Starting phenix.real_space_refine on Thu Jul 2 13:07:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pkp_71703/07_2026/9pkp_71703_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pkp_71703/07_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_71703/07_2026/9pkp_71703_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pkp_71703/07_2026/9pkp_71703_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pkp_71703/07_2026/9pkp_71703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pkp_71703/07_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-6108/lib/python3.11/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, 213 Ad-hoc single atom residues: {' K': 2} Unusual residues: {'LMT': 24} Classifications: {'undetermined': 24} Link IDs: {None: 23} Chain breaks: 2 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: 1.99, per 1000 atoms: 0.24 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: 0.67 Conformation dependent library (CDL) restraints added in 395.8 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: 0.21 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: 1.31 Time building geometry restraints manager: 0.91 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 3.590 nonbonded pdb=" O THR A 313 " pdb=" K K A 901 " model vdw 2.565 3.590 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: 2.400 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.080 Find NCS groups from input model: 0.180 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 : 0.317 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: 0.1013 time to fit residues: 18.4674 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 : 0.319 ------------------------------------------------------------------------------- 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... 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 = 0.3496 r_free = 0.3496 target = 0.089794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.071271 restraints weight = 22800.501| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.24 r_work: 0.2942 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8576 Z= 0.136 Angle : 0.516 5.761 11460 Z= 0.263 Chirality : 0.039 0.173 1294 Planarity : 0.004 0.026 1350 Dihedral : 5.977 58.086 1364 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.25 % Allowed : 5.58 % 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: 2.60 (0.27), residues: 1002 helix: 2.20 (0.18), residues: 782 sheet: None (None), residues: 0 loop : 0.02 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 699 TYR 0.013 0.001 TYR A 255 PHE 0.014 0.001 PHE B 264 TRP 0.009 0.001 TRP B 467 HIS 0.001 0.000 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 8576) covalent geometry : angle 0.51614 / 0.26 (11460) hydrogen bonds : bond 0.05085 / 3.44 ( 612) hydrogen bonds : angle 3.88510 / 2.79 ( 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 112 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.325 Fit side-chains REVERT: A 83 MET cc_start: 0.6117 (mpp) cc_final: 0.5338 (tpp) REVERT: A 268 GLN cc_start: 0.8713 (tp40) cc_final: 0.8408 (tp40) REVERT: A 269 ARG cc_start: 0.7982 (mtt90) cc_final: 0.7662 (mmm160) REVERT: A 392 MET cc_start: 0.8618 (mmm) cc_final: 0.8377 (tpp) REVERT: B 83 MET cc_start: 0.6073 (mpp) cc_final: 0.5314 (tpp) REVERT: B 268 GLN cc_start: 0.8664 (tp40) cc_final: 0.8352 (tp40) REVERT: B 269 ARG cc_start: 0.7925 (mtt90) cc_final: 0.7628 (mmm160) REVERT: B 392 MET cc_start: 0.8604 (mmm) cc_final: 0.8367 (tpp) REVERT: B 497 PHE cc_start: 0.8146 (m-80) cc_final: 0.7879 (m-80) outliers start: 11 outliers final: 6 residues processed: 103 average time/residue: 0.0986 time to fit residues: 14.1626 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 : 0.360 ------------------------------------------------------------------------------- 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: 0.5980 chunk 42 optimal weight: 0.0010 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.089622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.071498 restraints weight = 22651.181| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.22 r_work: 0.2930 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8576 Z= 