Starting phenix.real_space_refine on Mon Sep 23 23:05:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/09_2024/6y3y_10676.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/09_2024/6y3y_10676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/09_2024/6y3y_10676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/09_2024/6y3y_10676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/09_2024/6y3y_10676.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/09_2024/6y3y_10676.cif" } resolution = 3.39 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3778 2.51 5 N 886 2.21 5 O 1164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5854 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2707 Classifications: {'peptide': 332} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 316} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: G, H, J, B, I Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1 NAG A 406 " occ=0.81 ... (12 atoms not shown) pdb=" O7 NAG A 406 " occ=0.81 residue: pdb=" C1 NAG A 407 " occ=0.44 ... (12 atoms not shown) pdb=" O7 NAG A 407 " occ=0.44 residue: pdb=" C1 NAG B 406 " occ=0.81 ... (12 atoms not shown) pdb=" O7 NAG B 406 " occ=0.81 residue: pdb=" C1 NAG B 407 " occ=0.44 ... (12 atoms not shown) pdb=" O7 NAG B 407 " occ=0.44 Time building chain proxies: 5.29, per 1000 atoms: 0.90 Number of scatterers: 5854 At special positions: 0 Unit cell: (105.455, 73.255, 88.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1164 8.00 N 886 7.00 C 3778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 59 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 154 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 219 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 341 " distance=2.03 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 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA D 3 " - " MAN D 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 405 " - " ASN A 110 " " NAG A 406 " - " ASN A 145 " " NAG A 407 " - " ASN A 193 " " NAG B 405 " - " ASN B 110 " " NAG B 406 " - " ASN B 145 " " NAG B 407 " - " ASN B 193 " " NAG C 1 " - " ASN A 83 " " NAG D 1 " - " ASN A 286 " " NAG E 1 " - " ASN A 314 " " NAG F 1 " - " ASN A 328 " " NAG G 1 " - " ASN B 83 " " NAG H 1 " - " ASN B 286 " " NAG I 1 " - " ASN B 314 " " NAG J 1 " - " ASN B 328 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 771.7 milliseconds 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1260 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 17.2% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.738A pdb=" N ASP A 37 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 removed outlier: 3.518A pdb=" N LEU A 44 " --> pdb=" O ILE A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 113 through 132 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 310 through 313 removed outlier: 3.689A pdb=" N TYR A 313 " --> pdb=" O GLY A 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'B' and resid 33 through 37 removed outlier: 3.737A pdb=" N ASP B 37 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 44 removed outlier: 3.517A pdb=" N LEU B 44 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 Processing helix chain 'B' and resid 113 through 132 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 310 through 313 removed outlier: 3.689A pdb=" N TYR B 313 " --> pdb=" O GLY B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 8.627A pdb=" N SER A 65 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 30 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 29 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 91 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL A 259 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE A 93 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87 removed outlier: 8.426A pdb=" N LYS A 243 " --> pdb=" O PRO A 186 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 184 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 176 removed outlier: 3.733A pdb=" N VAL A 173 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 197 removed outlier: 4.276A pdb=" N VAL A 206 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY B 208 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY A 208 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL B 206 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 65 removed outlier: 8.627A pdb=" N SER B 65 