0.8431 (tp40) REVERT: A 269 ARG cc_start: 0.7979 (mtt90) cc_final: 0.7660 (mmm160) REVERT: A 392 MET cc_start: 0.8617 (mmm) cc_final: 0.8367 (tpp) REVERT: B 83 MET cc_start: 0.6068 (mpp) cc_final: 0.5324 (tpp) REVERT: B 268 GLN cc_start: 0.8661 (tp40) cc_final: 0.8364 (tp40) REVERT: B 269 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7608 (mmm160) REVERT: B 392 MET cc_start: 0.8616 (mmm) cc_final: 0.8365 (tpp) REVERT: B 497 PHE cc_start: 0.8137 (m-80) cc_final: 0.7918 (m-80) outliers start: 14 outliers final: 6 residues processed: 107 average time/residue: 0.0922 time to fit residues: 13.8325 Evaluate side-chains 89 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 0.6980 chunk 42 optimal weight: 0.0070 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.088606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.070437 restraints weight = 22502.088| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.09 r_work: 0.2923 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8576 Z= 0.150 Angle : 0.487 5.162 11460 Z= 0.248 Chirality : 0.039 0.168 1294 Planarity : 0.003 0.024 1350 Dihedral : 6.424 59.286 1364 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.25 % Allowed : 7.29 % Favored : 91.46 % 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: 3.10 (0.27), residues: 1002 helix: 2.66 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -0.22 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 699 TYR 0.008 0.001 TYR A 255 PHE 0.030 0.001 PHE A 497 TRP 0.009 0.001 TRP B 467 HIS 0.002 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 8576) covalent geometry : angle 0.48691 / 0.25 (11460) hydrogen bonds : bond 0.04539 / 3.06 ( 612) hydrogen bonds : angle 3.62738 / 2.62 ( 1824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.334 Fit side-chains REVERT: A 83 MET cc_start: 0.6147 (mpp) cc_final: 0.5445 (tpp) REVERT: A 268 GLN cc_start: 0.8744 (tp40) cc_final: 0.8151 (tp40) REVERT: A 269 ARG cc_start: 0.7882 (mtt90) cc_final: 0.7576 (mmm160) REVERT: A 696 MET cc_start: 0.9270 (mmt) cc_final: 0.9035 (mmt) REVERT: B 83 MET cc_start: 0.6164 (mpp) cc_final: 0.5511 (tpp) REVERT: B 269 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7594 (mmm160) REVERT: B 497 PHE cc_start: 0.8330 (m-80) cc_final: 0.8110 (m-80) REVERT: B 696 MET cc_start: 0.9307 (mmt) cc_final: 0.9064 (mmt) outliers start: 11 outliers final: 10 residues processed: 94 average time/residue: 0.0825 time to fit residues: 11.3645 Evaluate side-chains 93 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 0.0670 chunk 10 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.071749 restraints weight = 23089.620| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.21 r_work: 0.2939 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8576 Z= 0.110 Angle : 0.457 5.064 11460 Z= 0.232 Chirality : 0.038 0.154 1294 Planarity : 0.003 0.024 1350 Dihedral : 6.232 59.783 1364 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.94 % Allowed : 6.95 % Favored : 91.12 % 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: 3.34 (0.27), residues: 1002 helix: 2.83 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -0.15 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 699 TYR 0.007 0.001 TYR A 255 PHE 0.012 0.001 PHE A 497 TRP 0.008 0.001 TRP B 467 HIS 0.001 0.000 HIS B 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 8576) covalent geometry : angle 0.45719 / 0.23 (11460) hydrogen bonds : bond 0.03917 / 2.64 ( 612) hydrogen bonds : angle 3.48170 / 2.52 ( 1824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.304 Fit side-chains REVERT: A 83 MET cc_start: 0.6026 (mpp) cc_final: 0.5383 (tpp) REVERT: A 268 GLN cc_start: 0.8734 (tp40) cc_final: 0.7822 (tp40) REVERT: A 269 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7602 (mmm160) REVERT: A 633 MET cc_start: 0.7680 (ttm) cc_final: 0.7449 (ttp) REVERT: A 696 MET cc_start: 0.9297 (mmt) cc_final: 0.9044 (mmt) REVERT: B 83 MET cc_start: 0.6170 (mpp) cc_final: 0.5581 (tpp) REVERT: B 268 GLN