Starting phenix.real_space_refine on Wed Mar 12 20:20:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oqz_13035/03_2025/7oqz_13035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oqz_13035/03_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_13035/03_2025/7oqz_13035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oqz_13035/03_2025/7oqz_13035.map" model { file = "/net/cci-nas-00/data/ceres_data/7oqz_13035/03_2025/7oqz_13035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oqz_13035/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.41, per 1000 atoms: 0.68 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 837.2 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: 0.64 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: 2.15 Time building geometry restraints manager: 2.54 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.530 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.020 ------------------------------------------------------------------------------- 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 : 0.927 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: 0.1921 time to fit residues: 98.0105 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 : 0.884 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088269 restraints weight = 16445.674| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.64 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 : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8590 (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: 0.7407 (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: 0.8613 (m100) REVERT: B 50 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8611 (mm-30) REVERT: B 124 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7968 (mmmt) REVERT: B 143 HIS cc_start: 0.7749 (t70) cc_final: 0.7507 (t70) REVERT: B 146 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8029 (mp0) REVERT: B 170 GLU cc_start: 0.9146 (tt0) cc_final: 0.8890 (tt0) REVERT: B 211 ASP cc_start: 0.8087 (t0) cc_final: 0.7467 (t0) REVERT: B 227 TRP cc_start: 0.8765 (m100) cc_final: 0.8508 (m100) REVERT: C 5 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8265 (ttm170) REVERT: C 53 GLU cc_start: 0.8941 (pt0) cc_final: 0.8503 (pt0) REVERT: C 124 LYS cc_start: 0.8400 (mmmt) cc_final: 0.8099 (mmmt) REVERT: C 129 ASN cc_start: 0.9113 (t0) cc_final: 0.8906 (t0) REVERT: C 170 GLU cc_start: 0.9195 (tt0) cc_final: 0.8934 (tt0) REVERT: C 227 TRP cc_start: 0.8701 (m100) cc_final: 0.8437 (m-10) REVERT: C 235 ILE cc_start: 0.9140 (mt) cc_final: 0.8914 (mt) REVERT: D 124 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8203 (mmmt) REVERT: D 149 ASP cc_start: 0.7803 (t70) cc_final: 0.7559 (t0) REVERT: D 170 GLU cc_start: 0.9235 (tt0) cc_final: 0.9009 (tt0) REVERT: D 214 ASP cc_start: 0.6657 (t0) cc_final: 0.6340 (t0) REVERT: D 229 TYR cc_start: 0.9146 (t80) cc_final: 0.8941 (t80) REVERT: D 234 VAL cc_start: 0.9266 (t) cc_final: 0.9060 (p) REVERT: D 242 PHE cc_start: 0.8424 (t80) cc_final: 0.7802 (m-80) outliers start: 24 outliers final: 15 residues processed: 240 average time/residue: 0.2617 time to fit residues: 82.2982 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 : 0.890 ------------------------------------------------------------------------------- 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: 0.8980 chunk 77 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 0.0170 chunk 68 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7618 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.117972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.087554 restraints weight = 16576.247| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.62 r_work: 0.3068 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2828 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= 0.171 Angle : 0.500 7.932 11068 Z= 0.258 Chirality : 0.035 0.138 1220 Planarity : 0.003 0.031 1288 Dihedral : 16.042 88.642 1388 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.08 % Allowed : 16.84 % Favored : 79.08 % 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: 4.75 (0.26), residues: 932 helix: 3.81 (0.16), residues: 776 sheet: None (None), residues: 0 loop : -0.88 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 193 HIS 0.004 0.001 HIS C 215 PHE 0.017 0.001 PHE B 13 TYR 0.004 0.000 TYR C 229 ARG 0.005 0.001 ARG B 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 245 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.8418 (t80) cc_final: 0.7933 (t80) REVERT: A 48 ARG cc_start: 0.8864 (mmm-85) cc_final: 0.8428 (mtm110) REVERT: A 50 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8700 (mm-30) REVERT: A 147 MET cc_start: 0.8680 (ptp) cc_final: 0.8477 (ptt) REVERT: A 175 ASN cc_start: 0.9037 (m-40) cc_final: 0.8727 (p0) REVERT: A 214 ASP cc_start: 0.6804 (t0) cc_final: 0.6143 (t0) REVERT: A 217 ASN cc_start: 0.9324 (m-40) cc_final: 0.8993 (m-40) REVERT: A 227 TRP cc_start: 0.8815 (m100) cc_final: 0.8573 (m100) REVERT: B 48 ARG cc_start: 0.8879 (mmm-85) cc_final: 0.8331 (mtm110) REVERT: B 49 LEU cc_start: 0.9351 (mt) cc_final: 0.9096 (mt) REVERT: B 50 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8682 (mm-30) REVERT: B 111 LEU cc_start: 0.8743 (mt) cc_final: 0.8474 (mp) REVERT: B 129 ASN cc_start: 0.9192 (t0) cc_final: 0.8989 (t0) REVERT: B 146 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7311 (mp0) REVERT: B 211 ASP cc_start: 0.7864 (t0) cc_final: 0.7173 (t0) REVERT: B 215 HIS cc_start: 0.8601 (m-70) cc_final: 0.8113 (m-70) REVERT: B 227 TRP cc_start: 0.8743 (m100) cc_final: 0.8407 (m-10) REVERT: C 50 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8653 (mm-30) REVERT: C 53 GLU cc_start: 0.8904 (pt0) cc_final: 0.8594 (pt0) REVERT: C 111 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8516 (mp) REVERT: C 129 ASN cc_start: 0.9132 (t0) cc_final: 0.8907 (t0) REVERT: C 227 TRP cc_start: 0.8705 (m100) cc_final: 0.8425 (m-10) REVERT: C 235 ILE cc_start: 0.9115 (mt) cc_final: 0.8883 (mt) REVERT: D 49 LEU cc_start: 0.9450 (mt) cc_final: 0.9129 (mt) REVERT: D 50 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8506 (mm-30) REVERT: D 111 LEU cc_start: 0.8845 (mt) cc_final: 0.8599 (mp) REVERT: D 124 LYS cc_start: 0.8554 (mmmt) cc_final: 0.8101 (mmmt) REVERT: D 149 ASP cc_start: 0.7943 (t70) cc_final: 0.7702 (t0) REVERT: D 170 GLU cc_start: 0.9228 (tt0) cc_final: 0.8938 (tt0) REVERT: D 214 ASP cc_start: 0.6621 (t0) cc_final: 0.6187 (t0) REVERT: D 220 PHE cc_start: 0.9000 (t80) cc_final: 0.8730 (t80) REVERT: D 242 PHE cc_start: 0.8412 (t80) cc_final: 0.7721 (m-80) outliers start: 32 outliers final: 16 residues processed: 232 average time/residue: 0.1964 time to fit residues: 61.4755 Evaluate side-chains 223 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 31 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS C 143 HIS D 215 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.115352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.085380 restraints weight = 16573.521| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.48 r_work: 0.3055 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8216 Z= 0.242 Angle : 0.545 8.029 11068 Z= 0.286 Chirality : 0.035 0.142 1220 Planarity : 0.003 0.029 1288 Dihedral : 16.009 85.179 1388 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.87 % Allowed : 17.35 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.54 (0.27), residues: 932 helix: 3.68 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.77 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 193 HIS 0.006 0.001 HIS D 215 PHE 0.025 0.001 PHE B 242 TYR 0.005 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 260 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9473 (mt) cc_final: 0.9247 (mt) REVERT: A 50 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8759 (mm-30) REVERT: A 60 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8974 (ttm) REVERT: A 124 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8360 (mmmt) REVERT: A 129 ASN cc_start: 0.9453 (t0) cc_final: 0.9239 (t0) REVERT: A 146 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7306 (mp0) REVERT: A 147 MET cc_start: 0.8744 (ptp) cc_final: 0.8317 (ptt) REVERT: A 174 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8740 (mmt90) REVERT: A 214 ASP cc_start: 0.7068 (t0) cc_final: 0.6581 (t0) REVERT: A 217 ASN cc_start: 0.9320 (m-40) cc_final: 0.8976 (m-40) REVERT: B 48 ARG cc_start: 0.9009 (mmm-85) cc_final: 0.8520 (mtm110) REVERT: B 50 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8799 (mm-30) REVERT: B 60 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8940 (ttm) REVERT: B 111 LEU cc_start: 0.8809 (mt) cc_final: 0.8535 (mp) REVERT: B 124 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8263 (mmmt) REVERT: B 214 ASP cc_start: 0.6853 (t0) cc_final: 0.6602 (t0) REVERT: B 227 TRP cc_start: 0.8836 (m100) cc_final: 0.8471 (m-10) REVERT: C 50 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8719 (mm-30) REVERT: C 60 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8957 (ttm) REVERT: C 111 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8671 (mp) REVERT: C 124 LYS cc_start: 0.8739 (mmmt) cc_final: 0.8369 (mmmt) REVERT: C 170 GLU cc_start: 0.9268 (tt0) cc_final: 0.8921 (tt0) REVERT: C 227 TRP cc_start: 0.8835 (m100) cc_final: 0.8486 (m-10) REVERT: C 235 ILE cc_start: 0.9162 (mt) cc_final: 0.8909 (mt) REVERT: D 49 LEU cc_start: 0.9537 (mt) cc_final: 0.9262 (mt) REVERT: D 50 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8659 (mm-30) REVERT: D 111 LEU cc_start: 0.8908 (mt) cc_final: 0.8666 (mp) REVERT: D 124 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8302 (mmmt) REVERT: D 146 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7931 (mp0) REVERT: D 149 ASP cc_start: 0.8120 (t70) cc_final: 0.7866 (t0) REVERT: D 170 GLU cc_start: 0.9268 (tt0) cc_final: 0.9001 (tt0) REVERT: D 214 ASP cc_start: 0.6892 (t0) cc_final: 0.6436 (t0) REVERT: D 229 TYR cc_start: 0.9309 (t80) cc_final: 0.9031 (t80) REVERT: D 242 PHE cc_start: 0.8405 (t80) cc_final: 0.7695 (m-80) outliers start: 46 outliers final: 30 residues processed: 238 average time/residue: 0.1997 time to fit residues: 63.6960 Evaluate side-chains 234 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 199 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 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 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: 0.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 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: 0.9980 chunk 52 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 B 215 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 = 0.3708 r_free = 0.3708 target = 0.116313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.086295 restraints weight = 16335.692| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.49 r_work: 0.3074 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3495 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= 0.193 Angle : 0.545 9.958 11068 Z= 0.281 Chirality : 0.036 0.124 1220 Planarity : 0.003 0.029 1288 Dihedral : 15.443 81.174 1388 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.74 % Allowed : 17.98 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.35 (0.27), residues: 932 helix: 3.55 (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 0.009 0.001 TRP D 227 HIS 0.009 0.001 HIS B 143 PHE 0.032 0.001 PHE D 13 TYR 0.004 0.001 TYR C 229 ARG 0.006 0.001 ARG B 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 257 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 212 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9531 (mt) cc_final: 0.9308 (mt) REVERT: A 50 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8737 (mm-30) REVERT: A 96 PHE cc_start: 0.9243 (t80) cc_final: 0.8935 (t80) REVERT: A 129 ASN cc_start: 0.9462 (t0) cc_final: 0.9195 (t0) REVERT: A 147 MET cc_start: 0.8630 (ptp) cc_final: 0.8261 (ptt) REVERT: A 214 ASP cc_start: 0.6128 (t0) cc_final: 0.5596 (t0) REVERT: B 50 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8816 (mm-30) REVERT: B 96 PHE cc_start: 0.9168 (t80) cc_final: 0.8861 (t80) REVERT: B 111 LEU cc_start: 0.8870 (mt) cc_final: 0.8583 (mp) REVERT: B 214 ASP cc_start: 0.6781 (t0) cc_final: 0.6261 (t0) REVERT: B 227 TRP cc_start: 0.8834 (m100) cc_final: 0.8491 (m-10) REVERT: B 229 TYR cc_start: 0.9369 (t80) cc_final: 0.9133 (t80) REVERT: C 50 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8729 (mm-30) REVERT: C 96 PHE cc_start: 0.9218 (t80) cc_final: 0.8891 (t80) REVERT: C 111 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8624 (mp) REVERT: C 124 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8532 (mmmt) REVERT: C 213 MET cc_start: 0.6858 (mmm) cc_final: 0.5888 (mmm) REVERT: C 214 ASP cc_start: 0.6898 (t0) cc_final: 0.6579 (t0) REVERT: C 227 TRP cc_start: 0.8823 (m100) cc_final: 0.8511 (m-10) REVERT: C 235 ILE cc_start: 0.9218 (mt) cc_final: 0.8962 (mt) REVERT: D 49 LEU cc_start: 0.9561 (mt) cc_final: 0.9300 (mt) REVERT: D 50 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8665 (mm-30) REVERT: D 96 PHE cc_start: 0.9090 (t80) cc_final: 0.8710 (t80) REVERT: D 111 LEU cc_start: 0.8905 (mt) cc_final: 0.8620 (mp) REVERT: D 146 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7973 (mp0) REVERT: D 149 ASP cc_start: 0.8072 (t70) cc_final: 0.7833 (t0) REVERT: D 242 PHE cc_start: 0.8446 (t80) cc_final: 0.7753 (m-80) outliers start: 45 outliers final: 28 residues processed: 237 average time/residue: 0.1922 time to fit residues: 61.5562 Evaluate side-chains 230 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU 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 