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 30 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE B 29 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 91 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL B 259 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE B 93 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 removed outlier: 8.426A pdb=" N LYS B 243 " --> pdb=" O PRO B 186 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 184 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 165 through 168 Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 176 removed outlier: 3.732A pdb=" N VAL B 173 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 318 120 hydrogen bonds defined for protein. 312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 2.32 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: 1682 1.34 - 1.46: 1772 1.46 - 1.58: 2546 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 6028 Sorted by residual: bond pdb=" C PHE A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.20e+01 bond pdb=" C PHE B 108 " pdb=" N PRO B 109 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.20e+01 bond pdb=" C1 NAG B 405 " pdb=" O5 NAG B 405 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C1 NAG A 405 " pdb=" O5 NAG A 405 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.42e+00 ... (remaining 6023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 7885 2.41 - 4.81: 252 4.81 - 7.22: 51 7.22 - 9.63: 6 9.63 - 12.04: 4 Bond angle restraints: 8198 Sorted by residual: angle pdb=" C PHE A 108 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 119.84 131.88 -12.04 1.25e+00 6.40e-01 9.27e+01 angle pdb=" C PHE B 108 " pdb=" N PRO B 109 " pdb=" CA PRO B 109 " ideal model delta sigma weight residual 119.84 131.84 -12.00 1.25e+00 6.40e-01 9.22e+01 angle pdb=" CA PHE A 108 " pdb=" C PHE A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 118.56 125.78 -7.22 1.31e+00 5.83e-01 3.03e+01 angle pdb=" CA PHE B 108 " pdb=" C PHE B 108 " pdb=" N PRO B 109 " ideal model delta sigma weight residual 118.56 125.74 -7.18 1.31e+00 5.83e-01 3.00e+01 angle pdb=" CA PHE B 108 " pdb=" C PHE B 108 " pdb=" O PHE B 108 " ideal model delta sigma weight residual 119.22 114.87 4.35 1.02e+00 9.61e-01 1.82e+01 ... (remaining 8193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 3709 21.52 - 43.04: 132 43.04 - 64.56: 19 64.56 - 86.07: 38 86.07 - 107.59: 24 Dihedral angle restraints: 3922 sinusoidal: 1942 harmonic: 1980 Sorted by residual: dihedral pdb=" CA ASN A 168 " pdb=" C ASN A 168 " pdb=" N TYR A 169 " pdb=" CA TYR A 169 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ASN B 168 " pdb=" C ASN B 168 " pdb=" N TYR B 169 " pdb=" CA TYR B 169 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA SER A 147 " pdb=" C SER A 147 " pdb=" N LEU A 148 " pdb=" CA LEU A 148 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 3919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 780 0.076 - 0.152: 155 0.152 - 0.228: 17 0.228 - 0.305: 8 0.305 - 0.381: 4 Chirality restraints: 964 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 328 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG B 406 " pdb=" ND2 ASN B 145 " pdb=" C2 NAG B 406 " pdb=" O5 NAG B 406 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 961 not shown) Planarity restraints: 1006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 107 " 0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C CYS A 107 " -0.057 2.00e-02 2.50e+03 pdb=" O CYS A 107 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE A 108 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 107 " -0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C CYS B 107 " 0.057 2.00e-02 2.50e+03 pdb=" O CYS B 107 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE B 108 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 100 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO A 101 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.032 5.00e-02 4.00e+02 ... (remaining 1003 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 88 2.60 - 3.17: 4768 3.17 - 3.75: 9093 3.75 - 4.32: 13185 4.32 - 4.90: 21492 Nonbonded interactions: 48626 Sorted by model distance: nonbonded pdb=" SG CYS B 107 " pdb=" SG CYS B 154 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS B 277 " pdb=" SG CYS B 282 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 317 " pdb=" SG CYS B 341 