Starting phenix.real_space_refine on Sat Sep 12 05:08:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d1z_30551/09_2026/7d1z_30551.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d1z_30551/09_2026/7d1z_30551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d1z_30551/09_2026/7d1z_30551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d1z_30551/09_2026/7d1z_30551.map" model { file = "/net/cci-nas-00/data/ceres_data/7d1z_30551/09_2026/7d1z_30551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d1z_30551/09_2026/7d1z_30551.cif" } resolution = 3.15 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1358 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 20 5.16 5 C 7463 2.51 5 N 2499 2.21 5 O 3057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 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: 13327 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1330 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 3, 'TRANS': 162} Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 699 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 2.92, per 1000 atoms: 0.22 Number of scatterers: 13327 At special positions: 0 Unit cell: (118.65, 99.75, 123.9, 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 20 16.00 P 288 15.00 O 3057 8.00 N 2499 7.00 C 7463 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: 1.07 Conformation dependent library (CDL) restraints added in 409.4 milliseconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 64.5% alpha, 5.6% beta 138 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.805A 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 removed outlier: 3.544A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.399A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 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 124 removed outlier: 3.557A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.409A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.632A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) 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 194 through 211 Processing helix chain 'K' and resid 254 through 264 removed outlier: 3.805A pdb=" N GLU K 259 " --> pdb=" O ALA K 255 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA K 260 " --> pdb=" O LYS K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 347 Processing helix chain 'K' and resid 348 through 352 removed outlier: 3.729A pdb=" N LYS K 351 " --> pdb=" O PRO K 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.595A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.784A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.876A 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: 6.807A 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: 6.863A 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: 7.199A 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 218 through 223 removed outlier: 3.735A pdb=" N GLY K 227 " --> pdb=" O ILE K 223 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU K 330 " --> pdb=" O ALA K 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 240 through 244 removed outlier: 3.693A pdb=" N ASP K 240 " --> pdb=" O ALA K 322 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU K 320 " --> pdb=" O VAL K 242 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE K 321 " --> pdb=" O GLN K 306 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN K 306 " --> pdb=" O ILE K 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 248 through 250 removed outlier: 3.849A pdb=" N CYS K 283 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 276 through 277 Processing sheet with id=AB6, first strand: chain 'K' and resid 310 through 312 removed outlier: 3.966A pdb=" N VAL K 315 " --> pdb=" O ILE K 312 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 1.49 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: 2477 1.33 - 1.45: 4477 1.45 - 1.57: 6590 1.57 - 1.69: 576 1.69 - 1.81: 32 Bond restraints: 14152 Sorted by residual: bond pdb=" C3' DT I -71 " pdb=" C2' DT I -71 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DC I 7 " pdb=" O3' DC I 7 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG J 8 " pdb=" O3' DG J 8 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.98e+00 bond pdb=" C3' DA J -34 " pdb=" O3' DA J -34 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.93e+00 ... (remaining 14147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.42: 