0.117 Angle : 0.472 5.426 11460 Z= 0.237 Chirality : 0.038 0.184 1294 Planarity : 0.003 0.022 1350 Dihedral : 5.964 58.446 1364 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.25 % Allowed : 7.63 % 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: 3.27 (0.27), residues: 1002 helix: 2.71 (0.18), residues: 778 sheet: None (None), residues: 0 loop : 0.14 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 699 TYR 0.007 0.001 TYR B 255 PHE 0.034 0.001 PHE A 497 TRP 0.008 0.001 TRP B 467 HIS 0.001 0.000 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 8576) covalent geometry : angle 0.47152 / 0.24 (11460) hydrogen bonds : bond 0.04346 / 2.94 ( 612) hydrogen bonds : angle 3.60924 / 2.61 ( 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 104 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.328 Fit side-chains REVERT: A 83 MET cc_start: 0.6088 (mpp) cc_final: 0.5401 (tpp) REVERT: A 269 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7586 (mmm160) REVERT: A 392 MET cc_start: 0.8615 (mmm) cc_final: 0.8341 (tpp) REVERT: A 662 LYS cc_start: 0.8767 (tptt) cc_final: 0.8559 (tptt) REVERT: A 696 MET cc_start: 0.9207 (mmt) cc_final: 0.8985 (mmt) REVERT: B 83 MET cc_start: 0.6105 (mpp) cc_final: 0.5462 (tpp) REVERT: B 268 GLN cc_start: 0.8638 (tp40) cc_final: 0.8386 (tp40) REVERT: B 269 ARG cc_start: 0.7893 (mtt90) cc_final: 0.7576 (mmm160) REVERT: B 392 MET cc_start: 0.8620 (mmm) cc_final: 0.8341 (tpp) REVERT: B 497 PHE cc_start: 0.8265 (m-80) cc_final: 0.7994 (m-80) REVERT: B 633 MET cc_start: 0.7731 (ttm) cc_final: 0.7442 (ttp) REVERT: B 662 LYS cc_start: 0.8746 (tptt) cc_final: 0.8533 (tptt) REVERT: B 696 MET cc_start: 0.9229 (mmt) cc_final: 0.9018 (mmt) outliers start: 11 outliers final: 7 residues processed: 96 average time/residue: 0.0799 time to fit residues: 11.3719 Evaluate side-chains 92 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3431 r_free = 0.3431 target = 0.085856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.067073 restraints weight = 23473.299| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.19 r_work: 0.2849 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8576 Z= 0.201 Angle : 0.535 5.236 11460 Z= 0.274 Chirality : 0.040 0.160 1294 Planarity : 0.003 0.023 1350 Dihedral : 7.351 59.808 1364 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.94 % Allowed : 7.52 % Favored : 90.55 % 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: 3.30 (0.27), residues: 1002 helix: 2.71 (0.18), residues: 778 sheet: None (None), residues: 0 loop : 0.27 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 699 TYR 0.011 0.001 TYR A 255 PHE 0.014 0.001 PHE A 497 TRP 0.010 0.001 TRP B 467 HIS 0.003 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 ( 8576) covalent geometry : angle 0.53521 / 0.27 (11460) hydrogen bonds : bond 0.04554 / 3.08 ( 612) hydrogen bonds : angle 3.69390 / 2.68 ( 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 102 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.330 Fit side-chains REVERT: A 83 MET cc_start: 0.6236 (mpp) cc_final: 0.5511 (tpp) REVERT: A 268 GLN cc_start: 0.8825 (tp40) cc_final: 0.7780 (tp40) REVERT: A 269 ARG cc_start: 0.7920 (mtt90) cc_final: 0.7703 (mmm160) REVERT: B 83 MET cc_start: 0.6234 (mpp) cc_final: 0.5608 (tpp) REVERT: B 268 GLN cc_start: 0.8791 (tp40) cc_final: 0.7815 (tp40) REVERT: B 269 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7681 (mmm160) REVERT: B 497 PHE cc_start: 0.8374 (m-80) cc_final: 0.8162 (m-80) REVERT: B 696 MET cc_start: 0.9385 (mmt) cc_final: 0.9146 (mmt) outliers start: 17 outliers final: 13 residues processed: 90 average time/residue: 0.0819 time to fit residues: 10.9249 Evaluate side-chains 96 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 486 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: 0.7980 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.087833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.069691 restraints weight = 22898.181| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.10 r_work: 0.2905 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2753 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= 0.114 Angle : 0.481 7.733 11460 Z= 0.238 