Starting phenix.real_space_refine on Mon Dec 30 23:50:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xpx_33385/12_2024/7xpx_33385.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xpx_33385/12_2024/7xpx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xpx_33385/12_2024/7xpx_33385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xpx_33385/12_2024/7xpx_33385.map" model { file = "/net/cci-nas-00/data/ceres_data/7xpx_33385/12_2024/7xpx_33385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xpx_33385/12_2024/7xpx_33385.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 8.82, per 1000 atoms: 0.66 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: 3.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 6.62 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: 6.55 Time building geometry restraints manager: 4.10 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=" C2 SAM K 401 " pdb=" N3 SAM K 401 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" C8 SAM K 401 " pdb=" N7 SAM K 401 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 6.92e+00 bond pdb=" CB ECX B 20 " pdb=" SC ECX B 20 " ideal model delta sigma weight residual 1.819 1.767 0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" C2 SAM K 401 " pdb=" N1 SAM K 401 " ideal model delta sigma weight residual 1.329 1.380 -0.051 2.00e-02 2.50e+03 6.51e+00 bond pdb=" CD ECX B 20 " pdb=" SC ECX B 20 " ideal model delta sigma weight residual 1.817 1.770 0.047 2.00e-02 2.50e+03 5.51e+00 ... (remaining 14232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 19986 1.82 - 3.63: 436 3.63 - 5.45: 27 5.45 - 7.26: 3 7.26 - 9.08: 5 Bond angle restraints: 20457 Sorted by residual: angle pdb=" C LYS D 28 " pdb=" CA LYS D 28 " pdb=" CB LYS D 28 " ideal model delta sigma weight residual 116.54 111.52 5.02 1.15e+00 7.56e-01 1.91e+01 angle pdb=" N LYS K 195 " pdb=" CA LYS K 195 " pdb=" C LYS K 195 " ideal model delta sigma weight residual 111.81 107.04 4.77 1.44e+00 4.82e-01 1.10e+01 angle pdb=" CB MET K 272 " pdb=" CG MET K 272 " pdb=" SD MET K 272 " ideal model delta sigma weight residual 112.70 103.62 9.08 3.00e+00 1.11e-01 9.15e+00 angle pdb=" O SAM K 401 " pdb=" C SAM K 401 " pdb=" OXT SAM K 401 " ideal model delta sigma weight residual 126.77 118.08 8.69 3.00e+00 1.11e-01 8.39e+00 angle pdb=" CA LYS D 28 " pdb=" C LYS D 28 " pdb=" N THR D 29 " ideal model delta sigma weight residual 119.52 117.25 2.27 7.90e-01 1.60e+00 8.27e+00 ... (remaining 20452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 6410 35.48 - 70.96: 1429 70.96 - 106.44: 12 106.44 - 141.92: 2 141.92 - 177.40: 3 Dihedral angle restraints: 7856 sinusoidal: 5144 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 7853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1725 0.037 - 0.073: 476 0.073 - 0.110: 83 0.110 - 0.147: 25 0.147 - 0.183: 4 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.550 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.004 0.058 14237 Z= 0.213 Angle : 0.612 9.076 20457 Z= 0.359 Chirality : 0.036 0.183 2313 Planarity : 0.005 0.052 1588 Dihedral : 27.533 177.402 6108 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.001 TRP K 349 HIS 0.007 0.001 HIS B 75 PHE 0.013 0.002 PHE G 25 TYR 0.019 0.002 TYR K 262 ARG 0.014 0.001 ARG K 189 *********************** 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 : 1.050 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: 0.3833 time to fit residues: 59.9642 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 : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 104 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN D 92 GLN E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14237 Z= 0.305 Angle : 0.590 6.290 20457 Z= 0.347 Chirality : 0.036 0.159 2313 Planarity : 0.004 0.037 1588 Dihedral : 30.520 178.184 4244 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.77 % Allowed : 6.52 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.27), residues: 913 helix: 1.72 (0.21), residues: 587 sheet: -0.77 (0.82), residues: 38 loop : -0.63 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 349 HIS 0.006 0.001 HIS C 31 PHE 0.010 0.002 PHE A 78 TYR 0.014 0.002 TYR K 262 ARG 0.005 0.001 ARG H 96 *********************** 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 131 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7496 (tm-30) REVERT: C 95 LYS cc_start: 0.7605 (tttm) cc_final: 0.7292 (ttmt) REVERT: D 56 MET cc_start: 0.8266 (tpp) cc_final: 0.8020 (tpp) REVERT: G 73 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8160 (t0) REVERT: G 75 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8107 (mttm) outliers start: 6 outliers final: 4 residues processed: 125 average time/residue: 0.4193 time to fit residues: 68.1000 Evaluate side-chains 127 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 58 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 24 GLN D 44 GLN D 81 ASN F 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1471 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= 0.334 Angle : 0.580 6.908 20457 Z= 0.342 Chirality : 0.036 0.162 2313 Planarity : 0.004 0.038 1588 Dihedral : 30.379 179.445 4244 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.53 % Allowed : 9.