20325 5.42 - 10.85: 11 10.85 - 16.27: 1 16.27 - 21.70: 1 21.70 - 27.12: 1 Bond angle restraints: 20339 Sorted by residual: angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP1 DG J 21 " ideal model delta sigma weight residual 108.00 80.88 27.12 3.00e+00 1.11e-01 8.17e+01 angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.71 106.59 7.12 9.50e-01 1.11e+00 5.61e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP2 DG J 21 " ideal model delta sigma weight residual 108.00 87.24 20.76 3.00e+00 1.11e-01 4.79e+01 angle pdb=" N3 DT J 69 " pdb=" C4 DT J 69 " pdb=" O4 DT J 69 " ideal model delta sigma weight residual 119.90 122.75 -2.85 6.00e-01 2.78e+00 2.25e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 ... (remaining 20334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.83: 6034 31.83 - 63.67: 1699 63.67 - 95.50: 49 95.50 - 127.34: 0 127.34 - 159.17: 2 Dihedral angle restraints: 7784 sinusoidal: 5097 harmonic: 2687 Sorted by residual: dihedral pdb=" CA ALA G 12 " pdb=" C ALA G 12 " pdb=" N LYS G 13 " pdb=" CA LYS G 13 " ideal model delta harmonic sigma weight residual 180.00 -157.79 -22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 60.83 159.17 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 7781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.408: 2296 0.408 - 0.815: 0 0.815 - 1.223: 0 1.223 - 1.630: 0 1.630 - 2.038: 1 Chirality restraints: 2297 Sorted by residual: chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.34 0.30 2.04 2.00e-01 2.50e+01 1.04e+02 chirality pdb=" C3' DC I 4 " pdb=" C4' DC I 4 " pdb=" O3' DC I 4 " pdb=" C2' DC I 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" C3' DC I 7 " pdb=" C4' DC I 7 " pdb=" O3' DC I 7 " pdb=" C2' DC I 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 2294 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.028 2.00e-02 2.50e+03 1.22e-02 4.09e+00 pdb=" N9 DA I -35 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " 0.027 2.00e-02 2.50e+03 1.12e-02 3.76e+00 pdb=" N9 DG I 28 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " 0.026 2.00e-02 2.50e+03 1.09e-02 3.57e+00 pdb=" N9 DG I 26 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " -0.002 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 453 2.67 - 3.23: 11697 3.23 - 3.79: 25151 3.79 - 4.34: 32751 4.34 - 4.90: 46742 Nonbonded interactions: 116794 Sorted by model distance: nonbonded pdb=" O ALA K 255 " pdb=" OH TYR K 274 " model vdw 2.118 3.040 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.179 3.120 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.194 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.254 3.040 ... (remaining 116789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 14.620 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 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 : 0.008 0.047 14152 Z= 0.632 Angle : 0.863 27.121 20339 Z= 0.702 Chirality : 0.063 2.038 2297 Planarity : 0.003 0.035 1578 Dihedral : 28.096 159.170 6056 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.24), residues: 911 helix: -0.32 (0.19), residues: 582 sheet: -3.86 (0.67), residues: 28 loop : -3.32 (0.28), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 88 TYR 0.015 0.002 TYR G 50 PHE 0.018 0.002 PHE K 275 TRP 0.004 0.001 TRP K 349 HIS 0.006 0.001 HIS K 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00837 / 0.63 (14152) covalent geometry : angle 0.86327 / 0.70 (20339) hydrogen bonds : bond 0.07813 / 5.53 ( 814) hydrogen bonds : angle 3.85048 / 2.74 ( 2059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.384 Fit side-chains REVERT: A 59 GLU cc_start: 0.8147 (pp20) cc_final: 0.7642 (pp20) REVERT: B 88 TYR cc_start: 0.9097 (m-10) cc_final: 0.8749 (m-80) REVERT: C 75 LYS cc_start: 0.8629 (mttp) cc_final: 0.8408 (mtpt) REVERT: D 43 LYS cc_start: 0.8950 (mttt) cc_final: 0.8719 (mttm) REVERT: D 116 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8439 (ttmm) REVERT: E 50 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7909 (mt-10) REVERT: H 46 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8561 (mmtm) REVERT: H 116 LYS cc_start: 0.8901 (tttt) cc_final: 0.8639 (ttmt) REVERT: K 288 ARG cc_start: 0.5444 (ttp80) cc_final: 0.5185 (ttp80) REVERT: K 334 TYR cc_start: 0.7132 (p90) cc_final: 0.6895 (p90) REVERT: F 31 LYS cc_start: 0.9004 (tttt) cc_final: 0.8697 (tttm) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1854 