Starting phenix.real_space_refine on Sat Sep 12 07:32:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ccq_30339/09_2026/7ccq_30339.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ccq_30339/09_2026/7ccq_30339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ccq_30339/09_2026/7ccq_30339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ccq_30339/09_2026/7ccq_30339.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ccq_30339/09_2026/7ccq_30339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ccq_30339/09_2026/7ccq_30339.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 P 294 5.49 5 S 29 5.16 5 C 8443 2.51 5 N 2743 2.21 5 O 3348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14857 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "K" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2958 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 3.21, per 1000 atoms: 0.22 Number of scatterers: 14857 At special positions: 0 Unit cell: (125, 113, 139, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 294 15.00 O 3348 8.00 N 2743 7.00 C 8443 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: 1.17 Conformation dependent library (CDL) restraints added in 530.9 milliseconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 66.2% alpha, 6.0% beta 134 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.596A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.607A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.730A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.157A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.677A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.531A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.238A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.531A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 161 through 176 Processing helix chain 'K' and resid 178 through 198 removed outlier: 4.309A pdb=" N ALA K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS K 198 " --> pdb=" O LEU K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 204 removed outlier: 3.875A pdb=" N ARG K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 266 removed outlier: 3.663A pdb=" N GLN K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 289 removed outlier: 4.354A pdb=" N ASN K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 335 Processing helix chain 'K' and resid 345 through 354 Processing helix chain 'K' and resid 379 through 389 Processing helix chain 'K' and resid 405 through 424 Processing helix chain 'K' and resid 425 through 427 No H-bonds generated for 'chain 'K' and resid 425 through 427' Processing helix chain 'K' and resid 434 through 449 removed outlier: 3.911A pdb=" N VAL K 438 " --> pdb=" O SER K 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 458 removed outlier: 3.853A pdb=" N ASP K 456 " --> pdb=" O SER K 453 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ARG K 457 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LYS K 458 " --> pdb=" O TRP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 477 Processing helix chain 'K' and resid 497 through 513 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.030A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 5.959A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.264A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.859A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.737A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.991A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 206 through 208 removed outlier: 3.518A pdb=" N PHE K 230 " --> pdb=" O THR K 321 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 206 through 208 removed outlier: 3.518A pdb=" N PHE K 230 " --> pdb=" O THR K 321 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU K 311 " --> pdb=" O ILE K 297 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE K 297 " --> pdb=" O LEU K 311 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 237 through 241 Processing sheet with id=AB5, first strand: chain 'K' and resid 324 through 326 removed outlier: 3.893A pdb=" N TYR K 358 " --> pdb=" O SER K 378 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 336 hydrogen bonds 668 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2815 1.33 - 1.45: 4992 1.45 - 1.57: 7290 1.57 - 1.69: 584 1.69 - 1.81: 44 Bond restraints: 15725 Sorted by residual: bond pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " ideal model delta sigma weight residual 1.435 1.347 0.088 1.30e-02 5.92e+03 4.54e+01 bond pdb=" C3' DC J 6 " pdb=" O3' DC J 6 " ideal model delta sigma weight residual 1.435 1.350 0.085 1.30e-02 5.92e+03 4.31e+01 bond pdb=" C3' DG I 8 " pdb=" O3' DG I 8 " ideal model delta sigma weight residual 1.435 1.355 0.080 1.30e-02 5.92e+03 3.83e+01 bond pdb=" C3' DG I -8 " pdb=" C2' DG I -8 " ideal model delta sigma weight residual 1.516 1.565 -0.049 8.00e-03 1.56e+04 3.75e+01 bond pdb=" C3' DG I -4 " pdb=" O3' DG I -4 " ideal model delta sigma weight residual 1.435 1.356 0.079 1.30e-02 5.92e+03 3.65e+01 ... (remaining 15720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 20317 1.90 - 3.81: 1948 3.81 - 5.71: 169 5.71 - 7.61: 29 7.61 - 9.52: 10 Bond angle restraints: 22473 Sorted by residual: angle pdb=" O4' DG I -35 " pdb=" C1' DG I -35 " pdb=" N9 DG I -35 " ideal model delta sigma weight residual 108.00 101.73 6.27 7.00e-01 2.04e+00 8.03e+01 angle pdb=" O4' DG I -8 " pdb=" C1' DG I -8 " pdb=" N9 DG I -8 " ideal model delta sigma weight residual 108.00 102.10 5.90 7.00e-01 2.04e+00 7.11e+01 angle pdb=" O4' DA I -3 " pdb=" C1' DA I -3 " pdb=" N9 DA I -3 " ideal model delta sigma weight residual 108.00 102.60 5.40 7.00e-01 2.04e+00 5.95e+01 angle pdb=" O5' DT I 31 " pdb=" C5' DT I 31 " pdb=" C4' DT I 31 " ideal