Chirality : 0.038 0.148 1294 Planarity : 0.003 0.026 1350 Dihedral : 6.858 59.963 1364 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.05 % Allowed : 7.63 % Favored : 90.32 % 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: 3.49 (0.27), residues: 1002 helix: 2.83 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 0.36 (0.48), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 699 TYR 0.007 0.001 TYR A 439 PHE 0.010 0.001 PHE A 497 TRP 0.009 0.001 TRP B 467 HIS 0.001 0.000 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 8576) covalent geometry : angle 0.48145 / 0.24 (11460) hydrogen bonds : bond 0.03954 / 2.67 ( 612) hydrogen bonds : angle 3.49561 / 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 114 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.391 Fit side-chains REVERT: A 83 MET cc_start: 0.6195 (mpp) cc_final: 0.5566 (tpp) REVERT: A 268 GLN cc_start: 0.8759 (tp40) cc_final: 0.7115 (tp40) REVERT: A 269 ARG cc_start: 0.7823 (mtt90) cc_final: 0.7579 (mmm160) REVERT: A 392 MET cc_start: 0.8758 (mmm) cc_final: 0.8355 (tpp) REVERT: A 696 MET cc_start: 0.9293 (mmt) cc_final: 0.9070 (mmt) REVERT: B 83 MET cc_start: 0.6167 (mpp) cc_final: 0.5633 (tpp) REVERT: B 268 GLN cc_start: 0.8703 (tp40) cc_final: 0.7222 (tp40) REVERT: B 269 ARG cc_start: 0.7797 (mtt90) cc_final: 0.7554 (mmm160) REVERT: B 392 MET cc_start: 0.8756 (mmm) cc_final: 0.8350 (tpp) REVERT: B 696 MET cc_start: 0.9308 (mmt) cc_final: 0.9103 (mmt) outliers start: 18 outliers final: 10 residues processed: 103 average time/residue: 0.0893 time to fit residues: 13.2139 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 : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3465 r_free = 0.3465 target = 0.087147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.069050 restraints weight = 22893.652| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.10 r_work: 0.2893 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2875 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= 0.133 Angle : 0.495 6.683 11460 Z= 0.246 Chirality : 0.040 0.187 1294 Planarity : 0.003 0.028 1350 Dihedral : 6.879 56.816 1364 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.59 % Allowed : 9.34 % Favored : 89.07 % 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: 3.46 (0.27), residues: 1002 helix: 2.83 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 0.28 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.007 0.001 TYR A 255 PHE 0.019 0.001 PHE B 497 TRP 0.009 0.001 TRP B 467 HIS 0.002 0.000 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8576) covalent geometry : angle 0.49513 / 0.25 (11460) hydrogen bonds : bond 0.03949 / 2.69 ( 612) hydrogen bonds : angle 3.50731 / 2.54 ( 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 102 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.311 Fit side-chains REVERT: A 83 MET cc_start: 0.6168 (mpp) cc_final: 0.5537 (tpp) REVERT: A 268 GLN cc_start: 0.8755 (tp40) cc_final: 0.7134 (tp40) REVERT: A 269 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7566 (mmm160) REVERT: A 696 MET cc_start: 0.9293 (mmt) cc_final: 0.9047 (mmt) REVERT: B 83 MET cc_start: 0.6219 (mpp) cc_final: 0.5653 (tpp) REVERT: B 268 GLN cc_start: 0.8691 (tp40) cc_final: 0.8001 (tp40) REVERT: B 269 ARG cc_start: 0.7794 (mtt90) cc_final: 0.7529 (mmm-85) outliers start: 14 outliers final: 12 residues processed: 94 average time/residue: 0.0685 time to fit residues: 9.7876 Evaluate side-chains 98 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 88 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.087652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.069367 restraints weight = 22933.048| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.13 r_work: 0.2905 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8576 Z= 0.117 Angle : 0.496 7.745 11460 Z= 0.244 Chirality : 0.039 0.160 1294 Planarity : 0.003 0.029 1350 Dihedral : 6.773 59.433 1364 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.37 % Allowed : 9.91 % Favored : 88.72 % 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: 2.86 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 0.31 (0.48), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.007 