Starting phenix.real_space_refine on Wed Feb 12 19:33:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oqz_13035/02_2025/7oqz_13035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oqz_13035/02_2025/7oqz_13035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oqz_13035/02_2025/7oqz_13035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oqz_13035/02_2025/7oqz_13035.map" model { file = "/net/cci-nas-00/data/ceres_data/7oqz_13035/02_2025/7oqz_13035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oqz_13035/02_2025/7oqz_13035.cif" } resolution = 3.27 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= 0.002 sd= 0.037 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 52 5.16 5 C 5468 2.51 5 N 1196 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7996 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 5.34, per 1000 atoms: 0.67 Number of scatterers: 7996 At special positions: 0 Unit cell: (92.65, 92.65, 76.3, 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 52 16.00 P 8 15.00 O 1272 8.00 N 1196 7.00 C 5468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 814.3 milliseconds 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 84.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 3 through 34 Proline residue: A 10 - end of helix Processing helix chain 'A' and resid 42 through 69 removed outlier: 4.237A pdb=" N PHE A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 115 removed outlier: 4.063A pdb=" N HIS A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 141 removed outlier: 4.424A pdb=" N LYS A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 173 Processing helix chain 'A' and resid 176 through 202 Processing helix chain 'A' and resid 214 through 251 Processing helix chain 'B' and resid 4 through 34 Proline residue: B 10 - end of helix Processing helix chain 'B' and resid 42 through 69 removed outlier: 4.237A pdb=" N PHE B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 115 removed outlier: 4.063A pdb=" N HIS B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 141 removed outlier: 4.424A pdb=" N LYS B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 173 Processing helix chain 'B' and resid 176 through 202 Processing helix chain 'B' and resid 214 through 251 Processing helix chain 'C' and resid 4 through 34 Proline residue: C 10 - end of helix Processing helix chain 'C' and resid 42 through 69 removed outlier: 4.237A pdb=" N PHE C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 115 removed outlier: 4.063A pdb=" N HIS C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 141 removed outlier: 4.423A pdb=" N LYS C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 173 Processing helix chain 'C' and resid 176 through 202 Processing helix chain 'C' and resid 214 through 251 Processing helix chain 'D' and resid 4 through 34 Proline residue: D 10 - end of helix Processing helix chain 'D' and resid 42 through 69 removed outlier: 4.237A pdb=" N PHE D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 115 removed outlier: 4.063A pdb=" N HIS D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 141 removed outlier: 4.424A pdb=" N LYS D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 173 Processing helix chain 'D' and resid 176 through 202 Processing helix chain 'D' and resid 214 through 251 657 hydrogen bonds defined for protein. 1971 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: 2.07 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1104 1.31 - 1.43: 2440 1.43 - 1.56: 4461 1.56 - 1.68: 130 1.68 - 1.81: 81 Bond restraints: 8216 Sorted by residual: bond pdb=" C31 PC1 C 302 " pdb=" O31 PC1 C 302 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C31 PC1 A 301 " pdb=" O31 PC1 A 301 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C31 PC1 B 302 " pdb=" O31 PC1 B 302 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C31 PC1 C 303 " pdb=" O31 PC1 C 303 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C31 PC1 D 303 " pdb=" O31 PC1 D 303 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.94e+01 ... (remaining 8211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 10704 2.87 - 5.73: 324 5.73 - 8.60: 12 8.60 - 11.46: 20 11.46 - 14.33: 8 Bond angle restraints: 11068 Sorted by residual: angle pdb=" O12 PC1 D 303 " pdb=" P PC1 D 303 " pdb=" O14 PC1 D 303 " ideal model delta sigma weight residual 123.67 109.34 14.33 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 C 302 " pdb=" P PC1 C 302 " pdb=" O14 PC1 C 302 " ideal model delta sigma weight residual 123.67 109.35 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 A 302 " pdb=" P PC1 A 302 " pdb=" O14 PC1 A 302 " ideal model delta sigma weight residual 123.67 109.35 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 B 302 " pdb=" P PC1 B 302 " pdb=" O14 PC1 B 302 " ideal model delta sigma weight residual 123.67 109.36 14.31 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 A 301 " pdb=" P PC1 A 301 " pdb=" O14 PC1 A 301 " ideal model delta sigma weight