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 38 " pdb=" SG CYS B 59 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 188 " pdb=" SG CYS B 219 " model vdw 2.030 3.760 ... (remaining 48621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } 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=0.44 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.680 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.169 6028 Z= 0.482 Angle : 1.042 12.036 8198 Z= 0.512 Chirality : 0.067 0.381 964 Planarity : 0.007 0.058 992 Dihedral : 17.088 107.593 2644 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 0.33 % Allowed : 4.89 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -4.44 (0.27), residues: 660 helix: -2.69 (0.36), residues: 102 sheet: -2.19 (0.39), residues: 172 loop : -3.54 (0.25), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 116 HIS 0.004 0.001 HIS B 40 PHE 0.026 0.003 PHE B 93 TYR 0.025 0.003 TYR B 128 ARG 0.004 0.001 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7764 (pp20) cc_final: 0.7501 (pp20) REVERT: A 155 LYS cc_start: 0.7031 (pmtt) cc_final: 0.5975 (tptt) REVERT: A 316 SER cc_start: 0.8801 (m) cc_final: 0.8558 (p) REVERT: B 95 GLU cc_start: 0.7764 (pp20) cc_final: 0.7478 (pp20) REVERT: B 155 LYS cc_start: 0.7056 (pmtt) cc_final: 0.6018 (tptt) REVERT: B 316 SER cc_start: 0.8775 (m) cc_final: 0.8527 (p) outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 0.2004 time to fit residues: 36.9753 Evaluate side-chains 83 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain B residue 108 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 98 ASN B 55 HIS B 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6028 Z= 0.227 Angle : 0.718 9.281 8198 Z= 0.352 Chirality : 0.054 0.486 964 Planarity : 0.005 0.040 992 Dihedral : 15.900 78.508 1434 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.44 % Allowed : 8.31 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -3.50 (0.30), residues: 660 helix: -1.24 (0.49), residues: 102 sheet: -1.84 (0.39), residues: 172 loop : -2.99 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 116 HIS 0.003 0.001 HIS B 40 PHE 0.016 0.002 PHE A 78 TYR 0.016 0.002 TYR A 102 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7993 (pp20) cc_final: 0.7748 (pp20) REVERT: A 197 TYR cc_start: 0.8556 (m-80) cc_final: 0.8078 (m-80) REVERT: A 316 SER cc_start: 0.8768 (m) cc_final: 0.8528 (p) REVERT: B 95 GLU cc_start: 0.7922 (pp20) cc_final: 0.7604 (pp20) REVERT: B 316 SER cc_start: 0.8810 (m) cc_final: 0.8524 (p) REVERT: B 341 CYS cc_start: 0.8389 (t) cc_final: 0.7967 (m) outliers start: 15 outliers final: 10 residues processed: 106 average time/residue: 0.1666 time to fit residues: 23.8468 Evaluate side-chains 89 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN B 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6028 Z= 0.249 Angle : 0.668 8.487 8198 Z= 0.324 Chirality : 0.052 0.450 964 Planarity : 0.005 0.037 992 Dihedral : 13.035 66.250 1434 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 2.61 % Allowed : 10.42 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.99 (0.31), residues: 660 helix: -0.48 (0.55), residues: 102 sheet: -1.68 (0.39), residues: 180 loop : -2.66 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.003 0.001 HIS A 299 PHE 0.017 0.002 PHE A 151 TYR 0.016 0.002 TYR B 197 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7973 (pp20) cc_final: 0.7677 (pp20) REVERT: A 197 TYR cc_start: 0.8589 (m-80) cc_final: 0.8144 (m-80) REVERT: A 316 SER cc_start: 0.8792 (m) cc_final: 0.8501 (p) REVERT: B 95 GLU cc_start: 0.7994 (pp20) cc_final: 0.7649 (pp20) REVERT: B 316 SER cc_start: 0.8804 (m) cc_final: 0.8471 (p) outliers start: 16 outliers final: 12 residues processed: 98 average time/residue: 0.1721 time to fit residues: 22.4495 Evaluate side-chains 89 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 277 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.0770 chunk 28 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6028 Z= 0.188 Angle : 0.618 8.800 8198 Z= 0.300 Chirality : 0.051 0.425 964 Planarity : 0.005 0.038 992 Dihedral : 9.959 54.976 1434 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.12 % Allowed : 12.54 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.73 (0.32), residues: 660 helix: -0.04 (0.56), residues: 102 sheet: -1.54 (0.39), residues: 180 loop : -2.56 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.002 0.001 HIS