time to fit residues: 48.5047 Evaluate side-chains 158 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 30.0000 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS D 82 HIS D 84 ASN D 95 GLN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 49 HIS H 84 ASN K 347 HIS F 75 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.149953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.090978 restraints weight = 20820.094| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.88 r_work: 0.2914 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14152 Z= 0.137 Angle : 0.713 25.953 20339 Z= 0.392 Chirality : 0.063 1.988 2297 Planarity : 0.004 0.042 1578 Dihedral : 31.200 160.923 4211 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.78 % Allowed : 12.92 % Favored : 86.30 % 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: 0.11 (0.27), residues: 911 helix: 1.39 (0.20), residues: 588 sheet: -3.17 (0.64), residues: 43 loop : -2.30 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 131 TYR 0.022 0.001 TYR K 274 PHE 0.008 0.001 PHE E 67 TRP 0.005 0.001 TRP K 349 HIS 0.006 0.001 HIS K 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.14 (14152) covalent geometry : angle 0.71313 / 0.39 (20339) hydrogen bonds : bond 0.04368 / 2.98 ( 814) hydrogen bonds : angle 3.30860 / 2.41 ( 2059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 0.353 Fit side-chains REVERT: A 59 GLU cc_start: 0.8448 (pp20) cc_final: 0.7668 (pp20) REVERT: B 88 TYR cc_start: 0.9222 (m-10) cc_final: 0.8925 (m-80) REVERT: D 43 LYS cc_start: 0.9054 (mttt) cc_final: 0.8846 (mttm) REVERT: D 71 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7924 (tm-30) REVERT: E 52 ARG cc_start: 0.8296 (ttm110) cc_final: 0.7924 (mtp-110) REVERT: G 71 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8274 (ttp80) REVERT: H 86 ARG cc_start: 0.8778 (mmt90) cc_final: 0.8340 (mmt90) REVERT: H 116 LYS cc_start: 0.9108 (tttt) cc_final: 0.8756 (ttmt) REVERT: H 121 TYR cc_start: 0.9294 (t80) cc_final: 0.8996 (t80) REVERT: K 288 ARG cc_start: 0.5622 (ttp80) cc_final: 0.5329 (ttp80) REVERT: F 31 LYS cc_start: 0.8957 (tttt) cc_final: 0.8734 (tttm) REVERT: F 79 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8835 (mtpp) outliers start: 6 outliers final: 2 residues processed: 170 average time/residue: 0.1539 time to fit residues: 35.3775 Evaluate side-chains 161 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain F residue 79 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 47 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 50.0000 chunk 48 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 113 HIS G 31 HIS ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.149364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.089953 restraints weight = 21035.105| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.96 r_work: 0.2890 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14152 Z= 0.158 Angle : 0.691 26.137 20339 Z= 0.381 Chirality : 0.061 1.976 2297 Planarity : 0.004 0.030 1578 Dihedral : 31.016 161.540 4211 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.55 % Allowed : 14.34 % Favored : 84.11 % 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: 0.87 (0.28), residues: 911 helix: 1.96 (0.21), residues: 588 sheet: -2.85 (0.69), residues: 43 loop : -1.96 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 131 TYR 0.020 0.001 TYR K 274 PHE 0.010 0.001 PHE E 67 TRP 0.003 0.001 TRP K 349 HIS 0.005 0.001 HIS K 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (14152) covalent geometry : angle 0.69079 / 0.38 (20339) hydrogen bonds : bond 0.04244 / 2.88 ( 814) hydrogen bonds : angle 3.16445 / 2.30 ( 2059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9221 (m-10) cc_final: 0.8931 (m-80) REVERT: B 93 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8187 (mm-40) REVERT: D 71 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7954 (tm-30) REVERT: E 52 ARG cc_start: 0.8307 (ttm110) cc_final: 0.7955 (mtp-110) REVERT: H 86 ARG cc_start: 0.8790 (mmt90) cc_final: 0.8364 (mmt90) REVERT: H 101 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8915 (mm) REVERT: H 116 LYS cc_start: 0.9059 (tttt) cc_final: 0.8716 (ttmt) REVERT: H 121 TYR cc_start: 0.9293 (t80) cc_final: 0.9002 (t80) REVERT: K 208 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5943 (tm-30) REVERT: F 31 LYS cc_start: 0.8995 (tttt) cc_final: 0.8741 (tttm) outliers start: 12 outliers final: 7 residues processed: 169 average time/residue: 0.1541 time to fit residues: 35.2773 Evaluate side-chains 165 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 274 TYR Chi-restraints excluded: chain F residue 82 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 11 optimal weight: 0.0470 chunk 36 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 0.3980 chunk 45 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 50.0000 chunk 81 optimal weight: 20.0000 chunk 23 optimal weight: 0.6980 overall best weight: 2.