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.27), residues: 913 helix: 1.70 (0.21), residues: 587 sheet: -0.68 (0.82), residues: 38 loop : -0.64 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.002 PHE G 25 TYR 0.013 0.002 TYR B 51 ARG 0.007 0.000 ARG K 205 *********************** 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 134 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7473 (tm-30) REVERT: C 95 LYS cc_start: 0.7633 (tttm) cc_final: 0.7317 (ttmt) REVERT: D 56 MET cc_start: 0.8245 (tpp) cc_final: 0.8009 (tpp) REVERT: F 90 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8340 (mt) REVERT: G 73 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8214 (t0) REVERT: G 75 LYS cc_start: 0.8394 (mmtt) cc_final: 0.8189 (mttm) REVERT: H 96 ARG cc_start: 0.7714 (mtt-85) cc_final: 0.7439 (mtt-85) outliers start: 12 outliers final: 6 residues processed: 126 average time/residue: 0.4113 time to fit residues: 68.2042 Evaluate side-chains 128 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 99 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS B 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14237 Z= 0.313 Angle : 0.564 5.913 20457 Z= 0.335 Chirality : 0.036 0.149 2313 Planarity : 0.004 0.036 1588 Dihedral : 30.230 179.358 4244 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.66 % Allowed : 10.49 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 913 helix: 1.79 (0.21), residues: 587 sheet: -0.80 (0.81), residues: 38 loop : -0.57 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.004 0.001 HIS B 75 PHE 0.010 0.002 PHE A 67 TYR 0.011 0.001 TYR F 51 ARG 0.007 0.000 ARG C 35 *********************** 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 140 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7644 (tttm) cc_final: 0.7317 (ttmt) REVERT: D 56 MET cc_start: 0.8235 (tpp) cc_final: 0.8011 (tpp) REVERT: G 73 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8204 (t0) REVERT: G 75 LYS cc_start: 0.8470 (mmtt) cc_final: 0.8262 (mttm) REVERT: H 96 ARG cc_start: 0.7679 (mtt-85) cc_final: 0.7432 (mtt-85) outliers start: 12 outliers final: 9 residues processed: 130 average time/residue: 0.4429 time to fit residues: 73.0669 Evaluate side-chains 134 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN K 310 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14237 Z= 0.228 Angle : 0.540 6.320 20457 Z= 0.323 Chirality : 0.034 0.149 2313 Planarity : 0.004 0.036 1588 Dihedral : 30.159 179.364 4244 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.92 % Allowed : 10.36 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.27), residues: 913 helix: 1.98 (0.21), residues: 587 sheet: -0.86 (0.81), residues: 38 loop : -0.46 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR F 51 ARG 0.006 0.000 ARG A 129 *********************** 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 136 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7626 (tttm) cc_final: 0.7289 (ttmt) REVERT: F 90 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8248 (mt) REVERT: G 73 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8223 (t0) REVERT: H 96 ARG cc_start: 0.7667 (mtt-85) cc_final: 0.7415 (mtt-85) outliers start: 14 outliers final: 12 residues processed: 127 average time/residue: 0.4032 time to fit residues: 66.9771 Evaluate side-chains 136 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 62 ILE 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 197 GLU 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 100 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14237 Z= 0.212 Angle : 0.532 6.083 20457 Z= 0.318 Chirality : 0.034 0.155 2313 Planarity : 0.004 0.036 1588 Dihedral : 30.091 179.004 4244 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.17 % Allowed : 11.25 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.28), residues: 913 helix: 2.13 (0.21), residues: 584 sheet: -0.77 (0.81), residues: 38 loop : -0.40 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE A 67 TYR 0.009 0.001 TYR F 51 ARG 0.006 0.000 ARG E 129 *********************** 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 132 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.089 Fit side-chains REVERT: C 95 LYS cc_start: 0.7623 (tttm) cc_final: 0.7287 (ttmt) REVERT: F 90 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8241 (mt) REVERT: G 73 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8245 (t0) REVERT: K 214 LYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5126 (tttt) outliers start: 16 outliers final: 12 residues processed: 125 average time/residue: 0.3674 time to fit residues: 61.9702 Evaluate side-chains 130 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 58 THR 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 H residue 90 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 197 GLU 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 12 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 110 optimal weight: 30.0000 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14237 Z= 0.241 Angle : 0.535 6.329 20457 Z= 0.319 Chirality : 0.034 0.158 2313 Planarity : 0.004 0.037 1588 Dihedral : 30.085 178.531 4244 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.30 % Allowed : 11.38 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.27), residues: 913 helix: 2.11 (0.21), residues: 584 sheet: -0.71 (0.82), residues: 38 loop : -0.37 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.011 0.001 TYR G 57 ARG 0.005 0.000 ARG A 129 *********************** 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 141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7629 (tttm) cc_final: 0.7293 (ttmt) REVERT: F 90 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8236 (mt) REVERT: G 73 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8270 (t0) REVERT: K 214 LYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5009 (ttmt) outliers start: 17 outliers final: 13 residues processed: 132 average time/residue: 0.3831 time to fit residues: 66.8545 Evaluate side-chains 140 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE 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 H residue 98 LEU Chi-restraints excluded: chain K residue 197 GLU Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 204 LYS 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 66 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 87 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14237 Z= 0.220 Angle : 0.535 10.759 20457 Z= 0.318 Chirality : 0.034 0.152 2313 Planarity : 0.004 0.037 1588 Dihedral : 30.075 178.524 4244 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.43 % Allowed : 11.51 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.28), residues: 913 helix: 2.15 (0.21), residues: 584 sheet: -0.67 (0.82), residues: 38 loop : -0.34 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 349 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR G 57 ARG 0.006 0.000 ARG A 129 *********************** 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 141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7628 (tttm) cc_final: 0.7303 (ttmt) REVERT: F 90 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8240 (mt) REVERT: G 73 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8266 (t0) REVERT: K 214 LYS cc_start: 0.5974 (OUTLIER) cc_final: 0.5104 (tttt) outliers start: 18 outliers final: 15 residues processed: 132 average time/residue: 0.3738 time to fit residues: 64.8777 Evaluate side-chains 141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE 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 H residue 90 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 197 GLU Chi-restraints excluded: chain K residue 198 LEU 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 103 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14237 Z= 0.229 Angle : 0.535 8.425 20457 Z= 0.318 Chirality : 0.034 0.157 2313 Planarity : 0.004 0.048 1588 Dihedral : 30.054 178.408 4244 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.43 % Allowed : 11.51 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.27), residues: 913 helix: 2.14 (0.21), residues: 584 sheet: -0.63 (0.83), residues: 38 loop : -0.34 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.013 0.001 TYR G 39 ARG 0.008 0.000 ARG D 76 *********************** 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 142 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7618 (tttm) cc_final: 0.7300 (ttmt) REVERT: F 90 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8236 (mt) REVERT: G 73 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8292 (t0) REVERT: K 214 LYS cc_start: 0.5966 (OUTLIER) cc_final: 0.5093 (tttt) outliers start: 18 outliers final: 15 residues processed: 132 average time/residue: 0.3919 time to fit residues: 68.2492 Evaluate side-chains 142 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE 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 H residue 90 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 197 GLU Chi-restraints excluded: chain K residue 198 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 66 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14237 Z= 0.298 Angle : 0.554 8.371 20457 Z= 0.327 Chirality : 0.035 0.173 2313 Planarity : 0.004 0.038 1588 Dihedral : 30.117 177.825 4244 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.43 % Allowed : 11.51 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.27), residues: 913 helix: 2.02 (0.21), residues: 584 sheet: -0.63 (0.83), residues: 38 loop : -0.37 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE A 67 TYR 0.015 0.001 TYR G 39 ARG 0.009 0.000 ARG A 129 ********************** 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 160 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7868 (tpt90) cc_final: 0.7628 (tpt90) REVERT: C 95 LYS cc_start: 0.7645 (tttm) cc_final: 0.7330 (ttmt) REVERT: F 90 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8195 (mt) REVERT: G 73 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8233 (t0) outliers start: 18 outliers final: 15 residues processed: 151 average time/residue: 0.4090 time to fit residues: 80.3723 Evaluate side-chains 158 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE 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 H residue 90 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 197 GLU Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 204 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.221312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133508 restraints weight = 13944.260| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.95 r_work: 0.2946 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2477 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= 0.198 Angle : 0.537 12.375 20457 Z= 0.317 Chirality : 0.033 0.145 2313 Planarity : 0.004 0.045 1588 Dihedral : 29.983 178.223 4244 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.92 % Allowed : 13.17 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.27), residues: 913 helix: 2.22 (0.21), residues: 584 sheet: -0.83 (0.84), residues: 36 loop : -0.32 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.006 0.001 HIS K 317 PHE 0.008 0.001 PHE A 67 TYR 0.013 0.001 TYR G 39 ARG 0.009 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2506.98 seconds wall clock time: 47 minutes 11.22 seconds (2831.22 seconds total)