residual 123.67 109.36 14.31 3.00e+00 1.11e-01 2.28e+01 ... (remaining 11063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 4169 14.33 - 28.65: 331 28.65 - 42.98: 96 42.98 - 57.31: 76 57.31 - 71.63: 32 Dihedral angle restraints: 4704 sinusoidal: 1996 harmonic: 2708 Sorted by residual: dihedral pdb=" N PHE A 194 " pdb=" CA PHE A 194 " pdb=" CB PHE A 194 " pdb=" CG PHE A 194 " ideal model delta sinusoidal sigma weight residual -60.00 -118.53 58.53 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N PHE B 194 " pdb=" CA PHE B 194 " pdb=" CB PHE B 194 " pdb=" CG PHE B 194 " ideal model delta sinusoidal sigma weight residual -60.00 -118.52 58.52 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N PHE D 194 " pdb=" CA PHE D 194 " pdb=" CB PHE D 194 " pdb=" CG PHE D 194 " ideal model delta sinusoidal sigma weight residual -60.00 -118.51 58.51 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 811 0.024 - 0.049: 253 0.049 - 0.073: 128 0.073 - 0.098: 20 0.098 - 0.122: 8 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CA ILE A 71 " pdb=" N ILE A 71 " pdb=" C ILE A 71 " pdb=" CB ILE A 71 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE D 71 " pdb=" N ILE D 71 " pdb=" C ILE D 71 " pdb=" CB ILE D 71 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 1217 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 130 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.44e+00 pdb=" C ALA A 130 " 0.021 2.00e-02 2.50e+03 pdb=" O ALA A 130 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU A 131 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 130 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.44e+00 pdb=" C ALA B 130 " 0.021 2.00e-02 2.50e+03 pdb=" O ALA B 130 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU B 131 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 130 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.43e+00 pdb=" C ALA D 130 " -0.021 2.00e-02 2.50e+03 pdb=" O ALA D 130 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU D 131 " 0.007 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1712 2.79 - 3.31: 8076 3.31 - 3.84: 12946 3.84 - 4.37: 13510 4.37 - 4.90: 25055 Nonbonded interactions: 61299 Sorted by model distance: nonbonded pdb=" O LEU D 125 " pdb=" OG SER D 128 " model vdw 2.257 3.040 nonbonded pdb=" O LEU B 125 " pdb=" OG SER B 128 " model vdw 2.257 3.040 nonbonded pdb=" O LEU C 125 " pdb=" OG SER C 128 " model vdw 2.257 3.040 nonbonded pdb=" O LEU A 125 " pdb=" OG SER A 128 " model vdw 2.257 3.040 nonbonded pdb=" NE1 TRP B 21 " pdb=" OE2 GLU B 53 " model vdw 2.342 3.120 ... (remaining 61294 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'B' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'C' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'D' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.780 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.009 0.109 8216 Z= 0.561 Angle : 0.981 14.327 11068 Z= 0.384 Chirality : 0.030 0.122 1220 Planarity : 0.003 0.019 1288 Dihedral : 14.990 71.632 2960 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.51 % Allowed : 3.06 % Favored : 96.43 % 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: 4.83 (0.27), residues: 932 helix: 3.85 (0.17), residues: 780 sheet: None (None), residues: 0 loop : -0.84 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 193 HIS 0.003 0.001 HIS A 153 PHE 0.007 0.001 PHE A 96 TYR 0.005 0.001 TYR A 229 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 377 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 PHE cc_start: 0.8707 (m-10) cc_final: 0.8269 (m-80) REVERT: A 146 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7623 (mp0) REVERT: A 147 MET cc_start: 0.8447 (ptp) cc_final: 0.8195 (ptt) REVERT: A 211 ASP cc_start: 0.8161 (t0) cc_final: 0.7945 (t0) REVERT: A 215 HIS cc_start: 0.8117 (m-70) cc_final: 0.7588 (m90) REVERT: A 217 ASN cc_start: 0.9221 (m-40) cc_final: 0.8955 (m110) REVERT: B 13 PHE cc_start: 0.8648 (m-10) cc_final: 0.8179 (m-80) REVERT: B 146 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7652 (mp0) REVERT: B 211 ASP cc_start: 0.8173 (t0) cc_final: 0.7937 (t0) REVERT: B 217 ASN cc_start: 0.9219 (m-40) cc_final: 0.8888 (m-40) REVERT: B 227 TRP cc_start: 0.8554 (m100) cc_final: 0.8313 (m100) REVERT: B 235 ILE cc_start: 0.9282 (mt) cc_final: 0.9052 (mt) REVERT: C 13 PHE cc_start: 0.8630 (m-10) cc_final: 0.8138 (m-80) REVERT: C 143 HIS cc_start: 0.7095 (t70) cc_final: 0.6689 (t-90) REVERT: C 146 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7613 (mp0) REVERT: C 211 ASP cc_start: 0.8080 (t0) cc_final: 0.7872 (t0) REVERT: C 217 ASN cc_start: 0.9158 (m-40) cc_final: 0.8836 (m-40) REVERT: C 227 TRP cc_start: 0.8446 (m100) cc_final: 0.8241 (m-10) REVERT: C 235 ILE cc_start: 0.9292 (mt) cc_final: 0.9010 (mt) REVERT: C 242 PHE cc_start: 0.8377 (t80) cc_final: 0.7865 (m-80) REVERT: D 13 PHE cc_start: 0.8523 (m-10) cc_final: 0.8010 (m-80) REVERT: D 146 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7523 (mp0) REVERT: D 149 ASP cc_start: 0.7346 (t70) cc_final: 0.7142 (t0) REVERT: D 217 ASN cc_start: 0.9131 (m-40) cc_final: 0.8868 (m-40) REVERT: D 229 TYR cc_start: 0.9124 (t80) cc_final: 0.8709 (t80) REVERT: D 235 ILE cc_start: 0.9312 (mt) cc_final: 0.9037 (mt) REVERT: D 238 MET cc_start: 0.8067 (mtp) cc_final: 0.7832 (mtp) REVERT: D 242 PHE cc_start: 0.8396 (t80) cc_final: 0.7896 (m-80) outliers start: 4 outliers final: 4 residues processed: 381 average time/residue: 0.1996 time to fit residues: 101.8289 Evaluate side-chains 224 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 220 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain D residue 194 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 83 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN B 3 ASN B 215 HIS C 34 GLN C 94 HIS D 34 GLN D 215 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.119016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088268 restraints weight = 16445.674| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.63 r_work: 0.3114 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8216 Z= 0.174 Angle : 0.530 11.763 11068 Z= 0.265 Chirality : 0.034 0.118 1220 Planarity : 0.003 0.025 1288 Dihedral : 16.695 86.510 1388 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.06 % Allowed : 14.80 % Favored : 82.14 % 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: 4.83 (0.26), residues: 932 helix: 3.83 (0.16), residues: 780 sheet: None (None), residues: 0 loop : -0.75 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.006 0.001 HIS B 215 PHE 0.021 0.001 PHE B 4 TYR 0.004 0.000 TYR D 229 ARG 0.006 0.001 ARG C 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8591 (mm-30) REVERT: A 124 LYS cc_start: 0.8323 (mmmt) cc_final: 0.8072 (mmmt) REVERT: A 147 MET cc_start: 0.8815 (ptp) cc_final: 0.8449 (ptt) REVERT: A 170 GLU cc_start: 0.9234 (tt0) cc_final: 0.8932 (tt0) REVERT: A 175 ASN cc_start: 0.8977 (m-40) cc_final: 0.8703 (p0) REVERT: A 211 ASP cc_start: 0.7954 (t0) cc_final: 0.7408 (t0) REVERT: A 217 ASN cc_start: 0.9307 (m-40) cc_final: 0.8987 (m-40) REVERT: A 227 TRP cc_start: 0.8852 (m100) cc_final: 0.8614 (m100) REVERT: B 50 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8610 (mm-30) REVERT: B 124 LYS cc_start: 0.8285 (mmmt) cc_final: 0.7966 (mmmt) REVERT: B 143 HIS cc_start: 0.7748 (t70) cc_final: 0.7507 (t70) REVERT: B 146 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8030 (mp0) REVERT: B 170 GLU cc_start: 0.9145 (tt0) cc_final: 0.8888 (tt0) REVERT: B 211 ASP cc_start: 0.8088 (t0) cc_final: 0.7468 (t0) REVERT: B 227 TRP cc_start: 0.8765 (m100) cc_final: 0.8508 (m100) REVERT: C 5 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8266 (ttm170) REVERT: C 53 GLU cc_start: 0.8941 (pt0) cc_final: 0.8503 (pt0) REVERT: C 124 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8099 (mmmt) REVERT: C 129 ASN cc_start: 0.9114 (t0) cc_final: 0.8907 (t0) REVERT: C 170 GLU cc_start: 0.9194 (tt0) cc_final: 0.8932 (tt0) REVERT: C 227 TRP cc_start: 0.8702 (m100) cc_final: 0.8437 (m-10) REVERT: C 235 ILE cc_start: 0.9141 (mt) cc_final: 0.8915 (mt) REVERT: D 124 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8202 (mmmt) REVERT: D 149 ASP cc_start: 0.7804 (t70) cc_final: 0.7560 (t0) REVERT: D 170 GLU cc_start: 0.9234 (tt0) cc_final: 0.9007 (tt0) REVERT: D 214 ASP cc_start: 0.6656 (t0) cc_final: 0.6339 (t0) REVERT: D 229 TYR cc_start: 0.9145 (t80) cc_final: 0.8941 (t80) REVERT: D 234 VAL cc_start: 0.9266 (t) cc_final: 0.9061 (p) REVERT: D 242 PHE cc_start: 0.8425 (t80) cc_final: 0.7802 (m-80) outliers start: 24 outliers final: 15 residues processed: 240 average time/residue: 0.2266 time to fit residues: 71.2146 Evaluate side-chains 218 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 0.0170 chunk 68 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 GLN ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.117118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.086721 restraints weight = 16589.496| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.61 r_work: 0.3051 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8216 Z= 0.181 Angle : 0.504 7.827 11068 Z= 0.260 Chirality : 0.035 0.135 1220 Planarity : 0.003 0.030 1288 Dihedral : 16.085 89.228 1388 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.21 % Allowed : 16.96 % Favored : 78.83 % 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: 4.73 (0.26), residues: 932 helix: 3.84 (0.16), residues: 768 sheet: None (None), residues: 0 loop : -0.87 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 193 HIS 0.004 0.001 HIS C 215 PHE 0.019 0.001 PHE B 13 TYR 0.004 0.000 TYR C 229 ARG 0.005 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.8440 (t80) cc_final: 0.8001 (t80) REVERT: A 50 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8707 (mm-30) REVERT: A 147 MET cc_start: 0.8700 (ptp) cc_final: 0.8466 (ptt) REVERT: A 174 ARG cc_start: 0.9013 (mmm-85) cc_final: 0.8737 (mmt90) REVERT: A 211 ASP cc_start: 0.7918 (t0) cc_final: 