cc_start: 0.8805 (tp40) cc_final: 0.7670 (tp40) REVERT: B 269 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7603 (mmm160) REVERT: B 696 MET cc_start: 0.9290 (mmt) cc_final: 0.9055 (mmt) outliers start: 17 outliers final: 9 residues processed: 98 average time/residue: 0.0869 time to fit residues: 12.2576 Evaluate side-chains 93 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.087687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.069499 restraints weight = 23009.230| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.12 r_work: 0.2900 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8576 Z= 0.144 Angle : 0.494 5.835 11460 Z= 0.247 Chirality : 0.040 0.196 1294 Planarity : 0.003 0.025 1350 Dihedral : 6.533 59.327 1364 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.16 % Allowed : 7.86 % Favored : 89.98 % 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: 3.43 (0.27), residues: 1002 helix: 2.90 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -0.12 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.009 0.001 TYR A 255 PHE 0.019 0.001 PHE B 497 TRP 0.009 0.001 TRP B 467 HIS 0.002 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 8576) covalent geometry : angle 0.49386 / 0.25 (11460) hydrogen bonds : bond 0.04049 / 2.74 ( 612) hydrogen bonds : angle 3.51203 / 2.54 ( 1824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.6182 (mpp) cc_final: 0.5563 (tpp) REVERT: A 268 GLN cc_start: 0.8736 (tp40) cc_final: 0.7795 (tp40) REVERT: A 269 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7589 (mmm160) REVERT: A 696 MET cc_start: 0.9338 (mmt) cc_final: 0.9097 (mmt) REVERT: B 83 MET cc_start: 0.6191 (mpp) cc_final: 0.5562 (tpp) REVERT: B 268 GLN cc_start: 0.8784 (tp40) cc_final: 0.7660 (tp40) REVERT: B 269 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7616 (mmm160) outliers start: 19 outliers final: 15 residues processed: 96 average time/residue: 0.0913 time to fit residues: 12.6237 Evaluate side-chains 100 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.088396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.069609 restraints weight = 22972.710| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.20 r_work: 0.2898 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8576 Z= 0.124 Angle : 0.485 6.492 11460 Z= 0.241 Chirality : 0.039 0.148 1294 Planarity : 0.003 0.026 1350 Dihedral : 6.560 59.340 1364 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.05 % Allowed : 8.20 % Favored : 89.75 % 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: 3.45 (0.27), residues: 1002 helix: 2.90 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -0.10 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.008 0.001 TYR B 255 PHE 0.015 0.001 PHE A 497 TRP 0.009 0.001 TRP A 467 HIS 0.001 0.000 HIS B 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 8576) covalent geometry : angle 0.48515 / 0.24 (11460) hydrogen bonds : bond 0.03896 / 2.64 ( 612) hydrogen bonds : angle 3.46285 / 2.50 ( 1824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.317 Fit side-chains REVERT: A 83 MET cc_start: 0.6144 (mpp) cc_final: 0.5553 (tpp) REVERT: A 268 GLN cc_start: 0.8705 (tp40) cc_final: 0.7215 (tp40) REVERT: A 269 ARG cc_start: 0.7820 (mtt90) cc_final: 0.7571 (mmm160) REVERT: A 696 MET cc_start: 0.9305 (mmt) cc_final: 0.9053 (mmt) REVERT: B 83 MET cc_start: 0.6163 (mpp) cc_final: 0.5555 (tpp) REVERT: B 268 GLN cc_start: 0.8757 (tp40) cc_final: 0.7085 (tp40) REVERT: B 269 ARG cc_start: 0.7799 (mtt90) cc_final: 0.7568 (mmm160) REVERT: B 696 MET cc_start: 0.9309 (mmt) cc_final: 0.9064 (mmt) outliers start: 18 outliers final: 14 residues processed: 97 average time/residue: 0.0813 time to fit residues: 11.6016 Evaluate side-chains 97 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.088166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.069945 restraints weight = 22752.972| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.11 r_work: 0.2917 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8576 