model delta sigma weight residual 109.40 103.62 5.78 8.00e-01 1.56e+00 5.22e+01 angle pdb=" O5' DG I -49 " pdb=" C5' DG I -49 " pdb=" C4' DG I -49 " ideal model delta sigma weight residual 109.40 115.12 -5.72 8.00e-01 1.56e+00 5.11e+01 ... (remaining 22468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.00: 7258 32.00 - 63.99: 1432 63.99 - 95.99: 42 95.99 - 127.98: 1 127.98 - 159.98: 2 Dihedral angle restraints: 8735 sinusoidal: 5530 harmonic: 3205 Sorted by residual: dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual -180.00 -148.37 -31.63 0 5.00e+00 4.00e-02 4.00e+01 dihedral pdb=" CA PRO K 361 " pdb=" C PRO K 361 " pdb=" N LYS K 362 " pdb=" CA LYS K 362 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ILE K 312 " pdb=" C ILE K 312 " pdb=" N SER K 313 " pdb=" CA SER K 313 " ideal model delta harmonic sigma weight residual 180.00 154.05 25.95 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 8732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1883 0.077 - 0.153: 570 0.153 - 0.230: 74 0.230 - 0.307: 5 0.307 - 0.384: 4 Chirality restraints: 2536 Sorted by residual: chirality pdb=" C1' DC I -27 " pdb=" O4' DC I -27 " pdb=" C2' DC I -27 " pdb=" N1 DC I -27 " both_signs ideal model delta sigma weight residual False 2.43 2.05 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C1' DT J 13 " pdb=" O4' DT J 13 " pdb=" C2' DT J 13 " pdb=" N1 DT J 13 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C1' DT I 31 " pdb=" O4' DT I 31 " pdb=" C2' DT I 31 " pdb=" N1 DT I 31 " both_signs ideal model delta sigma weight residual False 2.43 2.10 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 2533 not shown) Planarity restraints: 1830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 31 " 0.052 2.00e-02 2.50e+03 5.17e-02 6.69e+01 pdb=" N1 DT I 31 " -0.131 2.00e-02 2.50e+03 pdb=" C2 DT I 31 " 0.079 2.00e-02 2.50e+03 pdb=" O2 DT I 31 " -0.012 2.00e-02 2.50e+03 pdb=" N3 DT I 31 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DT I 31 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT I 31 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DT I 31 " 0.007 2.00e-02 2.50e+03 pdb=" C7 DT I 31 " 0.017 2.00e-02 2.50e+03 pdb=" C6 DT I 31 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -2 " -0.048 2.00e-02 2.50e+03 4.15e-02 3.88e+01 pdb=" N1 DC I -2 " 0.102 2.00e-02 2.50e+03 pdb=" C2 DC I -2 " -0.050 2.00e-02 2.50e+03 pdb=" O2 DC I -2 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DC I -2 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DC I -2 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC I -2 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC I -2 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DC I -2 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 44 " -0.026 2.00e-02 2.50e+03 3.57e-02 3.18e+01 pdb=" N1 DT I 44 " 0.087 2.00e-02 2.50e+03 pdb=" C2 DT I 44 " -0.063 2.00e-02 2.50e+03 pdb=" O2 DT I 44 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DT I 44 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DT I 44 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT I 44 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DT I 44 " -0.006 2.00e-02 2.50e+03 pdb=" C7 DT I 44 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 44 " -0.013 2.00e-02 2.50e+03 ... (remaining 1827 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2684 2.77 - 3.30: 12926 3.30 - 3.83: 29462 3.83 - 4.37: 33969 4.37 - 4.90: 49238 Nonbonded interactions: 128279 Sorted by model distance: nonbonded pdb=" N2 DG I 21 " pdb=" O2 DC J -21 " model vdw 2.235 2.496 nonbonded pdb=" OH TYR H 40 " pdb=" OP1 DG I 48 " model vdw 2.291 3.040 nonbonded pdb=" NH2 ARG C 32 " pdb=" OE1 GLU D 35 " model vdw 2.321 3.120 nonbonded pdb=" OH TYR K 249 " pdb=" OG SER K 333 " model vdw 2.331 3.040 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.331 3.040 ... (remaining 128274 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 40 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 16 through 116) selection = (chain 'G' and resid 16 through 116) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 32 through 123) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.440 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.080 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.011 0.093 15725 Z= 0.848 Angle : 1.115 9.515 22473 Z= 0.862 Chirality : 0.072 0.384 2536 Planarity : 0.009 0.063 1830 Dihedral : 24.879 159.981 6661 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.89 (0.20), residues: 1081 helix: -1.61 (0.15), residues: 699 sheet: -2.19 (0.58), residues: 46 loop : -2.16 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 45 TYR 0.050 0.004 TYR F 98 PHE 0.028 0.004 PHE C 25 TRP 0.013 0.003 TRP K 375 HIS 0.010 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01080 / 0.85 (15725) covalent geometry : angle 1.11451 / 0.86 (22473) hydrogen bonds : bond 0.13252 / 8.57 ( 884) hydrogen bonds : angle 5.22451 / 3.73 ( 2285) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8909 (mt) cc_final: 0.8282 (mt) REVERT: A 52 ARG cc_start: 0.8806 (mtt90) cc_final: 0.8191 (mtm-85) REVERT: A 54 TYR cc_start: 0.8594 (m-80) cc_final: 0.8289 (m-80) REVERT: A 60 LEU cc_start: 0.8571 (mt) cc_final: 0.8320 (mt) REVERT: A 76 GLN cc_start: 0.8404 (tp40) cc_final: 0.8085 (tm-30) REVERT: A 79 LYS cc_start: 0.8130 (tttp) cc_final: 0.7800 (tttm) REVERT: A 93 GLN cc_start: 0.8955 (tt0) cc_final: 0.8104 (tt0) REVERT: C 18 SER cc_start: 0.9263 (m) cc_final: 0.8930 (p) REVERT: C 57 TYR cc_start: 0.8928 (t80) cc_final: 0.8187 (t80) REVERT: C 64 GLU cc_start: 0.8292 (tt0) cc_final: 0.8020 (tt0) REVERT: C 75 LYS cc_start: 0.9270 (mmtp) cc_final: 0.8824 (mmmt) REVERT: C 94 ASN cc_start: 0.8956 (t0) cc_final: 0.8433 (t0) REVERT: C 95 LYS cc_start: 