Starting phenix.real_space_refine on Sun Jul 21 11:55:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpx_33385/07_2024/7xpx_33385.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpx_33385/07_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpx_33385/07_2024/7xpx_33385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpx_33385/07_2024/7xpx_33385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpx_33385/07_2024/7xpx_33385.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpx_33385/07_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 Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 8.14, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 7.35 Conformation dependent library (CDL) restraints added in 1.5 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: 5.85 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: 6.36 Time building geometry restraints manager: 7.41 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: 98.52 - 105.61: 1409 105.61 - 112.71: 7942 112.71 - 119.81: 4840 119.81 - 126.91: 5509 126.91 - 134.01: 757 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 2.440 nonbonded pdb=" O GLU K 208 " pdb=" OG SER K 212 " model vdw 2.219 2.440 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.227 2.520 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.268 2.440 nonbonded pdb=" OE2 GLU D 68 " pdb=" NH2 ARG H 76 " model vdw 2.270 2.520 ... (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 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 44.140 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.470 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.990 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: 0.3801 time to fit residues: 59.4748 Evaluate side-chains 114 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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: 0.5980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 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: 0.0670 chunk 104 optimal weight: 5.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14237 Z= 0.290 Angle : 0.599 6.983 20457 Z= 0.351 Chirality : 0.037 0.154 2313 Planarity : 0.005 0.042 1588 Dihedral : 30.700 177.578 4244 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.77 % Allowed : 5.50 % Favored : 93.73 % 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: 1.22 (0.27), residues: 913 helix: 1.65 (0.21), residues: 584 sheet: -0.89 (0.81), residues: 38 loop : -0.62 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 349 HIS 0.013 0.001 HIS C 31 PHE 0.009 0.002 PHE A 78 TYR 0.017 0.002 TYR K 277 ARG 0.004 0.000 ARG B 55 *********************** 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 120 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7490 (tm-30) REVERT: C 95 LYS cc_start: 0.7631 (tttm) cc_final: 0.7332 (ttmt) REVERT: D 56 MET cc_start: 0.8263 (tpp) cc_final: 0.8018 (tpp) REVERT: G 73 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8194 (t0) REVERT: G 75 LYS cc_start: 0.8313 (mmtt) cc_final: 0.8035 (mttm) outliers start: 6 outliers final: 3 residues processed: 114 average time/residue: 0.3749 time to fit residues: 56.5326 Evaluate side-chains 114 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN D 92 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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 : 0.005 0.052 14237 Z= 0.280 Angle : 0.564 6.124 20457 Z= 0.335 Chirality : 0.035 0.139 2313 Planarity : 0.004 0.037 1588 Dihedral : 30.352 177.425 4244 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.02 % Allowed : 8.70 % Favored : 90.28 % 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: 1.48 (0.27), residues: 913 helix: 1.85 (0.21), residues: 587 sheet: -0.76 (0.83), residues: 38 loop : -0.53 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.007 0.001 HIS C 31 PHE 0.011 0.002 PHE G 25 TYR 0.013 0.002 TYR K 262 ARG 0.006 0.000 ARG A 129 *********************** 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 131 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7605 (tttm) cc_final: 0.7316 (ttmt) REVERT: D 56 MET cc_start: 0.8280 (tpp) cc_final: 0.8051 (tpp) REVERT: G 73 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8220 (t0) REVERT: H 96 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.7387 (mtt-85) outliers start: 8 outliers final: 7 residues processed: 125 average time/residue: 0.3901 time to fit residues: 63.4592 Evaluate side-chains 129 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 99 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1497 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= 0.296 Angle : 0.556 6.340 20457 Z= 0.331 Chirality : 0.035 0.162 2313 Planarity : 0.004 0.035 1588 Dihedral : 30.294 179.690 4244 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.92 % Allowed : 9.21 % Favored : 88.87 % 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: 1.56 (0.27), residues: 913 helix: 1.91 (0.21), residues: 583 sheet: -0.72 (0.84), residues: 38 loop : -0.48 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.002 PHE A 67 TYR 0.012 0.001 TYR K 262 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 