0.001 TYR A 439 PHE 0.011 0.001 PHE A 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 0.00262 / 0.12 ( 8576) covalent geometry : angle 0.49642 / 0.24 (11460) hydrogen bonds : bond 0.03784 / 2.57 ( 612) hydrogen bonds : angle 3.46664 / 2.52 ( 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 107 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.319 Fit side-chains REVERT: A 83 MET cc_start: 0.6113 (mpp) cc_final: 0.5496 (tpp) REVERT: A 268 GLN cc_start: 0.8725 (tp40) cc_final: 0.7121 (tp40) REVERT: A 269 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7535 (mmm160) REVERT: A 696 MET cc_start: 0.9261 (mmt) cc_final: 0.8978 (mmt) REVERT: B 83 MET cc_start: 0.6180 (mpp) cc_final: 0.5706 (tpp) REVERT: B 269 ARG cc_start: 0.7793 (mtt90) cc_final: 0.7535 (mmm-85) REVERT: B 632 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8949 (mt-10) REVERT: B 636 ASP cc_start: 0.9326 (m-30) cc_final: 0.9125 (m-30) REVERT: B 696 MET cc_start: 0.9295 (mmt) cc_final: 0.9075 (mmt) outliers start: 12 outliers final: 10 residues processed: 101 average time/residue: 0.0757 time to fit residues: 11.5245 Evaluate side-chains 99 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 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 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: 6.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.086476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.068174 restraints weight = 22819.991| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.11 r_work: 0.2879 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3094 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= 0.146 Angle : 0.526 10.262 11460 Z= 0.256 Chirality : 0.040 0.160 1294 Planarity : 0.003 0.030 1350 Dihedral : 6.922 55.245 1364 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.82 % Allowed : 9.91 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.51 (0.27), residues: 1002 helix: 2.86 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 0.29 (0.48), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.007 0.001 TYR A 255 PHE 0.011 0.001 PHE A 264 TRP 0.009 0.001 TRP A 467 HIS 0.002 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8576) covalent geometry : angle 0.52623 / 0.26 (11460) hydrogen bonds : bond 0.03937 / 2.67 ( 612) hydrogen bonds : angle 3.50194 / 2.54 ( 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 106 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6199 (mpp) cc_final: 0.5640 (tpp) REVERT: A 268 GLN cc_start: 0.8714 (tp40) cc_final: 0.7140 (tp40) REVERT: A 269 ARG cc_start: 0.7797 (mtt90) cc_final: 0.7581 (mmm160) REVERT: A 696 MET cc_start: 0.9124 (mmt) cc_final: 0.8873 (mmt) REVERT: B 83 MET cc_start: 0.6211 (mpp) cc_final: 0.5724 (tpp) REVERT: B 269 ARG cc_start: 0.7812 (mtt90) cc_final: 0.7565 (mmm-85) REVERT: B 696 MET cc_start: 0.9306 (mmt) cc_final: 0.9076 (mmt) outliers start: 16 outliers final: 16 residues processed: 99 average time/residue: 0.0748 time to fit residues: 11.2163 Evaluate side-chains 106 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 680 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 680 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: 2.9990 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.086811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.068461 restraints weight = 22863.899| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.13 r_work: 0.2882 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3161 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= 0.131 Angle : 0.515 10.446 11460 Z= 0.251 Chirality : 0.040 0.155 1294 Planarity : 0.003 0.030 1350 Dihedral : 6.842 54.676 1364 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.94 % Allowed : 9.68 % Favored : 88.38 % 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: 2.85 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 0.31 (0.48), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.009 0.001 TYR A 637 PHE 0.012 0.001 PHE A 264 TRP 0.009 0.001 TRP A 467 HIS 0.001 0.000 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8576) covalent geometry : angle 0.51466 / 0.25 (11460) hydrogen bonds : bond 0.03872 / 2.63 ( 612) hydrogen