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.148902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089301 restraints weight = 21018.075| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.93 r_work: 0.2881 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14152 Z= 0.180 Angle : 0.695 26.092 20339 Z= 0.379 Chirality : 0.062 1.973 2297 Planarity : 0.004 0.031 1578 Dihedral : 30.998 161.821 4211 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.45 % Allowed : 15.50 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.28), residues: 911 helix: 2.18 (0.21), residues: 586 sheet: -2.90 (0.69), residues: 43 loop : -1.69 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 32 TYR 0.019 0.001 TYR K 274 PHE 0.010 0.002 PHE E 67 TRP 0.002 0.001 TRP K 349 HIS 0.004 0.001 HIS K 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (14152) covalent geometry : angle 0.69456 / 0.38 (20339) hydrogen bonds : bond 0.04220 / 2.85 ( 814) hydrogen bonds : angle 3.11939 / 2.25 ( 2059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9216 (m-10) cc_final: 0.8940 (m-80) REVERT: B 93 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8224 (mm-40) REVERT: D 71 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7986 (tm-30) REVERT: E 52 ARG cc_start: 0.8319 (ttm110) cc_final: 0.7990 (mtp-110) REVERT: H 86 ARG cc_start: 0.8791 (mmt90) cc_final: 0.8408 (mmt90) REVERT: H 116 LYS cc_start: 0.9055 (tttt) cc_final: 0.8708 (ttmt) REVERT: H 121 TYR cc_start: 0.9299 (t80) cc_final: 0.9055 (t80) REVERT: K 208 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5963 (tm-30) REVERT: F 31 LYS cc_start: 0.9019 (tttt) cc_final: 0.8767 (tttm) outliers start: 19 outliers final: 14 residues processed: 168 average time/residue: 0.1489 time to fit residues: 34.3700 Evaluate side-chains 169 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 274 TYR Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 11 optimal weight: 0.0770 chunk 36 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 103 optimal weight: 40.0000 chunk 23 optimal weight: 0.0470 chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 2.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.149482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.090170 restraints weight = 20998.591| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.88 r_work: 0.2905 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14152 Z= 0.169 Angle : 0.683 26.100 20339 Z= 0.372 Chirality : 0.061 1.972 2297 Planarity : 0.004 0.033 1578 Dihedral : 30.932 162.509 4211 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.07 % Allowed : 16.02 % Favored : 81.91 % 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: 1.42 (0.28), residues: 911 helix: 2.31 (0.21), residues: 587 sheet: -2.82 (0.73), residues: 43 loop : -1.47 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.019 0.001 TYR K 274 PHE 0.010 0.001 PHE E 67 TRP 0.002 0.001 TRP K 349 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (14152) covalent geometry : angle 0.68347 / 0.37 (20339) hydrogen bonds : bond 0.04127 / 2.78 ( 814) hydrogen bonds : angle 3.07543 / 2.21 ( 2059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9199 (m-10) cc_final: 0.8921 (m-80) REVERT: B 93 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8186 (mm-40) REVERT: D 71 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7989 (tm-30) REVERT: E 52 ARG cc_start: 0.8291 (ttm110) cc_final: 0.8030 (mtp-110) REVERT: H 86 ARG cc_start: 0.8794 (mmt90) cc_final: 0.8365 (mmt90) REVERT: H 116 LYS cc_start: 0.9018 (tttt) cc_final: 0.8676 (ttmt) REVERT: H 121 TYR cc_start: 0.9282 (t80) cc_final: 0.8981 (t80) REVERT: K 208 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6023 (tm-30) REVERT: F 31 LYS cc_start: 0.9023 (tttt) cc_final: 0.8784 (tttm) outliers start: 16 