139 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7623 (tttm) cc_final: 0.7294 (ttmt) REVERT: D 56 MET cc_start: 0.8260 (tpp) cc_final: 0.8051 (tpp) REVERT: F 90 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8276 (mt) REVERT: G 73 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8239 (t0) REVERT: H 96 ARG cc_start: 0.7669 (mtt-85) cc_final: 0.7422 (mtt-85) outliers start: 14 outliers final: 7 residues processed: 128 average time/residue: 0.3716 time to fit residues: 62.3607 Evaluate side-chains 131 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 E residue 80 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 101 THR 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 63 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 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: 10.0000 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14237 Z= 0.280 Angle : 0.550 6.560 20457 Z= 0.327 Chirality : 0.035 0.163 2313 Planarity : 0.004 0.036 1588 Dihedral : 30.205 179.965 4244 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.79 % Allowed : 10.49 % 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: 1.66 (0.28), residues: 913 helix: 1.99 (0.21), residues: 583 sheet: -0.73 (0.86), residues: 38 loop : -0.46 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.006 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.011 0.001 TYR K 262 ARG 0.005 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 142 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7631 (tttm) cc_final: 0.7283 (ttmt) REVERT: D 56 MET cc_start: 0.8260 (tpp) cc_final: 0.8050 (tpp) REVERT: F 90 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8251 (mt) REVERT: G 73 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8234 (t0) REVERT: H 96 ARG cc_start: 0.7663 (mtt-85) cc_final: 0.7435 (mtt-85) outliers start: 13 outliers final: 10 residues processed: 133 average time/residue: 0.3914 time to fit residues: 68.0104 Evaluate side-chains 144 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 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 K residue 204 LYS Chi-restraints excluded: chain K residue 209 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 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: 0.7483 moved from start: 0.1794 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= 0.208 Angle : 0.536 6.602 20457 Z= 0.320 Chirality : 0.034 0.152 2313 Planarity : 0.004 0.036 1588 Dihedral : 30.184 179.956 4244 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.53 % Allowed : 11.00 % Favored : 87.47 % 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: 1.81 (0.28), residues: 913 helix: 2.12 (0.21), residues: 583 sheet: -0.71 (0.85), residues: 38 loop : -0.41 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 349 HIS 0.005 0.001 HIS B 75 PHE 0.010 0.001 PHE E 67 TYR 0.012 0.001 TYR K 262 ARG 0.007 0.000 ARG A 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 139 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7617 (tttm) cc_final: 0.7315 (ttmt) REVERT: E 129 ARG cc_start: 0.7832 (tpt90) cc_final: 0.7561 (tpt90) REVERT: F 90 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8238 (mt) REVERT: G 73 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8214 (t0) REVERT: H 96 ARG cc_start: 0.7657 (mtt-85) cc_final: 0.7414 (mtt-85) outliers start: 11 outliers final: 8 residues processed: 131 average time/residue: 0.3810 time to fit residues: 65.2341 Evaluate side-chains 136 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 90 LEU 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 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: 0.1980 chunk 93 optimal weight: 2.9990 chunk 110 optimal weight: 30.0000 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS B 93 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1892 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= 0.197 Angle : 0.528 6.515 20457 Z= 0.317 Chirality : 0.033 0.152 2313 Planarity : 0.004 0.036 1588 Dihedral : 30.123 179.799 4244 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.17 % Allowed : 11.00 % Favored : 86.83 % 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: 1.99 (0.28), residues: 913 helix: 2.29 (0.21), residues: 577 sheet: -0.67 (0.85), residues: 38 loop : -0.35 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 349 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.011 0.001 TYR K 262 ARG 0.009 0.000 ARG E 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 137 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7604 (tttm) cc_final: 0.7318 (ttmt) REVERT: F 90 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8237 (mt) REVERT: G 73 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8213 (t0) outliers start: 16 outliers final: 13 residues processed: 128 average time/residue: 0.3919 time to fit residues: 66.0221 Evaluate side-chains 136 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 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 H residue 98 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 209 LEU 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: 0.9990 chunk 21 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 