A 40 PHE 0.015 0.002 PHE B 151 TYR 0.013 0.001 TYR B 197 ARG 0.003 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8018 (pp20) cc_final: 0.7792 (pp20) REVERT: A 197 TYR cc_start: 0.8558 (m-80) cc_final: 0.8059 (m-80) REVERT: A 316 SER cc_start: 0.8779 (m) cc_final: 0.8475 (p) REVERT: B 95 GLU cc_start: 0.8015 (pp20) cc_final: 0.7747 (pp20) REVERT: B 316 SER cc_start: 0.8793 (m) cc_final: 0.8462 (p) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 0.1717 time to fit residues: 21.2784 Evaluate side-chains 79 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 182 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6028 Z= 0.227 Angle : 0.619 9.374 8198 Z= 0.302 Chirality : 0.050 0.403 964 Planarity : 0.004 0.037 992 Dihedral : 8.751 55.026 1434 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.77 % Allowed : 12.21 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.56 (0.32), residues: 660 helix: 0.12 (0.57), residues: 102 sheet: -1.37 (0.39), residues: 180 loop : -2.49 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.004 0.001 HIS A 299 PHE 0.014 0.002 PHE B 151 TYR 0.011 0.001 TYR B 169 ARG 0.002 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8034 (pp20) cc_final: 0.7757 (pp20) REVERT: A 197 TYR cc_start: 0.8569 (m-80) cc_final: 0.8140 (m-80) REVERT: A 316 SER cc_start: 0.8787 (m) cc_final: 0.8469 (p) REVERT: B 95 GLU cc_start: 0.8030 (pp20) cc_final: 0.7791 (pp20) REVERT: B 316 SER cc_start: 0.8762 (m) cc_final: 0.8435 (p) REVERT: B 341 CYS cc_start: 0.8408 (t) cc_final: 0.8020 (m) outliers start: 17 outliers final: 13 residues processed: 89 average time/residue: 0.1630 time to fit residues: 19.6639 Evaluate side-chains 82 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 242 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.0050 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 0.0170 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.3830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6028 Z= 0.161 Angle : 0.600 9.001 8198 Z= 0.292 Chirality : 0.049 0.400 964 Planarity : 0.004 0.041 992 Dihedral : 8.237 54.396 1434 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.12 % Allowed : 13.52 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.40 (0.32), residues: 660 helix: 0.20 (0.57), residues: 102 sheet: -1.25 (0.39), residues: 180 loop : -2.37 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.002 0.001 HIS B 23 PHE 0.015 0.001 PHE B 151 TYR 0.012 0.001 TYR B 197 ARG 0.002 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 TYR cc_start: 0.8522 (m-80) cc_final: 0.8062 (m-80) REVERT: A 316 SER cc_start: 0.8803 (m) cc_final: 0.8475 (p) REVERT: B 316 SER cc_start: 0.8800 (m) cc_final: 0.8458 (p) outliers start: 13 outliers final: 11 residues processed: 80 average time/residue: 0.1665 time to fit residues: 18.0515 Evaluate side-chains 77 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 182 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6028 Z= 0.216 Angle : 0.617 8.204 8198 Z= 0.301 Chirality : 0.049 0.394 964 Planarity : 0.004 0.040 992 Dihedral : 7.971 55.019 1434 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.44 % Allowed : 13.84 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.34 (0.32), residues: 660 helix: 0.28 (0.57), residues: 102 sheet: -1.22 (0.39), residues: 180 loop : -2.34 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.002 0.001 HIS A 23 PHE 0.016 0.002 PHE B 151 TYR 0.017 0.001 TYR A 295 ARG 0.003 0.000 ARG B 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7876 (pp20) cc_final: 0.7550 (pp20) REVERT: A 197 TYR cc_start: 0.8562 (m-80) cc_final: 0.8105 (m-80) REVERT: A 316 SER cc_start: 0.8787 (m) cc_final: 0.8455 (p) REVERT: B 95 GLU cc_start: 0.7857 (pp20) cc_final: 0.7535 (pp20) REVERT: B 316 SER cc_start: 0.8783 (m) cc_final: 0.8441 (p) REVERT: B 341 CYS cc_start: 0.8376 (t) cc_final: 0.7975 (m) outliers start: 15 outliers final: 12 residues processed: 84 average time/residue: 0.1617 time to fit residues: 18.6097 Evaluate side-chains 79 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 233 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 50 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 59 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6028 Z= 0.175 Angle : 0.607 7.875 8198 Z= 0.295 Chirality : 0.048 0.389 964 Planarity : 0.004 0.040 992 Dihedral : 7.687 55.093 1434 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.28 % Allowed : 14.33 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.28 (0.32), residues: 660 helix: 0.41 (0.57), residues: 100 sheet: -1.15 (0.39), residues: 180 loop : -2.33 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 HIS 0.002 0.001 HIS B 23 PHE 0.016 0.001 PHE B 151 TYR 0.016 0.001 TYR A 295 ARG 0.002 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7978 (pp20) cc_final: 0.7555 (pp20) REVERT: A 197 TYR cc_start: 0.8525 (m-80) cc_final: 0.8074 (m-80) REVERT: A 316 SER cc_start: 0.8806 (m) cc_final: 0.8459 (p) REVERT: B 95 GLU cc_start: 0.7949 (pp20) cc_final: 0.7544 (pp20) REVERT: B 316 SER cc_start: 0.8789 (m) cc_final: 0.8430 (p) outliers start: 14 outliers final: 12 residues processed: 82 average time/residue: 0.1646 time to fit residues: 18.4298 Evaluate side-chains 78 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 182 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 0.0270 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6028 Z= 0.180 Angle : 0.607 7.665 8198 Z= 0.296 Chirality : 0.048 0.384 964 Planarity : 0.004 0.039 992 Dihedral : 7.530 55.495 1434 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.61 % Allowed : 14.66 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.25 (0.32), residues: 660 helix: 0.49 (0.58), residues: 100 sheet: -1.07 (0.39), residues: 180 loop : -2.36 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 116 HIS 0.003 0.001 HIS A 77 PHE 0.017 0.002 PHE A 73 TYR 0.014 0.001 TYR A 295 ARG 0.002 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8012 (pp20) cc_final: 0.7587 (pp20) REVERT: A 197 TYR cc_start: 0.8537 (m-80) cc_final: 0.8097 (m-80) REVERT: A 262 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6460 (pmt100) REVERT: A 316 SER cc_start: 0.8807 (m) cc_final: 0.8454 (p) REVERT: B 95 GLU cc_start: 0.7992 (pp20) cc_final: 0.7586 (pp20) REVERT: B 262 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.6588 (pmt100) REVERT: B 316 SER cc_start: 0.8791 (m) cc_final: 0.8425 (p) outliers start: 16 outliers final: 13 residues processed: 84 average time/residue: 0.1862 time to fit residues: 20.6209 Evaluate side-chains 81 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 262 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6028 Z= 0.234 Angle : 0.625 8.509 8198 Z= 0.304 Chirality : 0.048 0.376 964 Planarity : 0.004 0.040 992 Dihedral : 7.492 56.228 1434 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.93 % Allowed : 14.82 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.27 (0.32), residues: 660 helix: 0.53 (0.58), residues: 100 sheet: -1.06 (0.39), residues: 180 loop : -2.41 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.003 0.001 HIS B 77 PHE 0.019 0.002 PHE B 151 TYR 0.017 0.001 TYR A 295 ARG 0.002 0.000 ARG B 267 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8038 (pp20) cc_final: 0.7575 (pp20) REVERT: A 197 TYR cc_start: 0.8551 (m-80) cc_final: 0.8071 (m-80) REVERT: A 262 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.6500 (pmt100) REVERT: A 316 SER cc_start: 0.8806 (m) cc_final: 0.8451 (p) REVERT: B 95 GLU cc_start: 0.8017 (pp20) cc_final: 0.7565 (pp20) REVERT: B 262 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.6672 (pmt100) REVERT: B 316 SER cc_start: 0.8797 (m) cc_final: 0.8429 (p) outliers start: 18 outliers final: 14 residues processed: 85 average time/residue: 0.1970 time to fit residues: 21.7370 Evaluate side-chains 82 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 262 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.123739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097187 restraints weight = 9129.471| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.04 r_work: 0.3185 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6028 Z= 0.220 Angle : 0.634 8.918 8198 Z= 0.305 Chirality : 0.048 0.368 964 Planarity : 0.004 0.040 992 Dihedral : 7.409 56.952 1434 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.61 % Allowed : 15.47 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.25 (0.32), residues: 660 helix: 0.58 (0.58), residues: 100 sheet: -1.08 (0.39), residues: 180 loop : -2.38 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 116 HIS 0.002 0.001 HIS B 23 PHE 0.018 0.002 PHE B 151 TYR 0.022 0.001 TYR A 295 ARG 0.002 0.000 ARG B 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1670.00 seconds wall clock time: 30 minutes 37.62 seconds (1837.62 seconds total)