bonds : angle 3.47846 / 2.52 ( 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 111 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6151 (mpp) cc_final: 0.5365 (tpp) REVERT: A 268 GLN cc_start: 0.8706 (tp40) cc_final: 0.7128 (tp40) REVERT: A 269 ARG cc_start: 0.7774 (mtt90) cc_final: 0.7558 (mmm160) REVERT: A 696 MET cc_start: 0.9057 (mmt) cc_final: 0.8846 (tmm) REVERT: B 83 MET cc_start: 0.6238 (mpp) cc_final: 0.5745 (tpp) REVERT: B 269 ARG cc_start: 0.7788 (mtt90) cc_final: 0.7544 (mmm-85) REVERT: B 696 MET cc_start: 0.9286 (mmt) cc_final: 0.9053 (mmt) outliers start: 17 outliers final: 17 residues processed: 103 average time/residue: 0.0718 time to fit residues: 11.0932 Evaluate side-chains 106 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET 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 680 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 680 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: 2.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.086819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.068193 restraints weight = 23075.441| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.21 r_work: 0.2868 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3234 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= 0.132 Angle : 0.524 10.487 11460 Z= 0.255 Chirality : 0.040 0.150 1294 Planarity : 0.003 0.029 1350 Dihedral : 6.749 53.410 1364 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.94 % Allowed : 9.57 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.52 (0.27), residues: 1002 helix: 2.87 (0.18), residues: 768 sheet: None (None), residues: 0 loop : 0.45 (0.46), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.014 0.001 TYR A 637 PHE 0.013 0.001 PHE A 264 TRP 0.009 0.001 TRP A 467 HIS 0.001 0.000 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8576) covalent geometry : angle 0.52421 / 0.26 (11460) hydrogen bonds : bond 0.03855 / 2.63 ( 612) hydrogen bonds : angle 3.49419 / 2.54 ( 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 109 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.6146 (mpp) cc_final: 0.5300 (tpp) REVERT: A 268 GLN cc_start: 0.8699 (tp40) cc_final: 0.7907 (tp40) REVERT: A 269 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7538 (mmm-85) REVERT: A 696 MET cc_start: 0.9054 (mmt) cc_final: 0.8829 (tmm) REVERT: B 83 MET cc_start: 0.6244 (mpp) cc_final: 0.5583 (tpp) REVERT: B 269 ARG cc_start: 0.7777 (mtt90) cc_final: 0.7545 (mmm-85) REVERT: B 696 MET cc_start: 0.9220 (mmt) cc_final: 0.8918 (tmm) outliers start: 17 outliers final: 16 residues processed: 102 average time/residue: 0.0712 time to fit residues: 10.9248 Evaluate side-chains 102 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 LEU 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 486 LEU Chi-restraints excluded: chain A residue 680 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 680 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: 1.9990 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 97 optimal weight: 0.0570 chunk 21 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.087677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.068998 restraints weight = 22968.141| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.24 r_work: 0.2886 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8576 Z= 0.113 Angle : 0.515 10.015 11460 Z= 0.250 Chirality : 0.039 0.150 1294 Planarity : 0.003 0.030 1350 Dihedral : 6.513 53.779 1364 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.94 % Allowed : 9.91 % Favored : 88.15 % 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: 3.64 (0.27), residues: 1002 helix: 3.00 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.50 (0.45), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.007 0.001 TYR B 439 PHE 0.013 0.001 PHE A 264 TRP 0.010 0.001 TRP A 661 HIS 0.001 0.000 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8576) covalent geometry : angle 0.51546 / 0.25 (11460) hydrogen bonds : bond 0.03714 / 2.53 ( 612) hydrogen bonds : angle 3.49163 / 2.54 ( 1824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.77 seconds wall clock time: 31 minutes 40.46 seconds (1900.46 seconds total)