0.9027 (tppt) cc_final: 0.8672 (tptm) REVERT: D 34 LYS cc_start: 0.8855 (mppt) cc_final: 0.8231 (mmmt) REVERT: D 45 LEU cc_start: 0.9503 (tp) cc_final: 0.9291 (tp) REVERT: D 46 LYS cc_start: 0.8999 (mmpt) cc_final: 0.8702 (mmtt) REVERT: D 71 GLU cc_start: 0.8269 (tp30) cc_final: 0.7850 (tp30) REVERT: D 86 ARG cc_start: 0.8149 (mmt90) cc_final: 0.7937 (mtt-85) REVERT: E 70 LEU cc_start: 0.9373 (tp) cc_final: 0.9125 (tt) REVERT: E 94 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8080 (mm-30) REVERT: F 34 ILE cc_start: 0.9611 (mt) cc_final: 0.9345 (mt) REVERT: F 46 ILE cc_start: 0.9502 (mt) cc_final: 0.9293 (mm) REVERT: F 59 LYS cc_start: 0.8730 (tttm) cc_final: 0.8441 (tttp) REVERT: F 88 TYR cc_start: 0.8578 (m-80) cc_final: 0.8131 (m-80) REVERT: G 38 ASN cc_start: 0.8359 (m110) cc_final: 0.7654 (m-40) REVERT: G 39 TYR cc_start: 0.8766 (m-80) cc_final: 0.7637 (m-80) REVERT: G 75 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8644 (mttm) REVERT: G 95 LYS cc_start: 0.8998 (tttt) cc_final: 0.8625 (mtpt) REVERT: H 34 LYS cc_start: 0.8443 (mttt) cc_final: 0.7974 (mmtm) REVERT: K 208 LEU cc_start: 0.8089 (tp) cc_final: 0.6984 (pt) REVERT: K 256 ASN cc_start: 0.7519 (t0) cc_final: 0.7296 (t0) REVERT: K 351 GLN cc_start: 0.8898 (tt0) cc_final: 0.8675 (tm-30) REVERT: K 432 LYS cc_start: 0.4770 (mmtm) cc_final: 0.4432 (tptt) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1780 time to fit residues: 80.2724 Evaluate side-chains 208 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN A 108 ASN C 24 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 84 ASN E 125 GLN F 75 HIS G 38 ASN ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 260 ASN K 449 ASN K 466 ASN K 494 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.098080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.065174 restraints weight = 48256.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.066668 restraints weight = 25845.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.067523 restraints weight = 18868.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.068014 restraints weight = 16326.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.068200 restraints weight = 15251.425| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 15725 Z= 0.262 Angle : 0.824 8.582 22473 Z= 0.454 Chirality : 0.052 0.255 2536 Planarity : 0.006 0.052 1830 Dihedral : 30.060 164.350 4426 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.11 % Allowed : 9.07 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.23), residues: 1081 helix: 0.03 (0.17), residues: 714 sheet: -1.36 (0.66), residues: 46 loop : -1.77 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 40 TYR 0.024 0.003 TYR K 242 PHE 0.016 0.002 PHE K 357 TRP 0.006 0.001 TRP K 375 HIS 0.015 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.26 (15725) covalent geometry : angle 0.82384 / 0.45 (22473) hydrogen bonds : bond 0.06310 / 4.12 ( 884) hydrogen bonds : angle 4.10130 / 2.92 ( 2285) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8683 (mt) cc_final: 0.7984 (mt) REVERT: A 52 ARG cc_start: 0.8934 (mtt90) cc_final: 0.8264 (mtm-85) REVERT: A 87 SER cc_start: 0.9248 (p) cc_final: 0.8947 (t) REVERT: B 84 MET cc_start: 0.8770 (tpt) cc_final: 0.8289 (tpp) REVERT: C 18 SER cc_start: 0.9330 (m) cc_final: 0.8977 (p) REVERT: C 74 LYS cc_start: 0.9191 (mtpt) cc_final: 0.8979 (mttt) REVERT: C 75 LYS cc_start: 0.9303 (mmtp) cc_final: 0.8879 (mmmt) REVERT: C 90 ASP cc_start: 0.8525 (t0) cc_final: 0.8289 (t0) REVERT: C 94 ASN cc_start: 0.8987 (t0) cc_final: 0.8510 (t0) REVERT: D 34 LYS cc_start: 0.8652 (mppt) cc_final: 0.7995 (mmmt) REVERT: D 71 GLU cc_start: 0.8418 (tp30) cc_final: 0.8017 (tp30) REVERT: D 86 ARG cc_start: 0.8140 (mmt90) cc_final: 0.7905 (mtt-85) REVERT: D 93 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8282 (mm-30) REVERT: D 101 LEU cc_start: 0.9265 (mt) cc_final: 0.9049 (mt) REVERT: E 76 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8243 (tm-30) REVERT: E 93 GLN cc_start: 0.8533 (tt0) cc_final: 0.8328 (tt0) REVERT: E 94 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8043 (mm-30) REVERT: E 106 ASP cc_start: 0.7957 (m-30) cc_final: 0.7732 (m-30) REVERT: E 107 THR cc_start: 0.9461 (m) cc_final: 0.9062 (t) REVERT: F 59 LYS cc_start: 0.8766 (tttm) cc_final: 0.8457 (tttp) REVERT: F 84 MET cc_start: 0.8390 (mmt) cc_final: 0.8021 (mmt) REVERT: F 88 TYR cc_start: 0.8626 (m-80) cc_final: 0.7659 (m-80) REVERT: G 38 ASN cc_start: 0.8267 (m-40) cc_final: 0.7660 (m-40) REVERT: G 39 TYR cc_start: 0.8640 (m-80) cc_final: 0.7680 (m-80) REVERT: G 75 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8682 (mttm) REVERT: G 95 LYS cc_start: 0.8970 (tttt) cc_final: 0.8594 (mtpt) REVERT: H 34 LYS cc_start: 0.8415 (mttt) cc_final: 0.8039 (mmtm) REVERT: H 47 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8329 (tm-30) REVERT: H 83 TYR cc_start: 0.8430 (m-10) cc_final: 0.8023 (m-10) REVERT: K 208 LEU cc_start: 0.8158 (tp) cc_final: 0.7002 (pt) REVERT: K 256 ASN cc_start: 0.7732 (t0) cc_final: 0.7387 (t0) outliers start: 20 outliers final: 12 residues processed: 245 average time/residue: 0.1242 time to fit residues: 43.9405 Evaluate side-chains 227 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 322 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 2 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN B 75 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS E 68 GLN G 38 ASN ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.098366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.065639 restraints weight = 48350.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.067152 restraints weight = 25901.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067943 restraints weight = 18812.