194 PHE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 27 LEU 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 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 246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 39 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.114818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.084742 restraints weight = 16421.850| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.48 r_work: 0.3016 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8216 Z= 0.230 Angle : 0.577 15.482 11068 Z= 0.298 Chirality : 0.036 0.133 1220 Planarity : 0.003 0.029 1288 Dihedral : 15.080 76.124 1388 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.48 % Allowed : 18.62 % Favored : 75.89 % 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: 4.17 (0.27), residues: 932 helix: 3.41 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.81 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 227 HIS 0.004 0.001 HIS D 215 PHE 0.033 0.001 PHE A 13 TYR 0.006 0.001 TYR D 229 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 254 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9535 (mt) cc_final: 0.9324 (mt) REVERT: A 50 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8762 (mm-30) REVERT: A 96 PHE cc_start: 0.9207 (t80) cc_final: 0.8924 (t80) REVERT: A 124 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8293 (mmmt) REVERT: A 147 MET cc_start: 0.8657 (ptp) cc_final: 0.8429 (ptt) REVERT: A 213 MET cc_start: 0.7156 (mmm) cc_final: 0.6811 (mmp) REVERT: A 214 ASP cc_start: 0.6396 (t0) cc_final: 0.5659 (t0) REVERT: B 50 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8837 (mm-30) REVERT: B 96 PHE cc_start: 0.9097 (t80) cc_final: 0.8823 (t80) REVERT: B 111 LEU cc_start: 0.8838 (mt) cc_final: 0.8561 (mp) REVERT: B 124 LYS cc_start: 0.8547 (mmmt) cc_final: 0.8252 (mmmt) REVERT: B 214 ASP cc_start: 0.6915 (t0) cc_final: 0.6274 (t0) REVERT: B 215 HIS cc_start: 0.8743 (m170) cc_final: 0.8243 (m-70) REVERT: B 227 TRP cc_start: 0.8882 (m100) cc_final: 0.8515 (m-10) REVERT: C 49 LEU cc_start: 0.9458 (mt) cc_final: 0.9233 (mt) REVERT: C 50 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8755 (mm-30) REVERT: C 96 PHE cc_start: 0.9158 (t80) cc_final: 0.8878 (t80) REVERT: C 111 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8610 (mp) REVERT: C 124 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8552 (mmmt) REVERT: C 213 MET cc_start: 0.6741 (mmm) cc_final: 0.6161 (mmm) REVERT: C 214 ASP cc_start: 0.6996 (t0) cc_final: 0.6605 (t0) REVERT: C 227 TRP cc_start: 0.8838 (m100) cc_final: 0.8507 (m-10) REVERT: C 235 ILE cc_start: 0.9184 (mt) cc_final: 0.8926 (mt) REVERT: D 49 LEU cc_start: 0.9558 (mt) cc_final: 0.9298 (mt) REVERT: D 50 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8708 (mm-30) REVERT: D 96 PHE cc_start: 0.9233 (t80) cc_final: 0.8888 (t80) REVERT: D 111 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8601 (mp) REVERT: D 124 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8317 (mmmt) REVERT: D 146 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7998 (mp0) REVERT: D 149 ASP cc_start: 0.8121 (t70) cc_final: 0.7865 (t0) REVERT: D 216 GLU cc_start: 0.8465 (mp0) cc_final: 0.8205 (pm20) REVERT: D 242 PHE cc_start: 0.8411 (t80) cc_final: 0.7695 (m-80) outliers start: 43 outliers final: 30 residues processed: 233 average time/residue: 0.2038 time to fit residues: 63.7649 Evaluate side-chains 238 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 27 LEU 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 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 234 VAL 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: 4.9990 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3690 r_free = 0.3690 target = 0.115550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.084907 restraints weight = 16638.008| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.53 r_work: 0.3002 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3909 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= 0.211 Angle : 0.567 15.574 11068 Z= 0.296 Chirality : 0.036 0.126 1220 Planarity : 0.003 0.030 1288 Dihedral : 14.615 73.939 1388 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.61 % Allowed : 18.75 % 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: 4.05 (0.27), residues: 932 helix: 3.33 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.85 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 227 HIS 0.006 0.001 HIS D 215 PHE 0.030 0.001 PHE B 242 TYR 0.009 0.001 TYR C 229 