0.7205 (t0) REVERT: A 214 ASP cc_start: 0.6832 (t0) cc_final: 0.6125 (t0) REVERT: A 217 ASN cc_start: 0.9324 (m-40) cc_final: 0.8995 (m-40) REVERT: A 227 TRP cc_start: 0.8802 (m100) cc_final: 0.8561 (m100) REVERT: B 48 ARG cc_start: 0.8883 (mmm-85) cc_final: 0.8333 (mtm110) REVERT: B 49 LEU cc_start: 0.9366 (mt) cc_final: 0.9111 (mt) REVERT: B 50 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8692 (mm-30) REVERT: B 111 LEU cc_start: 0.8775 (mt) cc_final: 0.8512 (mp) REVERT: B 129 ASN cc_start: 0.9196 (t0) cc_final: 0.8946 (t0) REVERT: B 146 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7328 (mp0) REVERT: B 211 ASP cc_start: 0.7991 (t0) cc_final: 0.7322 (t0) REVERT: B 227 TRP cc_start: 0.8758 (m100) cc_final: 0.8412 (m-10) REVERT: C 50 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8663 (mm-30) REVERT: C 53 GLU cc_start: 0.8914 (pt0) cc_final: 0.8607 (pt0) REVERT: C 111 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8537 (mp) REVERT: C 129 ASN cc_start: 0.9152 (t0) cc_final: 0.8921 (t0) REVERT: C 146 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7156 (mp0) REVERT: C 227 TRP cc_start: 0.8723 (m100) cc_final: 0.8437 (m-10) REVERT: C 235 ILE cc_start: 0.9126 (mt) cc_final: 0.8893 (mt) REVERT: D 49 LEU cc_start: 0.9455 (mt) cc_final: 0.9137 (mt) REVERT: D 50 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8526 (mm-30) REVERT: D 111 LEU cc_start: 0.8863 (mt) cc_final: 0.8619 (mp) REVERT: D 149 ASP cc_start: 0.7990 (t70) cc_final: 0.7746 (t0) REVERT: D 214 ASP cc_start: 0.6743 (t0) cc_final: 0.6247 (t0) REVERT: D 220 PHE cc_start: 0.9003 (t80) cc_final: 0.8744 (t80) REVERT: D 242 PHE cc_start: 0.8418 (t80) cc_final: 0.7726 (m-80) outliers start: 33 outliers final: 18 residues processed: 235 average time/residue: 0.2076 time to fit residues: 65.0372 Evaluate side-chains 226 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS B 215 HIS C 143 HIS D 215 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.115917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.085742 restraints weight = 16571.025| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.50 r_work: 0.3071 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8216 Z= 0.222 Angle : 0.538 8.222 11068 Z= 0.282 Chirality : 0.035 0.138 1220 Planarity : 0.003 0.030 1288 Dihedral : 15.958 85.624 1388 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.99 % Allowed : 17.09 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.57 (0.27), residues: 932 helix: 3.70 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.76 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 193 HIS 0.005 0.001 HIS D 215 PHE 0.024 0.001 PHE B 242 TYR 0.004 0.001 TYR A 29 ARG 0.006 0.001 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.8596 (t80) cc_final: 0.8391 (t80) REVERT: A 49 LEU cc_start: 0.9466 (mt) cc_final: 0.9238 (mt) REVERT: A 50 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8736 (mm-30) REVERT: A 60 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8957 (ttm) REVERT: A 96 PHE cc_start: 0.9150 (t80) cc_final: 0.8876 (t80) REVERT: A 124 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8327 (mmmt) REVERT: A 143 HIS cc_start: 0.7475 (t70) cc_final: 0.6506 (t70) REVERT: A 146 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7423 (mp0) REVERT: A 147 MET cc_start: 0.8785 (ptp) cc_final: 0.8236 (ptt) REVERT: A 174 ARG cc_start: 0.9028 (mmm-85) cc_final: 0.8693 (mmt90) REVERT: A 211 ASP cc_start: 0.7978 (t0) cc_final: 0.7248 (t0) REVERT: A 214 ASP cc_start: 0.6944 (t0) cc_final: 0.6450 (t0) REVERT: A 217 ASN cc_start: 0.9312 (m-40) cc_final: 0.8946 (m-40) REVERT: B 48 ARG cc_start: 0.8998 (mmm-85) cc_final: 0.8515 (mtm110) REVERT: B 49 LEU cc_start: 0.9446 (mt) cc_final: 0.9217 (mt) REVERT: B 50 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8726 (mm-30) REVERT: B 60 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8962 (ttm) REVERT: B 111 LEU cc_start: 0.8830 (mt) cc_final: 0.8551 (mp) REVERT: B 211 ASP cc_start: 0.7963 (t0) cc_final: 0.7272 (t0) REVERT: B 214 ASP cc_start: 0.6770 (t0) cc_final: 0.6326 (t0) REVERT: B 215 HIS cc_start: 0.8577 (m170) cc_final: 0.7946 (m-70) REVERT: B 227 TRP cc_start: 0.8789 (m100) cc_final: 0.8425 (m-10) REVERT: C 50 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8728 (mm-30) REVERT: C 60 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8948 (ttm) REVERT: C 65 MET cc_start: 0.8503 (ttt) cc_final: 0.8268 (tpt) REVERT: C 111 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8592 (mp) REVERT: C 124 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8365 (mmmt) REVERT: C 129 ASN cc_start: 0.9248 (t0) cc_final: 0.9027 (t0) REVERT: C 211 ASP cc_start: 0.7923 (t0) cc_final: 0.7282 (t0) REVERT: C 214 ASP cc_start: 0.6764 (t0) cc_final: 0.5782 (t0) REVERT: C 217 ASN cc_start: 0.9291 (m-40) cc_final: 0.8988 (m-40) REVERT: C 227 TRP cc_start: 0.8793 (m100) cc_final: 0.8463 (m-10) REVERT: C 235 ILE cc_start: 0.9160 (mt) cc_final: 0.8897 (mt) REVERT: D 49 LEU