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.068496 restraints weight = 16301.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.068721 restraints weight = 15164.444| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15725 Z= 0.204 Angle : 0.710 7.797 22473 Z= 0.401 Chirality : 0.047 0.270 2536 Planarity : 0.005 0.046 1830 Dihedral : 30.161 163.038 4426 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.27 % Allowed : 10.65 % Favored : 86.08 % 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: 0.07 (0.24), residues: 1081 helix: 0.88 (0.18), residues: 709 sheet: -1.12 (0.70), residues: 46 loop : -1.57 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 79 TYR 0.044 0.003 TYR D 83 PHE 0.014 0.002 PHE A 67 TRP 0.014 0.001 TRP K 375 HIS 0.014 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (15725) covalent geometry : angle 0.70970 / 0.40 (22473) hydrogen bonds : bond 0.05557 / 3.66 ( 884) hydrogen bonds : angle 3.76649 / 2.68 ( 2285) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8589 (mt) cc_final: 0.8152 (mt) REVERT: A 52 ARG cc_start: 0.8926 (mtt90) cc_final: 0.8230 (mtm-85) REVERT: A 87 SER cc_start: 0.9172 (p) cc_final: 0.8954 (t) REVERT: A 115 LYS cc_start: 0.9260 (mtmm) cc_final: 0.9046 (mtmt) REVERT: B 44 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8769 (mtpt) REVERT: B 80 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8618 (p) REVERT: B 84 MET cc_start: 0.8672 (tpt) cc_final: 0.8257 (tpp) REVERT: C 18 SER cc_start: 0.9328 (m) cc_final: 0.9003 (p) REVERT: C 75 LYS cc_start: 0.9235 (mmtp) cc_final: 0.8803 (mmmt) REVERT: C 90 ASP cc_start: 0.8491 (t0) cc_final: 0.8144 (t0) REVERT: C 94 ASN cc_start: 0.8971 (t0) cc_final: 0.8515 (t0) REVERT: D 34 LYS cc_start: 0.8611 (mppt) cc_final: 0.8003 (mmmt) REVERT: D 71 GLU cc_start: 0.8473 (tp30) cc_final: 0.8059 (tp30) REVERT: D 83 TYR cc_start: 0.7854 (m-10) cc_final: 0.7595 (m-80) REVERT: E 76 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8138 (tm-30) REVERT: E 90 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8112 (mtm) REVERT: E 93 GLN cc_start: 0.8607 (tt0) cc_final: 0.8310 (tt0) REVERT: E 106 ASP cc_start: 0.8019 (m-30) cc_final: 0.7724 (m-30) REVERT: E 107 THR cc_start: 0.9477 (m) cc_final: 0.9030 (t) REVERT: F 46 ILE cc_start: 0.9576 (mt) cc_final: 0.9340 (mm) REVERT: F 59 LYS cc_start: 0.8747 (tttm) cc_final: 0.8454 (tttp) REVERT: F 84 MET cc_start: 0.8350 (mmt) cc_final: 0.8050 (mmt) REVERT: F 88 TYR cc_start: 0.8583 (m-10) cc_final: 0.7484 (m-80) REVERT: G 39 TYR cc_start: 0.8739 (m-80) cc_final: 0.7993 (m-80) REVERT: G 75 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8694 (mttm) REVERT: G 90 ASP cc_start: 0.8802 (t0) cc_final: 0.8371 (t0) REVERT: G 91 GLU cc_start: 0.7340 (pm20) cc_final: 0.7020 (pm20) REVERT: G 95 LYS cc_start: 0.8986 (tttt) cc_final: 0.8555 (mtpt) REVERT: H 34 LYS cc_start: 0.8322 (mttt) cc_final: 0.7992 (mtmm) REVERT: H 47 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8371 (tm-30) REVERT: H 83 TYR cc_start: 0.8485 (m-10) cc_final: 0.7993 (m-10) REVERT: H 86 ARG cc_start: 0.8469 (mpt-90) cc_final: 0.8080 (mtt-85) REVERT: K 208 LEU cc_start: 0.8023 (tp) cc_final: 0.6767 (pt) REVERT: K 229 MET cc_start: 0.7944 (mmp) cc_final: 0.7627 (mmp) REVERT: K 236 ARG cc_start: 0.7721 (ptt90) cc_final: 0.7471 (ptt90) outliers start: 31 outliers final: 21 residues processed: 240 average time/residue: 0.1357 time to fit residues: 46.9831 Evaluate side-chains 231 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 410 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 91 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS C 110 ASN ** H 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.095491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.062487 restraints weight = 49109.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.063940 restraints weight = 26774.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.064800 restraints weight = 19605.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.065229 restraints weight = 16889.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.065402 restraints weight = 15768.192| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 15725 Z= 0.335 Angle : 0.822 9.982 22473 Z= 0.443 Chirality : 0.050 0.278 2536 Planarity : 0.006 0.045 1830 Dihedral : 30.452 163.561 4426 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.38 % Allowed : 12.76 % Favored : 83.86 % 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: 0.15 (0.24), residues: 1081 helix: 0.94 (0.18), residues: 715 sheet: -0.52 (0.83), residues: 39 loop : -1.64 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 86 TYR 0.032 0.003 TYR D 83 PHE 0.018 0.002 PHE K 471 TRP 0.006 0.002 TRP K 375 HIS 0.008 0.002 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.34 (15725) covalent geometry : angle 0.82196 / 0.44 (22473) hydrogen bonds : bond 0.06468 / 4.27 ( 884) hydrogen bonds : angle 3.98646 / 2.87 ( 2285) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8692 (mt) cc_final: 0.8091 (mt) REVERT: A 52 ARG cc_start: 0.9008 (mtt90) cc_final: 0.8245 (mtm-85) REVERT: A 59 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8406 (pm20) REVERT: B 44 LYS cc_start: 0.9200 (mtpt) cc_final: 0.8876 (mtpt) REVERT: B 84 MET cc_start: 0.8892 (tpt) cc_final: 0.8441 (tpp) REVERT: C 18 SER cc_start: 0.9350 (m) cc_final: 0.9085 (p) REVERT: C 57 TYR cc_start: 0.9204 (t80) cc_final: 0.8926 (t80) REVERT: C 75 LYS cc_start: 0.9335 (mmtp) cc_final: 0.8910 (mmmt) REVERT: D 34 LYS cc_start: 0.8786 (mppt) cc_final: 0.8088 (mmmt) REVERT: D 71 GLU cc_start: 0.8485 (tp30) cc_final: 0.8070 (tp30) REVERT: E 58 THR cc_start: 0.9538 (p) cc_final: 0.9216 (t) REVERT: E 107 THR cc_start: 0.9477 (m) cc_final: 0.9098 (t) REVERT: E 