Starting phenix.real_space_refine on Fri Jul 3 13:09:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xpx_33385/07_2026/7xpx_33385.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xpx_33385/07_2026/7xpx_33385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xpx_33385/07_2026/7xpx_33385.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xpx_33385/07_2026/7xpx_33385.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xpx_33385/07_2026/7xpx_33385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xpx_33385/07_2026/7xpx_33385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xpx_33385/07_2026/7xpx_33385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xpx_33385/07_2026/7xpx_33385.map" } resolution = 3.2 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 1341 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 7508 2.51 5 N 2521 2.21 5 O 3071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13408 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 820 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ECX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 756 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 808 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" 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: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2970 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2969 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1338 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1337 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 3, 'TRANS': 163} Conformer: "B" Number of residues, atoms: 167, 1337 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 3, 'TRANS': 163} bond proxies already assigned to first conformer: 1359 Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 3.60, per 1000 atoms: 0.27 Number of scatterers: 13408 At special positions: 0 Unit cell: (94, 120, 121, 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 3071 8.00 N 2521 7.00 C 7508 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: 1.20 Conformation dependent library (CDL) restraints added in 481.6 milliseconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 14 sheets defined 62.1% alpha, 7.0% beta 137 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.556A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.265A 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 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.798A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.567A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.289A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.565A 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 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 199 through 208 removed outlier: 3.720A pdb=" N ARG K 205 " --> pdb=" O GLU K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 265 removed outlier: 3.982A pdb=" N LYS K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 347 removed outlier: 3.577A pdb=" N GLU K 345 " --> pdb=" O LYS K 341 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA K 346 " --> pdb=" O ALA K 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.741A 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: 6.559A 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: 7.134A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.881A 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: 7.477A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 Processing sheet with id=AB3, first strand: chain 'K' and resid 241 through 245 removed outlier: 6.934A pdb=" N PHE K 241 " --> pdb=" O ALA K 322 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ALA K 322 " --> pdb=" O PHE K 241 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU K 318 " --> pdb=" O TYR K 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 248 through 250 Processing sheet with id=AB5, first strand: chain 'K' and resid 298 through 299 removed outlier: 6.611A pdb=" N ASN K 298 " --> pdb=" O TYR K 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 454 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3023 1.34 - 1.46: 4248 1.46 - 1.58: 6355 1.58 - 1.70: 576 1.70 - 1.82: 35 Bond restraints: 14237 Sorted by residual: bond pdb=" C3' DC I 34 " pdb=" C2' DC I 34 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DA J -22 " pdb=" C2' DA J -22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.72e+00 bond pdb=" C3' DC J 19 " pdb=" C2' DC J 19 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.37e+00 bond pdb=" C3' DG I 10 " pdb=" C2' DG I 10 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.12e+00 ... (remaining 14232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 19533 1.82 - 3.63: 883 3.63 - 5.45: 32 5.45 - 7.26: 4 7.26 - 9.08: 5 Bond angle restraints: 20457 Sorted by residual: angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT I -43 " pdb=" C4 DT I -43 " pdb=" O4 DT I -43 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 20452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 6390 35.48 - 70.96: 1417 70.96 - 106.44: 12 106.44 - 141.92: 2 141.92 - 177.40: 3 Dihedral angle restraints: 7824 sinusoidal: 5112 harmonic: 2712 Sorted by residual: dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 42.60 177.40 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT I 54 " pdb=" C3' DT I 54 " pdb=" O3' DT I 54 " pdb=" P DC I 55 " ideal model delta sinusoidal sigma weight residual -140.00 36.82 -176.82 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 44.40 175.60 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1445 0.037 - 0.073: 633 0.073 - 0.110: 187 0.110 - 0.147: 41 0.147 - 0.183: 7 Chirality restraints: 2313 Sorted by residual: chirality pdb=" CA GLU D 90 " pdb=" N GLU D 90 " pdb=" C GLU D 90 " pdb=" CB GLU D 90 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" C2' SAM K 401 " pdb=" C1' SAM K 401 " pdb=" C3' SAM K 401 " pdb=" O2' SAM K 401 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" C1' SAM K 401 " pdb=" C2' SAM K 401 " pdb=" N9 SAM K 401 " pdb=" O4' SAM K 401 " both_signs ideal model delta sigma weight residual False 2.30 2.47 -0.17 2.00e-01 2.50e+01 7.01e-01 ... (remaining 2310 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 55 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C ARG B 55 " 0.039 2.00e-02 2.50e+03 pdb=" O ARG B 55 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY B 56 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " 0.027 2.00e-02 2.50e+03 1.19e-02 3.88e+00 pdb=" N9 DA I 47 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL K 315 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO K 316 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO K 316 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 316 " -0.024 5.00e-02 4.00e+02 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 922 2.73 - 3.27: 12385 3.27 - 3.81: 27071 3.81 - 4.36: 31892 4.36 - 4.90: 45811 Nonbonded interactions: 118081 Sorted by model distance: nonbonded pdb=" O LYS C 15 " pdb=" OG SER C 19 " model vdw 2.185 3.040 nonbonded pdb=" O GLU K 208 " pdb=" OG SER K 212 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.227 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.268 3.040 nonbonded pdb=" OE2 GLU D 68 " pdb=" NH2 ARG H 76 " model vdw 2.270 3.120 ... (remaining 118076 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 38 through 134) selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 27 through 121) selection = (chain 'H' and resid 27 through 121) } ncs_group { reference = (chain 'I' and (resid -72 through -1 or resid 1 through 72)) selection = (chain 'J' and (resid -72 through -1 or resid 1 through 72)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.300 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 : 0.006 0.058 14237 Z= 0.494 Angle : 0.755 9.076 20457 Z= 0.637 Chirality : 0.044 0.183 2313 Planarity : 0.005 0.052 1588 Dihedral : 27.527 177.402 6076 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 0.82 (0.27), residues: 913 helix: 1.35 (0.21), residues: 572 sheet: -0.78 (0.81), residues: 38 loop : -0.77 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 189 TYR 0.019 0.002 TYR K 262 PHE 0.013 0.002 PHE G 25 TRP 0.003 0.001 TRP K 349 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.49 (14237) covalent geometry : angle 0.75544 / 0.64 (20457) hydrogen bonds : bond 0.10664 / 7.38 ( 808) hydrogen bonds : angle 4.14572 / 2.91 ( 2037) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7310 (tm-30) REVERT: C 95 LYS cc_start: 0.7621 (tttm) cc_final: 0.7349 (ttmt) REVERT: D 56 MET cc_start: 0.8281 (tpp) cc_final: 0.8077 (tpp) REVERT: G 75 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8093 (mttm) REVERT: K 195 LYS cc_start: 0.7410 (tmmt) cc_final: 0.7204 (tttt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1675 time to fit residues: 26.3422 Evaluate side-chains 114 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN D 44 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.210490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.124875 restraints weight = 14007.297| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.88 r_work: 0.2970 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (15 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14237 Z= 0.171 Angle : 0.655 7.834 20457 Z= 0.380 Chirality : 0.044 0.291 2313 Planarity : 0.005 0.041 1588 Dihedral : 30.956 179.809 4212 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.02 % Allowed : 5.88 % Favored : 93.09 % 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: 1.22 (0.27), residues: 913 helix: 1.66 (0.21), residues: 584 sheet: -0.87 (0.81), residues: 38 loop : -0.66 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 55 TYR 0.015 0.002 TYR K 277 PHE 0.008 0.001 PHE K 241 TRP 0.004 0.001 TRP K 349 HIS 0.007 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (14237) covalent geometry : angle 0.65490 / 0.38 (20457) hydrogen bonds : bond 0.04895 / 3.22 ( 808) hydrogen bonds : angle 3.53172 / 2.51 ( 2037) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.7839 (mmm) cc_final: 0.7486 (mmm) REVERT: C 35 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8183 (mtm-85) REVERT: C 95 LYS cc_start: 0.7695 (tttm) cc_final: 0.7150 (ttmt) REVERT: D 56 MET cc_start: 0.8660 (tpp) cc_final: 0.8417 (tpp) REVERT: G 73 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8528 (t0) REVERT: K 197 