outliers final: 13 residues processed: 166 average time/residue: 0.1406 time to fit residues: 32.1633 Evaluate side-chains 167 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 274 TYR Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 0.7980 chunk 105 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 30.0000 chunk 89 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 GLN G 104 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.150294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.090531 restraints weight = 21267.729| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.96 r_work: 0.2897 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14152 Z= 0.159 Angle : 0.676 26.077 20339 Z= 0.368 Chirality : 0.061 1.971 2297 Planarity : 0.004 0.034 1578 Dihedral : 30.859 163.171 4211 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.20 % Allowed : 16.28 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.28), residues: 911 helix: 2.43 (0.21), residues: 587 sheet: -2.87 (0.74), residues: 43 loop : -1.35 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.017 0.001 TYR K 274 PHE 0.010 0.001 PHE E 67 TRP 0.002 0.001 TRP K 349 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (14152) covalent geometry : angle 0.67632 / 0.37 (20339) hydrogen bonds : bond 0.04023 / 2.71 ( 814) hydrogen bonds : angle 3.03421 / 2.18 ( 2059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.343 Fit side-chains REVERT: A 77 ASP cc_start: 0.8552 (t0) cc_final: 0.8323 (t0) REVERT: B 88 TYR cc_start: 0.9209 (m-10) cc_final: 0.8976 (m-80) REVERT: B 93 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8164 (mm-40) REVERT: C 36 LYS cc_start: 0.9100 (mttp) cc_final: 0.8713 (mttp) REVERT: D 71 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7982 (tm-30) REVERT: D 99 ARG cc_start: 0.8688 (mtm-85) cc_final: 0.8415 (mtp85) REVERT: E 52 ARG cc_start: 0.8312 (ttm110) cc_final: 0.8048 (mtp-110) REVERT: H 86 ARG cc_start: 0.8798 (mmt90) cc_final: 0.8460 (mmt90) REVERT: H 116 LYS cc_start: 0.9013 (tttt) cc_final: 0.8717 (ttpt) REVERT: H 121 TYR cc_start: 0.9281 (t80) cc_final: 0.8989 (t80) REVERT: K 208 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5859 (tm-30) REVERT: F 31 LYS cc_start: 0.9030 (tttt) cc_final: 0.8792 (tttm) outliers start: 17 outliers final: 15 residues processed: 165 average time/residue: 0.1436 time to fit residues: 32.5860 Evaluate side-chains 165 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 24 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 65 optimal weight: 40.0000 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.149860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.090514 restraints weight = 20876.164| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.90 r_work: 0.2900 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14152 Z= 0.163 Angle : 0.682 26.092 20339 Z= 0.368 Chirality : 0.061 1.968 2297 Planarity : 0.004 0.035 1578 Dihedral : 30.836 163.499 4211 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.97 % Allowed : 16.67 % Favored : 80.36 % 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: 1.68 (0.28), residues: 911 helix: 2.47 (0.21), residues: 587 sheet: -2.82 (0.75), residues: 43 loop : -1.26 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.017 0.001 TYR H 40 PHE 0.010 0.001 PHE E 67 TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (14152) covalent geometry : angle 0.68236 / 0.37 (20339) hydrogen bonds : bond 0.04039 / 2.71 ( 814) hydrogen bonds : angle 3.03473 / 2.18 ( 2059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.380 Fit side-chains REVERT: A 77 ASP cc_start: 0.8571 (t0) cc_final: 0.8322 (t0) REVERT: B 84 MET cc_start: 0.8914 (mmm) cc_final: 0.8686 (mmm) REVERT: B 88 TYR cc_start: 0.9226 (m-10) cc_final: 0.8830 (m-80) REVERT: B 93 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8172 (mm-40) REVERT: C 36 LYS cc_start: 0.9096 (mttp) cc_final: 0.8878 (mttp) REVERT: D 71 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7997 (tm-30) REVERT: D 99 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8415 (mtp85) REVERT: E 52 ARG cc_start: 0.8308 (ttm110) cc_final: 0.8062 (mtp-110) REVERT: G 91 GLU cc_start: 0.8687 (tt0) cc_final: 0.8427 (tm-30) REVERT: H 86 ARG cc_start: 0.8783 (mmt90) cc_final: 0.8397 (mmt90) REVERT: H 116 LYS cc_start: 0.9013 (tttt) cc_final: 0.8663 (ttmt) REVERT: H 121 TYR cc_start: 0.9281 (t80) cc_final: 0.8984 (t80) REVERT: K 208 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5862 (tm-30) REVERT: F 31 LYS cc_start: 0.9033 (tttt) cc_final: 0.8795 (tttm) outliers start: 23 outliers final: 20 residues processed: 165 average time/residue: 0.1454 time to fit residues: 32.9722 Evaluate side-chains 170 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 50.0000 chunk 114 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 80 optimal weight: 30.