120 MET cc_start: 0.8925 (mtp) cc_final: 0.8412 (mtp) REVERT: F 59 LYS cc_start: 0.8843 (tttm) cc_final: 0.8581 (tttp) REVERT: F 88 TYR cc_start: 0.8631 (m-10) cc_final: 0.7646 (m-80) REVERT: G 39 TYR cc_start: 0.8919 (m-80) cc_final: 0.8078 (m-80) REVERT: G 57 TYR cc_start: 0.8810 (t80) cc_final: 0.8435 (t80) REVERT: G 75 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8734 (mttm) REVERT: G 95 LYS cc_start: 0.9028 (tttt) cc_final: 0.8608 (mtpt) REVERT: H 34 LYS cc_start: 0.8359 (mttt) cc_final: 0.7979 (mppt) REVERT: H 47 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8391 (tm-30) REVERT: H 71 GLU cc_start: 0.8900 (tp30) cc_final: 0.8437 (tp30) REVERT: H 83 TYR cc_start: 0.8555 (m-10) cc_final: 0.7640 (m-10) REVERT: H 86 ARG cc_start: 0.8540 (mpt-90) cc_final: 0.8041 (mtt-85) REVERT: K 208 LEU cc_start: 0.8018 (tp) cc_final: 0.6755 (pt) outliers start: 32 outliers final: 20 residues processed: 226 average time/residue: 0.1302 time to fit residues: 42.8873 Evaluate side-chains 218 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 410 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 106 optimal weight: 40.0000 chunk 19 optimal weight: 0.9990 chunk 107 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 71 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.097527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.064277 restraints weight = 48909.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.065837 restraints weight = 25471.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.066790 restraints weight = 18246.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.067260 restraints weight = 15556.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067412 restraints weight = 14471.357| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15725 Z= 0.172 Angle : 0.676 9.898 22473 Z= 0.380 Chirality : 0.045 0.279 2536 Planarity : 0.004 0.039 1830 Dihedral : 30.305 166.029 4426 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.48 % Allowed : 14.14 % Favored : 82.38 % 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: 0.74 (0.25), residues: 1081 helix: 1.42 (0.18), residues: 708 sheet: -0.42 (0.83), residues: 39 loop : -1.41 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 79 TYR 0.055 0.002 TYR D 83 PHE 0.016 0.002 PHE F 100 TRP 0.006 0.001 TRP K 375 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (15725) covalent geometry : angle 0.67628 / 0.38 (22473) hydrogen bonds : bond 0.04861 / 3.16 ( 884) hydrogen bonds : angle 3.59996 / 2.55 ( 2285) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8628 (mt) cc_final: 0.8230 (mt) REVERT: A 52 ARG cc_start: 0.9004 (mtt90) cc_final: 0.8246 (mtm-85) REVERT: A 59 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8381 (pm20) REVERT: B 44 LYS cc_start: 0.9139 (mtpt) cc_final: 0.8778 (mtpt) REVERT: B 80 THR cc_start: 0.9121 (m) cc_final: 0.8576 (p) REVERT: B 84 MET cc_start: 0.8766 (tpt) cc_final: 0.8433 (tpp) REVERT: C 18 SER cc_start: 0.9315 (m) cc_final: 0.9004 (p) REVERT: C 75 LYS cc_start: 0.9296 (mmtp) cc_final: 0.8837 (mmmt) REVERT: C 94 ASN cc_start: 0.9014 (t0) cc_final: 0.8473 (t0) REVERT: C 100 VAL cc_start: 0.9543 (OUTLIER) cc_final: 0.9238 (p) REVERT: D 34 LYS cc_start: 0.8749 (mppt) cc_final: 0.8050 (mmmt) REVERT: D 71 GLU cc_start: 0.8457 (tp30) cc_final: 0.8041 (tp30) REVERT: D 79 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7627 (mtm180) REVERT: D 105 GLU cc_start: 0.7443 (tp30) cc_final: 0.7199 (tp30) REVERT: E 58 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.9149 (t) REVERT: E 93 GLN cc_start: 0.8587 (tt0) cc_final: 0.8268 (tt0) REVERT: E 107 THR cc_start: 0.9429 (m) cc_final: 0.9001 (t) REVERT: F 59 LYS cc_start: 0.8750 (tttm) cc_final: 0.8436 (tttp) REVERT: F 88 TYR cc_start: 0.8296 (m-10) cc_final: 0.7577 (m-80) REVERT: F 98 TYR cc_start: 0.9217 (m-10) cc_final: 0.9004 (m-10) REVERT: G 39 TYR cc_start: 0.8751 (m-80) cc_final: 0.8155 (m-80) REVERT: G 75 LYS cc_start: 0.9020 (mmtm) cc_final: 0.8691 (mttm) REVERT: G 90 ASP cc_start: 0.8780 (t0) cc_final: 0.8505 (t0) REVERT: G 91 GLU cc_start: 0.7306 (pm20) cc_final: 0.7008 (pm20) REVERT: G 95 LYS cc_start: 0.8950 (tttt) cc_final: 0.8512 (mtpt) REVERT: H 34 LYS cc_start: 0.8330 (mttt) cc_final: 0.7935 (mppt) REVERT: H 47 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8316 (tm-30) REVERT: H 83 TYR cc_start: 0.8483 (m-10) cc_final: 0.7722 (m-10) REVERT: H 86 ARG cc_start: 0.8465 (mpt-90) cc_final: 0.8006 (mtt-85) REVERT: K 208 LEU cc_start: 0.7995 (tp) cc_final: 0.6747 (pt) REVERT: K 236 ARG cc_start: 0.8124 (ptt90) cc_final: 0.7880 (ptt90) outliers start: 33 outliers final: 18 residues processed: 244 average time/residue: 0.1215 time to fit residues: 43.2322 Evaluate side-chains 233 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 410 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 57 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 99 optimal weight: 0.8980 chunk 121 optimal weight: 40.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.098616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.065386 restraints weight = 48445.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.066956 restraints weight = 25455.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.067945 restraints weight = 18273.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.068413 restraints weight = 15596.