cc_start: 0.9533 (mt) cc_final: 0.9247 (mt) REVERT: D 50 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8641 (mm-30) REVERT: D 60 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.9025 (ttm) REVERT: D 111 LEU cc_start: 0.8886 (mt) cc_final: 0.8637 (mp) REVERT: D 124 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8381 (mmmt) REVERT: D 146 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7942 (mp0) REVERT: D 149 ASP cc_start: 0.8081 (t70) cc_final: 0.7837 (t0) REVERT: D 229 TYR cc_start: 0.9276 (t80) cc_final: 0.8994 (t80) REVERT: D 242 PHE cc_start: 0.8403 (t80) cc_final: 0.7697 (m-80) outliers start: 47 outliers final: 29 residues processed: 242 average time/residue: 0.2011 time to fit residues: 65.1581 Evaluate side-chains 240 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 70 optimal weight: 0.7980 chunk 88 optimal weight: 0.0070 chunk 35 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS B 143 HIS D 196 GLN D 215 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.119832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.089415 restraints weight = 16201.983| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.51 r_work: 0.3111 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8216 Z= 0.165 Angle : 0.547 9.668 11068 Z= 0.279 Chirality : 0.036 0.157 1220 Planarity : 0.003 0.030 1288 Dihedral : 15.196 82.963 1388 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.97 % Allowed : 19.39 % Favored : 75.64 % 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: 4.41 (0.27), residues: 932 helix: 3.60 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.82 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 193 HIS 0.008 0.001 HIS B 143 PHE 0.025 0.001 PHE A 242 TYR 0.005 0.000 TYR C 229 ARG 0.006 0.001 ARG C 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8813 (mm-30) REVERT: A 60 MET cc_start: 0.9164 (ttm) cc_final: 0.8954 (ttm) REVERT: A 96 PHE cc_start: 0.9070 (t80) cc_final: 0.8834 (t80) REVERT: A 129 ASN cc_start: 0.9242 (t0) cc_final: 0.9005 (t0) REVERT: A 147 MET cc_start: 0.8709 (ptp) cc_final: 0.8425 (ptt) REVERT: A 211 ASP cc_start: 0.7792 (t0) cc_final: 0.6978 (t0) REVERT: A 214 ASP cc_start: 0.5903 (t0) cc_final: 0.5244 (t0) REVERT: A 216 GLU cc_start: 0.8164 (pm20) cc_final: 0.7469 (pm20) REVERT: A 227 TRP cc_start: 0.8759 (m100) cc_final: 0.8470 (m-10) REVERT: B 49 LEU cc_start: 0.9410 (mt) cc_final: 0.9175 (mt) REVERT: B 50 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8759 (mm-30) REVERT: B 111 LEU cc_start: 0.8779 (mt) cc_final: 0.8491 (mp) REVERT: B 124 LYS cc_start: 0.8367 (mmmt) cc_final: 0.8010 (mttm) REVERT: B 143 HIS cc_start: 0.7660 (t-90) cc_final: 0.7458 (t70) REVERT: B 214 ASP cc_start: 0.6589 (t0) cc_final: 0.6063 (t0) REVERT: B 221 LEU cc_start: 0.9495 (mt) cc_final: 0.9248 (mp) REVERT: B 227 TRP cc_start: 0.8744 (m100) cc_final: 0.8430 (m-10) REVERT: B 229 TYR cc_start: 0.9262 (t80) cc_final: 0.8923 (t80) REVERT: C 50 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8714 (mm-30) REVERT: C 111 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8508 (mp) REVERT: C 129 ASN cc_start: 0.9179 (t0) cc_final: 0.8929 (t0) REVERT: C 213 MET cc_start: 0.6757 (mmm) cc_final: 0.5796 (mmm) REVERT: C 214 ASP cc_start: 0.6893 (t0) cc_final: 0.6520 (t0) REVERT: C 227 TRP cc_start: 0.8766 (m100) cc_final: 0.8462 (m-10) REVERT: C 235 ILE cc_start: 0.9099 (mt) cc_final: 0.8848 (mt) REVERT: D 49 LEU cc_start: 0.9500 (mt) cc_final: 0.9244 (mt) REVERT: D 50 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8682 (mm-30) REVERT: D 111 LEU cc_start: 0.8792 (mt) cc_final: 0.8488 (mp) REVERT: D 149 ASP cc_start: 0.7929 (t70) cc_final: 0.7677 (t0) REVERT: D 216 GLU cc_start: 0.8123 (pm20) cc_final: 0.7832 (pm20) REVERT: D 229 TYR cc_start: 0.9183 (t80) cc_final: 0.8918 (t80) REVERT: D 242 PHE cc_start: 0.8385 (t80) cc_final: 0.7678 (m-80) outliers start: 39 outliers final: 27 residues processed: 243 average time/residue: 0.1988 time to fit residues: 65.2340 Evaluate side-chains 228 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 39 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS D 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.120033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089751 restraints weight = 16235.288| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.50 r_work: 0.3097 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8216 Z= 0.178 Angle : 0.555 16.095 11068 Z= 0.281 Chirality : 0.035 0.151 1220 Planarity : 0.003 0.030 1288 Dihedral : 14.413 80.785 1388 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.36 % Allowed : 19.77 % Favored : 74.87 % 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: 4.27 (0.27), residues: 932 helix: 3.44 (0.17), residues: 776 sheet: None (None), residues: 0 loop : -0.79 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 227 HIS 0.006 0.001 HIS D 215 PHE 0.030 0.001 PHE C 13 TYR 0.008 0.000 TYR A 240 ARG 0.006 0.001 ARG C 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8836 (mm-30) REVERT: A 96 PHE cc_start: 0.9080 (t80) cc_final: 0.8803 (t80) REVERT: A 124 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8063 (mtpp) REVERT: A 129 ASN cc_start: 0.9215 (t0) cc_final: 0.9000 (t0) REVERT: A 147 MET cc_start: 0.8503 (ptp) cc_final: 0.8117 (ptt) REVERT: A 213 MET cc_start: 0.7195 (mmm) cc_final: 0.6427 (mmm) REVERT: A 214 ASP cc_start: 0.6087 (t0) cc_final: 0.5578 (t0) REVERT: A 216 GLU cc_start: 0.8335 (pm20) cc_final: 0.7636 (pm20) REVERT: A 227 TRP cc_start: 0.8754 (m100) cc_final: 0.8531 (m-10) REVERT: B 50 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8828 (mm-30) REVERT: B 111 LEU cc_start: 0.8724 (mt) cc_final: 0.8435 (mp) REVERT: B 214 ASP cc_start: 0.6804 (t0) cc_final: 0.6246 (t0) REVERT: B 221 LEU cc_start: 0.9498 (mt) cc_final: 0.9285 (mp) REVERT: B 227 TRP cc_start: 0.8755 (m100) cc_final: 0.8436 (m-10) REVERT: B 229 TYR cc_start: 0.9265 (t80) cc_final: 0.9003 (t80) REVERT: C 50 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8719 (mm-30) REVERT: C 96 PHE cc_start: 0.9037 (t80) cc_final: 0.8787 (t80) REVERT: C 111 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8495 (mp) REVERT: C 124 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8243 (mmmt) REVERT: C 129 ASN cc_start: 0.9194 (t0) cc_final: 0.8943 (t0) REVERT: C 170 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8917 (tt0) REVERT: C 211 ASP cc_start: 0.7754 (t0) cc_final: 0.7033 (t0) REVERT: C 214 ASP cc_start: 0.6665 (t0) cc_final: 0.6125 (t0) REVERT: C 227 TRP cc_start: 0.8744 (m100) cc_final: 0.8449 (m-10) REVERT: C 235 ILE cc_start: 0.9122 (mt) cc_final: 0.8875 (mt) REVERT: D 49 LEU cc_start: 0.9531 (mt) cc_final: 0.9279 (mt) REVERT: D 50 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8685 (mm-30) REVERT: D 111 LEU cc_start: 0.8821 (mt) cc_final: 0.8518 (mp) REVERT: D 124 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8004 (mttm) REVERT: D 149 ASP cc_start: 0.7947 (t70) cc_final: 0.7688 (t0) REVERT: D 214 ASP cc_start: 0.6528 (t0) cc_final: 0.6325 (t0) REVERT: D 229 TYR cc_start: 0.9213 (t80) cc_final: 0.8973 (t80) REVERT: D 242 PHE cc_start: 0.8381 (t80) cc_final: 0.7669 (m-80) outliers start: 42 outliers final: 28 residues processed: 226 average time/residue: 0.1961 time to fit residues: 59.6832 Evaluate side-chains 230 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.119238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.088754 restraints weight = 16546.249| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.55 r_work: 0.3079 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8216 Z= 0.183 Angle : 0.572 15.982 11068 Z= 0.288 Chirality : 0.036 0.135 1220 Planarity : 0.003 0.030 1288 Dihedral : 14.041 79.761 1388 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 5.23 % Allowed : 19.77 % Favored : 75.00 % 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: 4.22 (0.27), residues: 932 helix: 3.41 (0.17), residues: 776 sheet: None (None), residues: 0 loop : -0.78 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 227 HIS 0.011 0.001 HIS C 143 PHE 0.028 0.001 PHE A 13 TYR 0.006 0.000 TYR A 240 ARG 0.007 0.001 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8874 (mm-30) REVERT: A 96 PHE cc_start: 0.9126 (t80) cc_final: 0.8859 (t80) REVERT: A 129 ASN cc_start: 0.9221 (t0) cc_final: 0.8998 (t0) REVERT: A 147 MET cc_start: 0.8581 (ptp) cc_final: 0.8173 (ptt) REVERT: A 213 MET cc_start: 0.7147 (mmm) cc_final: 0.6442 (mmm) REVERT: A 214 ASP cc_start: 0.6092 (t0) cc_final: 0.5681 (t0) REVERT: A 216 GLU cc_start: 0.8416 (pm20) cc_final: 0.7809 (pm20) REVERT: A 227 TRP cc_start: 0.8770 (m100) cc_final: 0.8555 (m-10) REVERT: B 50 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8927 (mm-30) REVERT: B 111 LEU cc_start: 0.8755 (mt) cc_final: 0.8458 (mp) REVERT: B 124 LYS cc_start: 0.8344 (mmmt) cc_final: 0.7950 (mttm) REVERT: B 213 MET cc_start: 0.7016 (mmm) cc_final: 0.4951 (mmm) REVERT: B 214 ASP cc_start: 0.6677 (t0) cc_final: 0.6008 (t0) REVERT: B 221 LEU cc_start: 0.9502 (mt) cc_final: 0.9285 (mp) REVERT: B 227 TRP cc_start: 0.8772 (m100) cc_final: 0.8449 (m-10) REVERT: B 229 TYR cc_start: 0.9279 (t80) cc_final: 0.9020 (t80) REVERT: C 49 LEU cc_start: 0.9456 (mt) cc_final: 0.9230 (mt) REVERT: C 50 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8860 (mm-30) REVERT: C 96 PHE cc_start: 0.9118 (t80) cc_final: 0.8786 (t80) REVERT: C 111 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8481 (mp) REVERT: C 129 ASN cc_start: 0.9237 (t0) cc_final: 0.8970 (t0) REVERT: C 211 ASP cc_start: 0.7757 (t0) cc_final: 0.7016 (t0) REVERT: C 214 ASP cc_start: 0.6702 (t0) cc_final: 0.6016 (t0) REVERT: C 227 TRP cc_start: 0.8765 (m100) cc_final: 0.8475 (m-10) REVERT: C 229 TYR cc_start: 0.9175 (t80) cc_final: 0.8970 (t80) REVERT: C 235 ILE cc_start: 0.9127 (mt) cc_final: 0.8887 (mt) REVERT: D 49 LEU cc_start: 0.9540 (mt) cc_final: 0.9318 (mt) REVERT: D 50 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8789 (mm-30) REVERT: D 111 LEU