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6665 (mt-10) outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 0.1543 time to fit residues: 23.4643 Evaluate side-chains 113 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 204 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 80 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 97 optimal weight: 10.0000 chunk 67 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 46 HIS D 81 ASN D 92 GLN F 93 GLN G 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.211717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.124659 restraints weight = 14100.557| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.97 r_work: 0.2962 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14237 Z= 0.146 Angle : 0.593 6.854 20457 Z= 0.350 Chirality : 0.043 0.292 2313 Planarity : 0.004 0.038 1588 Dihedral : 30.930 179.901 4212 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.02 % Allowed : 8.18 % Favored : 90.79 % 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: 1.61 (0.28), residues: 913 helix: 1.98 (0.21), residues: 587 sheet: -0.81 (0.81), residues: 38 loop : -0.56 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 35 TYR 0.014 0.001 TYR K 262 PHE 0.010 0.001 PHE G 25 TRP 0.003 0.001 TRP K 349 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (14237) covalent geometry : angle 0.59288 / 0.35 (20457) hydrogen bonds : bond 0.04124 / 2.71 ( 808) hydrogen bonds : angle 3.19635 / 2.28 ( 2037) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8031 (mmm) cc_final: 0.7549 (mmm) REVERT: C 95 LYS cc_start: 0.7664 (tttm) cc_final: 0.7080 (ttmt) REVERT: D 56 MET cc_start: 0.8710 (tpp) cc_final: 0.8484 (tpp) REVERT: F 90 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7433 (mt) REVERT: G 73 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8483 (t0) REVERT: K 197 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6590 (mt-10) REVERT: K 205 ARG cc_start: 0.7783 (tmm160) cc_final: 0.7547 (tmm-80) outliers start: 8 outliers final: 5 residues processed: 119 average time/residue: 0.1612 time to fit residues: 24.9881 Evaluate side-chains 121 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 214 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 110 optimal weight: 40.0000 chunk 98 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 40 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 75 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.211726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.123990 restraints weight = 14156.340| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.96 r_work: 0.2961 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14237 Z= 0.147 Angle : 0.575 6.968 20457 Z= 0.341 Chirality : 0.042 0.290 2313 Planarity : 0.004 0.037 1588 Dihedral : 30.838 179.401 4212 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.15 % Allowed : 9.46 % Favored : 89.39 % 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: 1.79 (0.28), residues: 913 helix: 2.11 (0.21), residues: 584 sheet: -0.85 (0.82), residues: 38 loop : -0.42 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.013 0.001 TYR K 262 PHE 0.008 0.001 PHE A 67 TRP 0.002 0.001 TRP K 349 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (14237) covalent geometry : angle 0.57456 / 0.34 (20457) hydrogen bonds : bond 0.03931 / 2.58 ( 808) hydrogen bonds : angle 3.10856 / 2.21 ( 2037) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8704 (ttpp) cc_final: 0.8485 (tttm) REVERT: B 92 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8248 (ttp80) REVERT: C 35 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.8020 (mtm-85) REVERT: C 95 LYS cc_start: 0.7664 (tttm) cc_final: 0.7163 (ttmt) REVERT: D 56 MET cc_start: 0.8704 (tpp) cc_final: 0.8450 (tpp) REVERT: G 73 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8489 (t0) REVERT: K 197 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6538 (mt-10) outliers start: 8 outliers final: 6 residues processed: 115 average time/residue: 0.1642 time to fit residues: 24.8146 Evaluate side-chains 119 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain K residue 204 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 30.0000 chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 72 optimal weight: 30.0000 chunk 12 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.212727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.123483 restraints weight = 14252.619| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.04 r_work: 0.2943 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14237 Z= 0.149 Angle : 0.570 6.988 20457 Z= 0.337 Chirality : 0.042 0.285 2313 Planarity : 0.004 0.036 1588 Dihedral : 30.791 178.477 4212 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.66 % Allowed : 8.95 % Favored : 89.39 % 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: 1.84 (0.28), residues: 913 helix: 2.14 (0.21), residues: 584 sheet: -0.80 (0.82), residues: 38 loop : -0.38 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 96 TYR 0.011 0.001 TYR K 262 PHE 0.007 0.001 PHE A 67 TRP 0.001 0.000 TRP K 349 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (14237) covalent geometry : angle 