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068679 restraints weight = 14520.220| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15725 Z= 0.145 Angle : 0.655 11.787 22473 Z= 0.367 Chirality : 0.044 0.279 2536 Planarity : 0.004 0.041 1830 Dihedral : 30.087 167.175 4426 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.27 % Allowed : 16.03 % Favored : 80.70 % 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: 1.05 (0.25), residues: 1081 helix: 1.70 (0.18), residues: 708 sheet: -0.33 (1.01), residues: 29 loop : -1.37 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 35 TYR 0.061 0.003 TYR D 83 PHE 0.012 0.001 PHE A 67 TRP 0.008 0.001 TRP K 375 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (15725) covalent geometry : angle 0.65546 / 0.37 (22473) hydrogen bonds : bond 0.04555 / 2.95 ( 884) hydrogen bonds : angle 3.45291 / 2.44 ( 2285) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8525 (mt) cc_final: 0.8141 (mt) REVERT: A 52 ARG cc_start: 0.8970 (mtt90) cc_final: 0.8171 (mtm-85) REVERT: A 59 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: B 44 LYS cc_start: 0.9114 (mtpt) cc_final: 0.8744 (mtpt) REVERT: B 84 MET cc_start: 0.8587 (tpt) cc_final: 0.8382 (tpp) REVERT: C 18 SER cc_start: 0.9295 (m) cc_final: 0.9042 (p) REVERT: C 75 LYS cc_start: 0.9260 (mmtp) cc_final: 0.8832 (mmmt) REVERT: C 94 ASN cc_start: 0.8902 (t0) cc_final: 0.8455 (t0) REVERT: C 100 VAL cc_start: 0.9589 (OUTLIER) cc_final: 0.9262 (p) REVERT: D 34 LYS cc_start: 0.8581 (mppt) cc_final: 0.7981 (mmmt) REVERT: D 71 GLU cc_start: 0.8433 (tp30) cc_final: 0.8042 (tp30) REVERT: D 79 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7636 (mtm180) REVERT: E 107 THR cc_start: 0.9424 (m) cc_final: 0.8913 (t) REVERT: E 108 ASN cc_start: 0.8742 (t0) cc_final: 0.8421 (t0) REVERT: F 59 LYS cc_start: 0.8760 (tttm) cc_final: 0.8447 (tttp) REVERT: F 88 TYR cc_start: 0.8636 (m-10) cc_final: 0.7683 (m-80) REVERT: G 39 TYR cc_start: 0.8697 (m-80) cc_final: 0.8335 (m-80) REVERT: G 57 TYR cc_start: 0.8644 (t80) cc_final: 0.8139 (t80) REVERT: G 75 LYS cc_start: 0.8998 (mmtm) cc_final: 0.8704 (mttm) REVERT: G 90 ASP cc_start: 0.8803 (t0) cc_final: 0.8385 (t0) REVERT: G 91 GLU cc_start: 0.7366 (pm20) cc_final: 0.7145 (pm20) REVERT: G 95 LYS cc_start: 0.8917 (tttt) cc_final: 0.8420 (mtpt) REVERT: H 34 LYS cc_start: 0.8260 (mttt) cc_final: 0.7856 (mppt) REVERT: H 47 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8261 (tm-30) REVERT: H 83 TYR cc_start: 0.8445 (m-10) cc_final: 0.7863 (m-10) REVERT: H 86 ARG cc_start: 0.8441 (mpt-90) cc_final: 0.8052 (mtt-85) REVERT: K 208 LEU cc_start: 0.7985 (tp) cc_final: 0.6768 (pt) outliers start: 31 outliers final: 19 residues processed: 242 average time/residue: 0.1268 time to fit residues: 44.9374 Evaluate side-chains 233 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 298 MET Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 374 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 119 optimal weight: 40.0000 chunk 61 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 20 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.097355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.064154 restraints weight = 48933.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.065667 restraints weight = 26019.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.066631 restraints weight = 18816.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.067068 restraints weight = 16068.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.067151 restraints weight = 14997.047| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15725 Z= 0.209 Angle : 0.685 11.283 22473 Z= 0.379 Chirality : 0.044 0.276 2536 Planarity : 0.004 0.044 1830 Dihedral : 30.135 167.002 4426 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.16 % Allowed : 17.19 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.25), residues: 1081 helix: 1.68 (0.18), residues: 708 sheet: -0.41 (0.85), residues: 39 loop : -1.36 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 35 TYR 0.056 0.002 TYR D 83 PHE 0.013 0.002 PHE E 67 TRP 0.007 0.001 TRP K 375 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.21 (15725) covalent geometry : angle 0.68488 / 0.38 (22473) hydrogen bonds : bond 0.04881 / 3.19 ( 884) hydrogen bonds : angle 3.54691 / 2.52 ( 2285) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8510 (mt) cc_final: 0.7958 (mt) REVERT: A 52 ARG cc_start: 0.8987 (mtt90) cc_final: 0.8188 (mtm-85) REVERT: A 59 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8325 (pm20) REVERT: B 44 LYS cc_start: 0.9159 (mtpt) cc_final: 0.8768 (mtpt) REVERT: C 18 SER cc_start: 0.9296 (m) cc_final: 0.9013 (p) REVERT: C 75 LYS cc_start: 0.9326 (mmtp) cc_final: 0.8899 (mmmt) REVERT: C 92 GLU cc_start: 0.8062 (tt0) cc_final: 0.7857 (tt0) REVERT: C 94 ASN cc_start: 0.8990 (t0) cc_final: 0.8503 (t0) REVERT: C 100 VAL cc_start: 0.9585 (t) cc_final: 0.9318 (p) REVERT: D 34 LYS cc_start: 0.8586 (mppt) cc_final: 0.7951 (mmmt) REVERT: D 71 GLU cc_start: 0.8493 (tp30) cc_final: 0.8049 (tp30) REVERT: D 79 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7722 (mtm180) REVERT: E 93 GLN cc_start: 0.8628 (tt0) cc_final: 0.8241 (tt0) REVERT: E 107 THR cc_start: 0.9447 (m) cc_final: 0.8956 (t) REVERT: F 59 LYS cc_start: 0.8791 (tttm) cc_final: 0.8461 (tttp) REVERT: F 88 TYR cc_start: 0.8396 (m-10) cc_final: 0.7744 (m-80) REVERT: G 39 TYR cc_start: 0.8796 (m-80) cc_final: 0.8392 (m-80) REVERT: G 75 LYS cc_start: 0.9028 (mmtm) cc_final: 0.8722 (mttm) REVERT: G 95 LYS cc_start: 0.8938 (tttt) cc_final: 0.8463 (mtpt) REVERT: H 34 LYS cc_start: 0.8280 (mttt) cc_final: 0.7872 (mppt) REVERT: H 47 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8306 (tm-30) REVERT: H 71 GLU cc_start: 0.8906 (tp30) cc_final: 0.8577 (tp30) REVERT: H 83 TYR cc_start: 0.8545 (m-10) cc_final: 0.7888 (m-10) REVERT: H 86 ARG cc_start: 0.8503 (mpt-90) cc_final: 0.8124 (mtt-85) REVERT: K 208 LEU cc_start: 0.8046 (tp) cc_final: 0.6837 (pt) outliers start: 30 outliers final: 22 residues processed: 227 average time/residue: 0.1190 time to fit residues: 40.0553 Evaluate side-chains 230 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 298 MET Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 410 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 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 = 0.3779 r_free = 0.3779 target = 0.097810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.064594 restraints weight = 48941.