cc_start: 0.8838 (mt) cc_final: 0.8545 (mp) REVERT: D 124 LYS cc_start: 0.8479 (mmmt) cc_final: 0.7997 (mttm) REVERT: D 149 ASP cc_start: 0.7938 (t70) cc_final: 0.7686 (t0) REVERT: D 214 ASP cc_start: 0.6238 (t0) cc_final: 0.5047 (t0) REVERT: D 217 ASN cc_start: 0.9215 (m-40) cc_final: 0.8795 (m-40) REVERT: D 221 LEU cc_start: 0.9540 (mt) cc_final: 0.9280 (mp) REVERT: D 229 TYR cc_start: 0.9233 (t80) cc_final: 0.8970 (t80) REVERT: D 242 PHE cc_start: 0.8375 (t80) cc_final: 0.7660 (m-80) outliers start: 41 outliers final: 32 residues processed: 230 average time/residue: 0.2047 time to fit residues: 64.1782 Evaluate side-chains 239 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 3 ASN Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 44 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.117455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.087359 restraints weight = 16581.768| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.58 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8216 Z= 0.215 Angle : 0.601 15.855 11068 Z= 0.305 Chirality : 0.037 0.199 1220 Planarity : 0.003 0.031 1288 Dihedral : 14.053 78.113 1388 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.10 % Allowed : 20.54 % Favored : 74.36 % 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: 4.13 (0.27), residues: 932 helix: 3.38 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.78 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 227 HIS 0.009 0.001 HIS C 143 PHE 0.029 0.001 PHE A 242 TYR 0.005 0.000 TYR A 229 ARG 0.007 0.001 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8822 (mm-30) REVERT: A 96 PHE cc_start: 0.9214 (t80) cc_final: 0.8790 (t80) REVERT: A 129 ASN cc_start: 0.9228 (t0) cc_final: 0.8994 (t0) REVERT: A 147 MET cc_start: 0.8361 (ptp) cc_final: 0.7851 (ptt) REVERT: A 170 GLU cc_start: 0.9033 (tt0) cc_final: 0.8586 (tt0) REVERT: A 213 MET cc_start: 0.7459 (mmm) cc_final: 0.6644 (mmm) REVERT: A 214 ASP cc_start: 0.6569 (t0) cc_final: 0.5870 (t0) REVERT: A 215 HIS cc_start: 0.8247 (m-70) cc_final: 0.7977 (m90) REVERT: A 227 TRP cc_start: 0.8685 (m100) cc_final: 0.8461 (m-10) REVERT: B 50 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8866 (mm-30) REVERT: B 111 LEU cc_start: 0.8900 (mt) cc_final: 0.8628 (mp) REVERT: B 214 ASP cc_start: 0.7057 (t0) cc_final: 0.6500 (t0) REVERT: B 221 LEU cc_start: 0.9502 (mt) cc_final: 0.9284 (mp) REVERT: B 227 TRP cc_start: 0.8638 (m100) cc_final: 0.8332 (m-10) REVERT: C 96 PHE cc_start: 0.9239 (t80) cc_final: 0.8786 (t80) REVERT: C 111 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8621 (mp) REVERT: C 124 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8142 (mmmt) REVERT: C 170 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8667 (tt0) REVERT: C 214 ASP cc_start: 0.7073 (t0) cc_final: 0.6551 (t0) REVERT: C 227 TRP cc_start: 0.8611 (m100) cc_final: 0.8349 (m-10) REVERT: C 235 ILE cc_start: 0.9157 (mt) cc_final: 0.8878 (mt) REVERT: D 50 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8747 (mm-30) REVERT: D 111 LEU cc_start: 0.8913 (mt) cc_final: 0.8627 (mp) REVERT: D 149 ASP cc_start: 0.7950 (t70) cc_final: 0.7696 (t0) REVERT: D 214 ASP cc_start: 0.6465 (t0) cc_final: 0.5950 (t0) REVERT: D 221 LEU cc_start: 0.9537 (mt) cc_final: 0.9303 (mp) REVERT: D 242 PHE cc_start: 0.8343 (t80) cc_final: 0.7686 (m-80) outliers start: 40 outliers final: 30 residues processed: 226 average time/residue: 0.2021 time to fit residues: 61.2528 Evaluate side-chains 231 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 86 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 HIS D 3 ASN ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.119643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.089314 restraints weight = 16782.505| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.71 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8216 Z= 0.189 Angle : 0.618 16.031 11068 Z= 0.308 Chirality : 0.037 0.194 1220 Planarity : 0.003 0.030 1288 Dihedral : 13.671 77.849 1388 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.95 % Allowed : 21.43 % Favored : 74.62 % 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: 4.05 (0.27), residues: 932 helix: 3.34 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.87 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 227 HIS 0.009 0.001 HIS C 143 PHE 0.038 0.001 PHE D 13 TYR 0.016 0.001 TYR A 229 ARG 0.007 0.001 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.8354 (t80) cc_final: 0.8062 (t80) REVERT: A 50 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8861 (mm-30) REVERT: A 96 PHE cc_start: 0.9256 (t80) cc_final: 0.8734 (t80) REVERT: A 124 LYS cc_start: 0.8364 (mmmt) cc_final: 0.7904 (mtpp) REVERT: A 214 ASP cc_start: 0.7073 (t0) cc_final: 0.6524 (t0) REVERT: A 227 TRP cc_start: 0.8644 (m100) cc_final: 0.8415 (m-10) REVERT: B 50 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8802 (mm-30) REVERT: B 111 LEU cc_start: 0.8798 (mt) cc_final: 0.8509 (mp) REVERT: B 124 