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.150441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.091253 restraints weight = 20674.572| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.89 r_work: 0.2910 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14152 Z= 0.140 Angle : 0.677 26.106 20339 Z= 0.366 Chirality : 0.061 1.973 2297 Planarity : 0.004 0.035 1578 Dihedral : 30.824 163.590 4211 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.10 % Allowed : 16.54 % Favored : 80.36 % 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: 1.77 (0.29), residues: 911 helix: 2.54 (0.21), residues: 587 sheet: -2.78 (0.76), residues: 43 loop : -1.23 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.017 0.001 TYR H 40 PHE 0.010 0.001 PHE E 67 TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS K 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (14152) covalent geometry : angle 0.67707 / 0.37 (20339) hydrogen bonds : bond 0.03962 / 2.66 ( 814) hydrogen bonds : angle 3.02411 / 2.17 ( 2059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.369 Fit side-chains REVERT: A 77 ASP cc_start: 0.8567 (t0) cc_final: 0.8315 (t0) REVERT: A 79 LYS cc_start: 0.8548 (tttm) cc_final: 0.8323 (tttm) REVERT: B 74 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8492 (mm-30) REVERT: B 84 MET cc_start: 0.8922 (mmm) cc_final: 0.8692 (mmm) REVERT: B 88 TYR cc_start: 0.9220 (m-10) cc_final: 0.8813 (m-80) REVERT: B 93 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8147 (mm-40) REVERT: D 71 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7989 (tm-30) REVERT: D 99 ARG cc_start: 0.8672 (mtm-85) cc_final: 0.8407 (mtp85) REVERT: E 52 ARG cc_start: 0.8318 (ttm110) cc_final: 0.8078 (mtp-110) REVERT: G 91 GLU cc_start: 0.8676 (tt0) cc_final: 0.8428 (tm-30) REVERT: H 86 ARG cc_start: 0.8771 (mmt90) cc_final: 0.8383 (mmt90) REVERT: H 116 LYS cc_start: 0.8999 (tttt) cc_final: 0.8705 (ttpt) REVERT: H 121 TYR cc_start: 0.9276 (t80) cc_final: 0.8976 (t80) REVERT: K 208 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5881 (tm-30) REVERT: F 31 LYS cc_start: 0.9036 (tttt) cc_final: 0.8804 (tttm) outliers start: 24 outliers final: 20 residues processed: 170 average time/residue: 0.1356 time to fit residues: 31.9727 Evaluate side-chains 175 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 272 MET Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 73 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 115 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.150698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.091564 restraints weight = 20909.758| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.88 r_work: 0.2921 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14152 Z= 0.130 Angle : 0.675 26.102 20339 Z= 0.364 Chirality : 0.060 1.972 2297 Planarity : 0.004 0.039 1578 Dihedral : 30.792 163.836 4211 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.33 % Allowed : 17.57 % Favored : 80.10 % 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: 1.81 (0.28), residues: 911 helix: 2.55 (0.21), residues: 588 sheet: -2.78 (0.75), residues: 43 loop : -1.18 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.017 0.001 TYR H 40 PHE 0.010 0.001 PHE A 67 TRP 0.002 0.000 TRP K 349 HIS 0.003 0.001 HIS K 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (14152) covalent geometry : angle 0.67509 / 0.36 (20339) hydrogen bonds : bond 0.03883 / 2.61 ( 814) hydrogen bonds : angle 3.00001 / 2.16 ( 2059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.325 Fit side-chains REVERT: A 77 ASP cc_start: 0.8551 (t0) cc_final: 0.8304 (t0) REVERT: A 79 LYS cc_start: 0.8554 (tttm) cc_final: 0.8331 (tttm) REVERT: B 74 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8486 (mm-30) REVERT: B 84 MET cc_start: 0.8907 (mmm) cc_final: 0.8686 (mmm) REVERT: B 88 TYR cc_start: 0.9214 (m-10) cc_final: 0.8855 (m-80) REVERT: B 93 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8125 (mm-40) REVERT: C 36 LYS cc_start: 0.9049 (mttp) cc_final: 0.8684 (mttp) REVERT: D 99 ARG cc_start: 0.8660 (mtm-85) cc_final: 0.8420 (mtp85) REVERT: E 52 ARG cc_start: 0.8314 (ttm110) cc_final: 0.8076 (mtp-110) REVERT: G 91 GLU cc_start: 0.8672 (tt0) cc_final: 0.8436 (tm-30) REVERT: H 86 ARG cc_start: 0.8766 (mmt90) cc_final: 0.8386 (mmt90) REVERT: H 116 LYS cc_start: 0.8989 (tttt) cc_final: 0.8696 (ttpt) REVERT: H 121 TYR cc_start: 0.9267 (t80) cc_final: 0.9006 (t80) REVERT: K 208 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5879 (tm-30) REVERT: F 31 LYS cc_start: 0.9028 (tttt) cc_final: 0.8802 (tttm) outliers start: 18 outliers final: 16 residues processed: 167 average time/residue: 0.1348 time to fit residues: 31.3752 Evaluate side-chains 169 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain F residue 22 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.149674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.090105 restraints weight = 20836.061| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.90 r_work: 0.2890 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14152 Z= 0.179 Angle : 0.692 26.130 20339 Z= 0.370 Chirality : 0.061 1.964 2297 Planarity : 0.004 0.035 1578 Dihedral : 30.820 163.999 4211 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.58 % Allowed : 17.44 % Favored : 79.97 % 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: 1.80 (0.28), residues: 911 helix: 2.56 (0.21), residues: 585 sheet: -2.79 (0.76), residues: 43 loop : -1.18 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.016 0.001 TYR H 40 PHE 0.010 0.002 PHE E 67 TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (14152) covalent geometry : angle 0.69169 / 0.37 (20339) hydrogen bonds : bond 0.04176 / 2.80 ( 814) hydrogen bonds : angle 3.05680 / 2.19 ( 2059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.373 Fit side-chains REVERT: A 77 ASP cc_start: 0.8574 (t0) cc_final: 0.8311 (t0) REVERT: A 79 LYS cc_start: 0.8573 (tttm) cc_final: 0.8346 (tttm) REVERT: B 74 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8495 (mm-30) REVERT: B 84 MET cc_start: 0.8964 (mmm) cc_final: 0.8693 (mmm) REVERT: B 88 TYR cc_start: 0.9244 (m-10) cc_final: 0.8828 (m-80) REVERT: B 93 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8161 (mm-40) REVERT: C 36 LYS cc_start: 0.9126 (mttp) cc_final: 0.8797 (mttp) REVERT: D 71 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8015 (tm-30) REVERT: D 99 ARG cc_start: 0.8687 (mtm-85) cc_final: 0.8406 (mtp85) REVERT: E 52 ARG cc_start: 0.8302 (ttm110) cc_final: 0.8058 (mtp-110) REVERT: G 91 GLU cc_start: 0.8712 (tt0) cc_final: 0.8450 (tm-30) REVERT: H 86 ARG cc_start: 0.8791 (mmt90) cc_final: 0.8408 (mmt90) REVERT: H 116 LYS cc_start: 0.8999 (tttt) cc_final: 0.8700 (ttpt) REVERT: H 121 TYR cc_start: 0.9286 (t80) cc_final: 0.9043 (t80) REVERT: K 208 GLU cc_start: 0.6129 (OUTLIER) cc_final: 0.5827 (tm-30) REVERT: F 31 LYS cc_start: 0.9041 (tttt) cc_final: 0.8800 (tttm) outliers start: 20 outliers final: 18 residues processed: 164 average time/residue: 0.1341 time to fit residues: 30.6635 Evaluate side-chains 169 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 113 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 100 optimal weight: 30.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.149160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.088950 restraints weight = 21276.006| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.92 r_work: 0.2874 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14152 Z= 0.208 Angle : 0.710 26.116 20339 Z= 0.377 Chirality : 0.062 1.963 2297 Planarity : 0.004 0.034 1578 Dihedral : 30.891 164.250 4211 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.58 % Allowed : 17.31 % Favored : 80.10 % 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: 1.68 (0.29), residues: 911 helix: 2.45 (0.21), residues: 585 sheet: -2.88 (0.75), residues: 43 loop : -1.16 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.016 0.001 TYR H 40 PHE 0.010 0.002 PHE E 67 TRP 0.002 0.001 TRP K 349 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (14152) covalent geometry : angle 0.70983 / 0.38 (20339) hydrogen bonds : bond 0.04382 / 2.93 ( 814) hydrogen bonds : angle 3.12798 / 2.24 ( 2059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3326.60 seconds wall clock time: 57 minutes 33.57 seconds (3453.57 seconds total)