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.066119 restraints weight = 25983.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.067071 restraints weight = 18787.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067538 restraints weight = 16047.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.067748 restraints weight = 14931.223| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15725 Z= 0.181 Angle : 0.666 12.188 22473 Z= 0.371 Chirality : 0.044 0.276 2536 Planarity : 0.004 0.044 1830 Dihedral : 30.114 168.439 4426 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.43 % Allowed : 18.46 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.25), residues: 1081 helix: 1.74 (0.18), residues: 701 sheet: -0.39 (0.86), residues: 39 loop : -1.24 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 35 TYR 0.039 0.002 TYR D 83 PHE 0.012 0.001 PHE E 67 TRP 0.006 0.001 TRP K 375 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (15725) covalent geometry : angle 0.66594 / 0.37 (22473) hydrogen bonds : bond 0.04689 / 3.06 ( 884) hydrogen bonds : angle 3.49444 / 2.47 ( 2285) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8527 (mt) cc_final: 0.7968 (mt) REVERT: A 52 ARG cc_start: 0.8982 (mtt90) cc_final: 0.8167 (mtm-85) REVERT: A 59 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8283 (pm20) REVERT: B 44 LYS cc_start: 0.9152 (mtpt) cc_final: 0.8752 (mtpt) REVERT: C 18 SER cc_start: 0.9321 (m) cc_final: 0.9071 (p) REVERT: C 75 LYS cc_start: 0.9299 (mmtp) cc_final: 0.8896 (mmmt) REVERT: C 94 ASN cc_start: 0.8994 (t0) cc_final: 0.8523 (t0) REVERT: C 100 VAL cc_start: 0.9608 (t) cc_final: 0.9257 (p) REVERT: D 34 LYS cc_start: 0.8591 (mppt) cc_final: 0.7941 (mmmt) REVERT: D 71 GLU cc_start: 0.8468 (tp30) cc_final: 0.8067 (tp30) REVERT: D 79 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7786 (mtm180) REVERT: E 93 GLN cc_start: 0.8596 (tt0) cc_final: 0.8317 (tt0) REVERT: E 107 THR cc_start: 0.9447 (m) cc_final: 0.8948 (t) REVERT: F 59 LYS cc_start: 0.8772 (tttm) cc_final: 0.8434 (tttp) REVERT: F 88 TYR cc_start: 0.8648 (m-10) cc_final: 0.7785 (m-80) REVERT: G 39 TYR cc_start: 0.8767 (m-80) cc_final: 0.8406 (m-80) REVERT: G 75 LYS cc_start: 0.9038 (mmtm) cc_final: 0.8722 (mttm) REVERT: G 90 ASP cc_start: 0.8702 (t0) cc_final: 0.8418 (t0) REVERT: G 95 LYS cc_start: 0.8923 (tttt) cc_final: 0.8467 (mtpt) REVERT: H 34 LYS cc_start: 0.8263 (mttt) cc_final: 0.7841 (mppt) REVERT: H 47 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8330 (tm-30) REVERT: H 71 GLU cc_start: 0.8895 (tp30) cc_final: 0.8666 (tp30) REVERT: H 83 TYR cc_start: 0.8472 (m-10) cc_final: 0.7838 (m-10) REVERT: H 86 ARG cc_start: 0.8483 (mpt-90) cc_final: 0.8114 (mtt-85) REVERT: K 208 LEU cc_start: 0.8050 (tp) cc_final: 0.6838 (pt) outliers start: 23 outliers final: 21 residues processed: 227 average time/residue: 0.1294 time to fit residues: 43.0586 Evaluate side-chains 226 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 298 MET Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 410 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 109 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 79 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 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 = 0.3799 r_free = 0.3799 target = 0.098858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.065735 restraints weight = 48896.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.067316 restraints weight = 25683.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.068267 restraints weight = 18490.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068783 restraints weight = 15717.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.069016 restraints weight = 14584.351| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15725 Z= 0.145 Angle : 0.636 10.339 22473 Z= 0.359 Chirality : 0.043 0.277 2536 Planarity : 0.004 0.040 1830 Dihedral : 29.975 170.007 4426 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.53 % Allowed : 18.67 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.25), residues: 1081 helix: 1.80 (0.19), residues: 706 sheet: -0.41 (0.85), residues: 39 loop : -1.18 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 35 TYR 0.027 0.002 TYR G 57 PHE 0.013 0.001 PHE E 67 TRP 0.007 0.001 TRP K 375 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (15725) covalent geometry : angle 0.63592 / 0.36 (22473) hydrogen bonds : bond 0.04404 / 2.87 ( 884) hydrogen bonds : angle 3.41418 / 2.40 ( 2285) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8496 (mt) cc_final: 0.7891 (mt) REVERT: A 52 ARG cc_start: 0.9011 (mtt90) cc_final: 0.8144 (mtm-85) REVERT: A 59 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: B 35 ARG cc_start: 0.9139 (ttm-80) cc_final: 0.8882 (mtp-110) REVERT: B 44 LYS cc_start: 0.9164 (mtpt) cc_final: 0.8753 (mtpt) REVERT: C 18 SER cc_start: 0.9295 (m) cc_final: 0.9028 (p) REVERT: C 75 LYS cc_start: 0.9286 (mmtp) cc_final: 0.8893 (mmmt) REVERT: C 94 ASN cc_start: 0.8962 (t0) cc_final: 0.8531 (t0) REVERT: D 34 LYS cc_start: 0.8478 (mppt) cc_final: 0.7873 (mmmt) REVERT: D 71 GLU cc_start: 0.8445 (tp30) cc_final: 0.8080 (tp30) REVERT: D 79 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7540 (mtm180) REVERT: E 93 GLN cc_start: 0.8531 (tt0) cc_final: 0.8245 (tt0) REVERT: E 125 GLN cc_start: 0.8924 (mt0) cc_final: 0.8683 (mt0) REVERT: F 59 LYS cc_start: 0.8751 (tttm) cc_final: 