0.56963 / 0.34 (20457) hydrogen bonds : bond 0.03878 / 2.55 ( 808) hydrogen bonds : angle 3.04138 / 2.17 ( 2037) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8557 (tttm) REVERT: C 95 LYS cc_start: 0.7671 (tttm) cc_final: 0.7157 (ttmt) REVERT: D 56 MET cc_start: 0.8720 (tpp) cc_final: 0.8462 (tpp) REVERT: F 90 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7828 (mt) REVERT: G 73 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8500 (t0) REVERT: K 197 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6603 (mt-10) outliers start: 12 outliers final: 9 residues processed: 115 average time/residue: 0.1570 time to fit residues: 23.8443 Evaluate side-chains 122 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 214 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 51 optimal weight: 0.5980 chunk 104 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.212163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.124146 restraints weight = 14039.270| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.95 r_work: 0.2960 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14237 Z= 0.147 Angle : 0.564 7.007 20457 Z= 0.334 Chirality : 0.041 0.282 2313 Planarity : 0.004 0.051 1588 Dihedral : 30.730 177.792 4212 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.41 % Allowed : 9.85 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.28), residues: 913 helix: 2.19 (0.21), residues: 584 sheet: -0.80 (0.82), residues: 38 loop : -0.33 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 35 TYR 0.010 0.001 TYR K 262 PHE 0.008 0.001 PHE A 67 TRP 0.000 0.000 TRP K 349 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (14237) covalent geometry : angle 0.56372 / 0.33 (20457) hydrogen bonds : bond 0.03813 / 2.52 ( 808) hydrogen bonds : angle 3.00283 / 2.14 ( 2037) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8761 (ttpp) cc_final: 0.8553 (tttm) REVERT: C 95 LYS cc_start: 0.7661 (tttm) cc_final: 0.7150 (ttmt) REVERT: D 56 MET cc_start: 0.8690 (tpp) cc_final: 0.8438 (tpp) REVERT: F 64 ASN cc_start: 0.8193 (m-40) cc_final: 0.7972 (m-40) REVERT: F 90 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7850 (mt) REVERT: G 73 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8524 (t0) outliers start: 10 outliers final: 8 residues processed: 116 average time/residue: 0.1761 time to fit residues: 26.7460 Evaluate side-chains 123 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 214 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 114 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS D 60 ASN E 125 GLN F 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.218446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.129132 restraints weight = 14136.031| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.03 r_work: 0.2926 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14237 Z= 0.156 Angle : 0.567 8.489 20457 Z= 0.334 Chirality : 0.041 0.279 2313 Planarity : 0.004 0.036 1588 Dihedral : 30.725 177.275 4212 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.79 % Allowed : 10.23 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.28), residues: 913 helix: 2.20 (0.21), residues: 583 sheet: -0.66 (0.84), residues: 38 loop : -0.34 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 96 TYR 0.010 0.001 TYR K 262 PHE 0.009 0.001 PHE A 67 TRP 0.000 0.000 TRP K 349 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (14237) covalent geometry : angle 0.56747 / 0.33 (20457) hydrogen bonds : bond 0.03830 / 2.53 ( 808) hydrogen bonds : angle 3.00982 / 2.15 ( 2037) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8795 (ttpp) cc_final: 0.8575 (tttm) REVERT: C 95 LYS cc_start: 0.7692 (tttm) cc_final: 0.7178 (ttmt) REVERT: D 56 MET cc_start: 0.8723 (tpp) cc_final: 0.8466 (tpp) REVERT: F 90 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7857 (mt) REVERT: G 73 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8447 (t0) outliers start: 13 outliers final: 11 residues processed: 123 average time/residue: 0.1750 time to fit residues: 28.2888 Evaluate side-chains 130 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 214 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 101 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.219006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.129407 restraints weight = 14041.194| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.10 r_work: 0.2923 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14237 Z= 0.143 Angle : 0.555 7.059 20457 Z= 0.329 Chirality : 0.041 0.277 2313 Planarity : 0.004 0.036 1588 Dihedral : 30.693 177.027 4212 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.79 % Allowed : 10.23 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.28), residues: 913 helix: 2.25 (0.21), residues: 583 sheet: -0.59 (0.85), residues: 38 loop : -0.30 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 96 TYR 0.010 0.001 TYR G 57 PHE 0.007 0.001 PHE E 67 TRP 0.000 0.000 TRP K 349 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (14237) covalent geometry : angle 0.55536 / 0.33 (20457) hydrogen bonds : bond 0.03757 / 2.49 ( 808) hydrogen bonds : angle 2.97652 / 2.13 ( 2037) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8774 (ttpp) cc_final: 0.8550 (tttm) REVERT: C 95 LYS cc_start: 0.7703 (tttm) cc_final: 0.7183 (ttmt) REVERT: D 56 MET cc_start: 0.8744 (tpp) cc_final: 0.8492 (tpp) REVERT: F 90 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7857 (mt) REVERT: G 73 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8516 (t0) outliers start: 13 outliers final: 9 residues processed: 119 average time/residue: 0.1725 time to fit residues: 27.2566 Evaluate side-chains 121 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 214 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 84 optimal weight: 30.0000 chunk 18 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.212715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.123680 restraints weight = 14036.959| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.03 r_work: 0.2940 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14237 Z= 0.145 Angle : 0.574 15.980 20457 Z= 0.332 Chirality : 0.041 0.284 2313 Planarity : 0.004 0.036 1588 Dihedral : 30.675 176.724 4212 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.66 % Allowed : 10.74 % Favored : 87.60 % 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: 2.01 (0.28), residues: 913 helix: 2.25 (0.21), residues: 583 sheet: -0.51 (0.86), residues: 38 loop : -0.28 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 96 TYR 0.010 0.001 TYR G 57 PHE 0.008 0.001 PHE A 67 TRP 0.000 0.000 TRP K 349 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (14237) covalent geometry : angle 0.57355 / 0.33 (20457) hydrogen bonds : bond 0.03756 / 2.50 ( 808) hydrogen bonds : angle 2.99251 / 2.14 ( 2037) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7694 (tttm) cc_final: 0.7172 (ttmt) REVERT: D 56 MET cc_start: 0.8733 (tpp) cc_final: 0.8477 (tpp) REVERT: F 90 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7880 (mt) REVERT: G 73 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8506 (t0) outliers start: 12 outliers final: 10 residues processed: 122 average time/residue: 0.1747 time to fit residues: 27.9974 Evaluate side-chains 129 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 214 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 108 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 chunk 83 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.0070 chunk 42 optimal weight: 0.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.218870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.129153 restraints weight = 14127.970| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.07 r_work: 0.2958 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14237 Z= 0.129 Angle : 0.555 12.096 20457 Z= 0.327 Chirality : 0.040 0.274 2313 Planarity : 0.004 0.036 1588 Dihedral : 30.646 176.622 4212 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.53 % Allowed : 11.25 % Favored : 87.21 % 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: 2.06 (0.28), residues: 913 helix: 2.29 (0.21), residues: 583 sheet: -0.54 (0.86), residues: 38 loop : -0.26 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 96 TYR 0.011 0.001 TYR K 262 PHE 0.007 0.001 PHE A 67 TRP 0.000 0.000 TRP K 349 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.13 (14237) covalent geometry : angle 0.55512 / 0.33 (20457) hydrogen bonds : bond 0.03689 / 2.46 ( 808) hydrogen bonds : angle 2.94493 / 2.10 ( 2037) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7727 (tttm) cc_final: 0.7207 (ttmt) REVERT: D 34 TYR cc_start: 0.9240 (m-80) cc_final: 0.8792 (m-80) REVERT: D 56 MET cc_start: 0.8760 (tpp) cc_final: 0.8517 (tpp) REVERT: E 131 ARG cc_start: 0.8717 (mtp85) cc_final: 0.8486 (mtp85) REVERT: F 90 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7878 (mt) REVERT: G 73 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8517 (t0) outliers start: 11 outliers final: 9 residues processed: 116 average time/residue: 0.1769 time to fit residues: 27.0727 Evaluate side-chains 119 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 214 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 61 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.223476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135472 restraints weight = 14189.240| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.98 r_work: 0.2972 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14237 Z= 0.142 Angle : 0.554 12.062 20457 Z= 0.325 Chirality : 0.040 0.270 2313 Planarity : 0.004 0.036 1588 Dihedral : 30.646 176.205 4212 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.66 % Allowed : 11.13 % Favored : 87.21 % 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: 2.07 (0.28), residues: 913 helix: 2.29 (0.21), residues: 584 sheet: -0.51 (0.86), residues: 38 loop : -0.24 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 129 TYR 0.013 0.001 TYR K 262 PHE 0.009 0.001 PHE A 67 TRP 0.001 0.000 TRP K 349 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (14237) covalent geometry : angle 0.55358 / 0.33 (20457) hydrogen bonds : bond 0.03732 / 2.49 ( 808) hydrogen bonds : angle 2.94949 / 2.11 ( 2037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3759.93 seconds wall clock time: 64 minutes 58.40 seconds (3898.40 seconds total)