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7676 (mttm) REVERT: B 214 ASP cc_start: 0.7369 (t0) cc_final: 0.6770 (t0) REVERT: B 221 LEU cc_start: 0.9471 (mt) cc_final: 0.9241 (mp) REVERT: B 227 TRP cc_start: 0.8607 (m100) cc_final: 0.8285 (m-10) REVERT: C 96 PHE cc_start: 0.9231 (t80) cc_final: 0.8714 (t80) REVERT: C 111 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8461 (mp) REVERT: C 124 LYS cc_start: 0.8335 (mmmt) cc_final: 0.8114 (mmmt) REVERT: C 211 ASP cc_start: 0.8052 (t0) cc_final: 0.7300 (t0) REVERT: C 214 ASP cc_start: 0.7053 (t0) cc_final: 0.6456 (t0) REVERT: C 227 TRP cc_start: 0.8587 (m100) cc_final: 0.8348 (m-10) REVERT: C 235 ILE cc_start: 0.9126 (mt) cc_final: 0.8875 (mt) REVERT: D 50 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8799 (mm-30) REVERT: D 65 MET cc_start: 0.7929 (mmm) cc_final: 0.7260 (tpt) REVERT: D 111 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8567 (mp) REVERT: D 149 ASP cc_start: 0.7907 (t70) cc_final: 0.7665 (t0) REVERT: D 214 ASP cc_start: 0.6450 (t0) cc_final: 0.5966 (t0) REVERT: D 221 LEU cc_start: 0.9503 (mt) cc_final: 0.9254 (mp) REVERT: D 242 PHE cc_start: 0.8319 (t80) cc_final: 0.7665 (m-80) outliers start: 31 outliers final: 29 residues processed: 229 average time/residue: 0.2054 time to fit residues: 63.3000 Evaluate side-chains 232 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 215 HIS B 129 ASN ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.113864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.082544 restraints weight = 16737.896| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.65 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8216 Z= 0.289 Angle : 0.681 15.581 11068 Z= 0.345 Chirality : 0.038 0.139 1220 Planarity : 0.003 0.031 1288 Dihedral : 14.309 75.111 1388 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.57 % Allowed : 22.58 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.27), residues: 932 helix: 3.30 (0.17), residues: 764 sheet: None (None), residues: 0 loop : -0.94 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 227 HIS 0.008 0.001 HIS C 143 PHE 0.049 0.002 PHE A 13 TYR 0.011 0.001 TYR A 229 ARG 0.007 0.001 ARG D 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.8454 (t80) cc_final: 0.8009 (t80) REVERT: A 50 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8887 (mm-30) REVERT: A 96 PHE cc_start: 0.9243 (t80) cc_final: 0.8760 (t80) REVERT: A 214 ASP cc_start: 0.7393 (t0) cc_final: 0.6788 (t0) REVERT: A 227 TRP cc_start: 0.8806 (m100) cc_final: 0.8481 (m-10) REVERT: B 50 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8857 (mm-30) REVERT: B 111 LEU cc_start: 0.8908 (mt) cc_final: 0.8639 (mp) REVERT: B 214 ASP cc_start: 0.7568 (t0) cc_final: 0.7109 (t0) REVERT: B 227 TRP cc_start: 0.8688 (m100) cc_final: 0.8404 (m-10) REVERT: B 229 TYR cc_start: 0.9260 (t80) cc_final: 0.8879 (t80) REVERT: C 96 PHE cc_start: 0.9263 (t80) cc_final: 0.8796 (t80) REVERT: C 111 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8668 (mp) REVERT: C 124 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8287 (mmmt) REVERT: C 170 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8627 (tt0) REVERT: C 214 ASP cc_start: 0.6986 (t0) cc_final: 0.5665 (t0) REVERT: C 217 ASN cc_start: 0.9245 (m-40) cc_final: 0.8933 (m-40) REVERT: C 227 TRP cc_start: 0.8746 (m100) cc_final: 0.8490 (m-10) REVERT: C 235 ILE cc_start: 0.9155 (mt) cc_final: 0.8883 (mt) REVERT: D 111 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8692 (mp) REVERT: D 124 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7602 (mttm) REVERT: D 149 ASP cc_start: 0.8113 (t70) cc_final: 0.7854 (t0) REVERT: D 214 ASP cc_start: 0.6829 (t0) cc_final: 0.6342 (t0) REVERT: D 242 PHE cc_start: 0.8363 (t80) cc_final: 0.7681 (m-80) outliers start: 28 outliers final: 23 residues processed: 222 average time/residue: 0.2026 time to fit residues: 60.1873 Evaluate side-chains 218 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 69 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS B 129 ASN B 215 HIS D 129 ASN ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.115134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.084199 restraints weight = 16756.509| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.67 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8216 Z= 0.248 Angle : 0.713 15.849 11068 Z= 0.357 Chirality : 0.038 0.139 1220 Planarity : 0.003 0.031 1288 Dihedral : 14.182 72.314 1388 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.95 % Allowed : 23.34 % Favored : 72.70 % 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: 3.94 (0.27), residues: 932 helix: 3.29 (0.17), residues: 764 sheet: None (None), residues: 0 loop : -0.97 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 227 HIS 0.009 0.001 HIS C 143 PHE 0.044 0.001 PHE A 13 TYR 0.014 0.001 TYR A 229 ARG 0.007 0.001 ARG B 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.47 seconds wall clock time: 62 minutes 23.12 seconds (3743.12 seconds total)