0.8391 (tttp) REVERT: F 88 TYR cc_start: 0.8614 (m-10) cc_final: 0.7858 (m-10) REVERT: G 39 TYR cc_start: 0.8710 (m-80) cc_final: 0.8438 (m-80) REVERT: G 75 LYS cc_start: 0.9024 (mmtm) cc_final: 0.8730 (mttm) REVERT: G 90 ASP cc_start: 0.8729 (t0) cc_final: 0.8466 (t0) REVERT: G 91 GLU cc_start: 0.7342 (pm20) cc_final: 0.7101 (pm20) REVERT: G 95 LYS cc_start: 0.8899 (tttt) cc_final: 0.8413 (mtpt) REVERT: H 34 LYS cc_start: 0.8249 (mttt) cc_final: 0.7832 (mppt) REVERT: H 47 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8322 (tm-30) REVERT: H 71 GLU cc_start: 0.8874 (tp30) cc_final: 0.8662 (tp30) REVERT: H 83 TYR cc_start: 0.8470 (m-10) cc_final: 0.8201 (m-10) REVERT: H 86 ARG cc_start: 0.8448 (mpt-90) cc_final: 0.8088 (mtt-85) REVERT: K 208 LEU cc_start: 0.8007 (tp) cc_final: 0.6811 (pt) outliers start: 24 outliers final: 16 residues processed: 235 average time/residue: 0.1261 time to fit residues: 43.2724 Evaluate side-chains 225 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 298 MET Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 374 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 121 optimal weight: 40.0000 chunk 33 optimal weight: 2.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS K 217 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.094613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.061019 restraints weight = 49271.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.062393 restraints weight = 28146.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.063204 restraints weight = 21050.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.063669 restraints weight = 18297.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.063847 restraints weight = 17093.390| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.107 15725 Z= 0.437 Angle : 0.925 11.564 22473 Z= 0.484 Chirality : 0.054 0.276 2536 Planarity : 0.007 0.052 1830 Dihedral : 30.500 167.038 4426 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.11 % Allowed : 19.20 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1081 helix: 0.95 (0.18), residues: 715 sheet: -0.07 (0.89), residues: 39 loop : -1.57 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 79 TYR 0.035 0.003 TYR D 83 PHE 0.043 0.003 PHE A 67 TRP 0.016 0.003 TRP K 343 HIS 0.012 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00942 / 0.44 (15725) covalent geometry : angle 0.92527 / 0.48 (22473) hydrogen bonds : bond 0.07681 / 5.11 ( 884) hydrogen bonds : angle 4.19330 / 3.00 ( 2285) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8675 (mt) cc_final: 0.8087 (mt) REVERT: A 52 ARG cc_start: 0.9055 (mtt90) cc_final: 0.8194 (mtm-85) REVERT: A 59 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8377 (pm20) REVERT: B 39 ARG cc_start: 0.9441 (mmt-90) cc_final: 0.9221 (mmt180) REVERT: B 44 LYS cc_start: 0.9256 (mtpt) cc_final: 0.9030 (mtpt) REVERT: C 18 SER cc_start: 0.9329 (m) cc_final: 0.9095 (p) REVERT: C 75 LYS cc_start: 0.9378 (mmtp) cc_final: 0.8941 (mmmt) REVERT: D 34 LYS cc_start: 0.8662 (mppt) cc_final: 0.7907 (mmmt) REVERT: D 61 ILE cc_start: 0.9670 (mm) cc_final: 0.9417 (mt) REVERT: D 71 GLU cc_start: 0.8504 (tp30) cc_final: 0.8181 (tp30) REVERT: D 79 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7739 (mtm180) REVERT: E 93 GLN cc_start: 0.8765 (tt0) cc_final: 0.8307 (tt0) REVERT: E 107 THR cc_start: 0.9502 (m) cc_final: 0.9128 (t) REVERT: F 59 LYS cc_start: 0.8884 (tttm) cc_final: 0.8563 (tttp) REVERT: F 88 TYR cc_start: 0.8718 (m-10) cc_final: 0.7714 (m-80) REVERT: G 95 LYS cc_start: 0.9044 (tttt) cc_final: 0.8603 (mtpt) REVERT: H 34 LYS cc_start: 0.8311 (mttt) cc_final: 0.7879 (mppt) REVERT: H 47 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8551 (tm-30) REVERT: H 83 TYR cc_start: 0.8617 (m-10) cc_final: 0.7878 (m-10) REVERT: H 86 ARG cc_start: 0.8671 (mpt-90) cc_final: 0.8339 (mtt-85) REVERT: K 208 LEU cc_start: 0.8147 (tp) cc_final: 0.6921 (pt) outliers start: 20 outliers final: 16 residues processed: 210 average time/residue: 0.1325 time to fit residues: 40.3221 Evaluate side-chains 207 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 298 MET Chi-restraints excluded: chain K residue 322 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 46 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 49 optimal weight: 0.0570 chunk 81 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.098218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.065278 restraints weight = 48853.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.066804 restraints weight = 26850.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.067589 restraints weight = 19646.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.068225 restraints weight = 17053.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.068429 restraints weight = 15779.747| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15725 Z= 0.158 Angle : 0.687 10.334 22473 Z= 0.383 Chirality : 0.045 0.275 2536 Planarity : 0.005 0.059 1830 Dihedral : 30.286 172.313 4426 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.79 % Allowed : 19.94 % Favored : 78.27 % 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: 0.95 (0.25), residues: 1081 helix: 1.47 (0.18), residues: 716 sheet: -0.15 (0.87), residues: 39 loop : -1.14 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 35 TYR 0.036 0.003 TYR D 83 PHE 0.040 0.002 PHE A 67 TRP 0.008 0.001 TRP K 455 HIS 0.007 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (15725) covalent geometry : angle 0.68683 / 0.38 (22473) hydrogen bonds : bond 0.04744 / 3.11 ( 884) hydrogen bonds : angle 3.57919 / 2.52 ( 2285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2826.06 seconds wall clock time: 49 minutes 28.03 seconds (2968.03 seconds total)