87 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 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: 0.7470 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14237 Z= 0.211 Angle : 0.530 9.824 20457 Z= 0.317 Chirality : 0.033 0.154 2313 Planarity : 0.004 0.036 1588 Dihedral : 30.078 179.336 4244 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.30 % Allowed : 11.13 % 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: 2.05 (0.28), residues: 913 helix: 2.33 (0.21), residues: 577 sheet: -0.56 (0.85), residues: 38 loop : -0.32 (0.35), residues: 298 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 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 131 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7616 (tttm) cc_final: 0.7314 (ttmt) REVERT: F 90 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8263 (mt) REVERT: G 73 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8244 (t0) outliers start: 17 outliers final: 15 residues processed: 123 average time/residue: 0.3625 time to fit residues: 58.8319 Evaluate side-chains 131 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 24 ASP 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 E residue 80 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 98 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 209 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 30.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN K 310 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14237 Z= 0.331 Angle : 0.574 14.177 20457 Z= 0.333 Chirality : 0.036 0.175 2313 Planarity : 0.004 0.035 1588 Dihedral : 30.136 178.490 4244 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.17 % Allowed : 12.02 % Favored : 85.81 % 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: 1.76 (0.28), residues: 913 helix: 2.07 (0.21), residues: 577 sheet: -0.54 (0.85), residues: 38 loop : -0.38 (0.35), residues: 298 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 0.014 0.001 TYR K 262 ARG 0.007 0.000 ARG A 129 *********************** 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 149 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7615 (tttm) cc_final: 0.7297 (ttmt) REVERT: F 90 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8196 (mt) REVERT: G 73 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8278 (t0) outliers start: 16 outliers final: 14 residues processed: 141 average time/residue: 0.3658 time to fit residues: 68.0900 Evaluate side-chains 148 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 E residue 80 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 98 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 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: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 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: 0.7508 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14237 Z= 0.298 Angle : 0.555 8.807 20457 Z= 0.328 Chirality : 0.035 0.166 2313 Planarity : 0.004 0.037 1588 Dihedral : 30.097 178.756 4244 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.30 % Allowed : 11.76 % Favored : 85.93 % 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: 1.78 (0.28), residues: 913 helix: 2.09 (0.21), residues: 577 sheet: -0.49 (0.86), residues: 38 loop : -0.36 (0.35), residues: 298 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 0.015 0.001 TYR B 88 ARG 0.007 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 150 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7816 (tpt90) cc_final: 0.7487 (tpt90) REVERT: C 95 LYS cc_start: 0.7612 (tttm) cc_final: 0.7296 (ttmt) REVERT: E 129 ARG cc_start: 0.7953 (tpt90) cc_final: 0.7686 (tpt90) REVERT: F 90 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8234 (mt) REVERT: G 73 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8278 (t0) outliers start: 17 outliers final: 15 residues processed: 141 average time/residue: 0.3606 time to fit residues: 66.6717 Evaluate side-chains 149 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 24 ASP 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 E residue 80 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 98 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 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 = 0.4283 r_free = 0.4283 target = 0.218175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.130138 restraints weight = 13956.718| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.95 r_work: 0.2928 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2206 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= 0.202 Angle : 0.531 8.485 20457 Z= 0.316 Chirality : 0.033 0.147 2313 Planarity : 0.004 0.038 1588 Dihedral : 30.030 178.946 4244 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: 2.04 (0.28), residues: 913 helix: 2.31 (0.21), residues: 577 sheet: -0.44 (0.87), residues: 38 loop : -0.30 (0.35), residues: 298 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 0.010 0.001 PHE E 67 TYR 0.011 0.001 TYR G 39 ARG 0.007 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.35 seconds wall clock time: 48 minutes 6.96 seconds (2886.96 seconds total)