Z= 0.112 Angle : 0.496 8.277 11460 Z= 0.241 Chirality : 0.039 0.148 1294 Planarity : 0.003 0.026 1350 Dihedral : 6.464 58.053 1364 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.82 % Allowed : 9.23 % Favored : 88.95 % 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: 3.49 (0.27), residues: 1002 helix: 2.96 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -0.19 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.006 0.001 TYR B 439 PHE 0.011 0.001 PHE A 264 TRP 0.008 0.001 TRP A 467 HIS 0.001 0.000 HIS B 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 8576) covalent geometry : angle 0.49562 / 0.24 (11460) hydrogen bonds : bond 0.03746 / 2.54 ( 612) hydrogen bonds : angle 3.41510 / 2.47 ( 1824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.372 Fit side-chains REVERT: A 83 MET cc_start: 0.6133 (mpp) cc_final: 0.5521 (tpp) REVERT: A 268 GLN cc_start: 0.8671 (tp40) cc_final: 0.7991 (tp40) REVERT: A 269 ARG cc_start: 0.7785 (mtt90) cc_final: 0.7528 (mmm-85) REVERT: B 83 MET cc_start: 0.6170 (mpp) cc_final: 0.5650 (tpp) REVERT: B 268 GLN cc_start: 0.8714 (tp40) cc_final: 0.7093 (tp40) REVERT: B 269 ARG cc_start: 0.7753 (mtt90) cc_final: 0.7534 (mmm160) REVERT: B 636 ASP cc_start: 0.9309 (m-30) cc_final: 0.9102 (t0) REVERT: B 696 MET cc_start: 0.9311 (mmt) cc_final: 0.9060 (mmt) outliers start: 16 outliers final: 13 residues processed: 102 average time/residue: 0.0764 time to fit residues: 11.7869 Evaluate side-chains 100 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.086776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.068403 restraints weight = 22901.877| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.14 r_work: 0.2883 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8576 Z= 0.148 Angle : 0.525 10.498 11460 Z= 0.257 Chirality : 0.040 0.159 1294 Planarity : 0.003 0.028 1350 Dihedral : 6.669 55.847 1364 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.82 % Allowed : 10.48 % Favored : 87.70 % 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: 3.50 (0.27), residues: 1002 helix: 3.01 (0.18), residues: 768 sheet: None (None), residues: 0 loop : -0.15 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.008 0.001 TYR B 255 PHE 0.010 0.001 PHE B 264 TRP 0.010 0.001 TRP A 661 HIS 0.003 0.001 HIS B 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8576) covalent geometry : angle 0.52520 / 0.26 (11460) hydrogen bonds : bond 0.03959 / 2.69 ( 612) hydrogen bonds : angle 3.52591 / 2.55 ( 1824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.481 Fit side-chains REVERT: A 83 MET cc_start: 0.6236 (mpp) cc_final: 0.5679 (tpp) REVERT: A 269 ARG cc_start: 0.7830 (mtt90) cc_final: 0.7579 (mmm-85) REVERT: A 696 MET cc_start: 0.9293 (mmt) cc_final: 0.9034 (mmt) REVERT: B 83 MET cc_start: 0.6170 (mpp) cc_final: 0.5683 (tpp) REVERT: B 268 GLN cc_start: 0.8721 (tp40) cc_final: 0.7099 (tp40) REVERT: B 269 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7565 (mmm160) REVERT: B 636 ASP cc_start: 0.9302 (m-30) cc_final: 0.9097 (t0) REVERT: B 696 MET cc_start: 0.9294 (mmt) cc_final: 0.9053 (mmt) outliers start: 16 outliers final: 14 residues processed: 97 average time/residue: 0.0743 time to fit residues: 10.9431 Evaluate side-chains 101 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 99 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.087206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.068824 restraints weight = 22879.781| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.13 r_work: 0.2894 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8576 Z= 0.128 Angle : 0.534 11.262 11460 Z= 0.256 Chirality : 0.040 0.150 1294 Planarity : 0.003 0.028 1350 Dihedral : 6.682 55.248 1364 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.71 % Allowed : 10.59 % Favored : 87.70 % 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: 3.52 (0.27), residues: 1002 helix: 3.02 (0.18), residues: 768 sheet: None (None), residues: 0 loop : -0.14 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.006 0.001 TYR B 305 PHE 0.013 0.001 PHE B 264 TRP 0.009 0.001 TRP B 467 HIS 0.001 0.000 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8576) covalent geometry : angle 0.53358 / 0.26 (11460) hydrogen bonds : bond 0.03869 / 2.63 ( 612) hydrogen bonds : angle 3.51179 / 2.54 ( 1824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.417 Fit side-chains REVERT: A 83 MET cc_start: 0.6180 (mpp) cc_final: 0.5627 (tpp) REVERT: A 269 ARG cc_start: 0.7806 (mtt90) cc_final: 0.7563 (mmm-85) REVERT: A 696 MET cc_start: 0.9278 (mmt) cc_final: 0.9012 (mmt) REVERT: B 83 MET cc_start: 0.6156 (mpp) cc_final: 0.5671 (tpp) REVERT: B 268 GLN cc_start: 0.8714 (tp40) cc_final: 0.7879 (tp40) REVERT: B 269 ARG cc_start: 0.7776 (mtt90) cc_final: 0.7555 (mmm-85) REVERT: B 636 ASP cc_start: 0.9323 (m-30) cc_final: 0.9109 (t0) REVERT: B 696 MET cc_start: 0.9286 (mmt) cc_final: 0.9001 (mmt) outliers start: 15 outliers final: 15 residues processed: 100 average time/residue: 0.0789 time to fit residues: 11.8287 Evaluate side-chains 102 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.088491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.069709 restraints weight = 23002.906| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.18 r_work: 0.2901 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8576 Z= 0.117 Angle : 0.529 11.357 11460 Z= 0.253 Chirality : 0.039 0.149 1294 Planarity : 0.003 0.028 1350 Dihedral : 6.504 55.176 1364 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.59 % Allowed : 10.48 % Favored : 87.93 % 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: 3.59 (0.27), residues: 1002 helix: 3.07 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.05 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.006 0.001 TYR B 637 PHE 0.013 0.001 PHE B 264 TRP 0.009 0.001 TRP B 467 HIS 0.001 0.000 HIS B 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8576) covalent geometry : angle 0.52907 / 0.25 (11460) hydrogen bonds : bond 0.03779 / 2.58 ( 612) hydrogen bonds : angle 3.47486 / 2.52 ( 1824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.385 Fit side-chains REVERT: A 83 MET cc_start: 0.6156 (mpp) cc_final: 0.5531 (tpp) REVERT: A 268 GLN cc_start: 0.8606 (tp40) cc_final: 0.7921 (tp40) REVERT: A 269 ARG cc_start: 0.7758 (mtt90) cc_final: 0.7528 (mmm-85) REVERT: A 696 MET cc_start: 0.9256 (mmt) cc_final: 0.8994 (mmt) REVERT: B 83 MET cc_start: 0.6147 (mpp) cc_final: 0.5585 (tpp) REVERT: B 268 GLN cc_start: 0.8711 (tp40) cc_final: 0.7868 (tp40) REVERT: B 269 ARG cc_start: 0.7752 (mtt90) cc_final: 0.7527 (mmm-85) REVERT: B 636 ASP cc_start: 0.9346 (m-30) cc_final: 0.9132 (t0) REVERT: B 696 MET cc_start: 0.9203 (mmt) cc_final: 0.8952 (mmt) outliers start: 14 outliers final: 13 residues processed: 101 average time/residue: 0.0823 time to fit residues: 12.1557 Evaluate side-chains 101 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.088563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.070335 restraints weight = 22685.636| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.12 r_work: 0.2918 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8576 Z= 0.109 Angle : 0.536 10.855 11460 Z= 0.255 Chirality : 0.039 0.149 1294 Planarity : 0.003 0.029 1350 Dihedral : 6.404 55.130 1364 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.82 % Allowed : 10.71 % Favored : 87.47 % 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: 3.65 (0.27), residues: 1002 helix: 3.10 (0.18), residues: 754 sheet: None (None), residues: 0 loop : 0.15 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.008 0.001 TYR B 658 PHE 0.014 0.001 PHE B 264 TRP 0.009 0.001 TRP B 467 HIS 0.001 0.000 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 8576) covalent geometry : angle 0.53623 / 0.26 (11460) hydrogen bonds : bond 0.03696 / 2.51 ( 612) hydrogen bonds : angle 3.47388 / 2.53 ( 1824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1865.51 seconds wall clock time: 32 minutes 53.61 seconds (1973.61 seconds total)