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 251 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9548 (mt) cc_final: 0.9339 (mt) REVERT: A 50 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8831 (mm-30) REVERT: A 96 PHE cc_start: 0.9194 (t80) cc_final: 0.8863 (t80) REVERT: A 124 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8114 (mttm) REVERT: A 147 MET cc_start: 0.8667 (ptp) cc_final: 0.8389 (ptt) REVERT: A 214 ASP cc_start: 0.7008 (t0) cc_final: 0.6521 (t0) REVERT: A 216 GLU cc_start: 0.8410 (pm20) cc_final: 0.7855 (pm20) REVERT: A 229 TYR cc_start: 0.9359 (t80) cc_final: 0.9087 (t80) REVERT: B 50 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8908 (mm-30) REVERT: B 96 PHE cc_start: 0.9057 (t80) cc_final: 0.8767 (t80) REVERT: B 111 LEU cc_start: 0.8828 (mt) cc_final: 0.8544 (mp) REVERT: B 214 ASP cc_start: 0.7073 (t0) cc_final: 0.6514 (t0) REVERT: B 221 LEU cc_start: 0.9529 (mp) cc_final: 0.9311 (mp) REVERT: B 227 TRP cc_start: 0.8805 (m100) cc_final: 0.8452 (m-10) REVERT: C 49 LEU cc_start: 0.9477 (mt) cc_final: 0.9255 (mt) REVERT: C 50 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8762 (mm-30) REVERT: C 96 PHE cc_start: 0.9190 (t80) cc_final: 0.8863 (t80) REVERT: C 111 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8594 (mp) REVERT: C 124 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8586 (mmmt) REVERT: C 214 ASP cc_start: 0.7045 (t0) cc_final: 0.6531 (t0) REVERT: C 215 HIS cc_start: 0.8666 (m-70) cc_final: 0.8236 (m90) REVERT: C 235 ILE cc_start: 0.9183 (mt) cc_final: 0.8918 (mt) REVERT: D 49 LEU cc_start: 0.9567 (mt) cc_final: 0.9320 (mt) REVERT: D 50 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8731 (mm-30) REVERT: D 111 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8565 (mp) REVERT: D 129 ASN cc_start: 0.9340 (t0) cc_final: 0.9104 (t0) REVERT: D 146 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7954 (mp0) REVERT: D 149 ASP cc_start: 0.8105 (t70) cc_final: 0.7867 (t0) REVERT: D 216 GLU cc_start: 0.8381 (mp0) cc_final: 0.8084 (pm20) REVERT: D 229 TYR cc_start: 0.9279 (t80) cc_final: 0.9046 (t80) REVERT: D 242 PHE cc_start: 0.8404 (t80) cc_final: 0.7679 (m-80) outliers start: 44 outliers final: 32 residues processed: 232 average time/residue: 0.2077 time to fit residues: 65.2478 Evaluate side-chains 237 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 170 GLU 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 143 HIS 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 234 VAL 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: 6.9990 chunk 83 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.115438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.085221 restraints weight = 16717.769| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.64 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4079 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= 0.213 Angle : 0.588 15.682 11068 Z= 0.304 Chirality : 0.036 0.125 1220 Planarity : 0.003 0.029 1288 Dihedral : 14.340 72.622 1388 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.74 % Allowed : 19.64 % 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: 4.00 (0.27), residues: 932 helix: 3.30 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.88 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 227 HIS 0.006 0.001 HIS D 215 PHE 0.036 0.001 PHE B 96 TYR 0.006 0.001 TYR B 229 ARG 0.007 0.001 ARG B 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 251 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8806 (mm-30) REVERT: A 96 PHE cc_start: 0.9246 (t80) cc_final: 0.8840 (t80) REVERT: A 214 ASP cc_start: 0.6991 (t0) cc_final: 0.6473 (t0) REVERT: A 229 TYR cc_start: 0.9298 (t80) cc_final: 0.9044 (t80) REVERT: B 96 PHE cc_start: 0.9245 (t80) cc_final: 0.8930 (t80) REVERT: B 111 LEU cc_start: 0.8840 (mt) cc_final: 0.8559 (mp) REVERT: B 124 LYS cc_start: 0.8385 (mmmt) cc_final: 0.8175 (mmmt) REVERT: B 214 ASP cc_start: 0.7099 (t0) cc_final: 0.6540 (t0) REVERT: B 221 LEU cc_start: 0.9508 (mp) cc_final: 0.9294 (mp) REVERT: B 227 TRP cc_start: 0.8662 (m100) cc_final: 0.8437 (m100) REVERT: C 50 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8743 (mm-30) REVERT: C 96 PHE cc_start: 0.9257 (t80) cc_final: 0.8789 (t80) REVERT: C 111 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8613 (mp) REVERT: C 124 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8399 (mmmt) REVERT: C 213 MET cc_start: 0.6679 (mmm) cc_final: 0.6458 (mmm) REVERT: C 214 ASP cc_start: 0.7032 (t0) cc_final: 0.6513 (t0) REVERT: C 215 HIS cc_start: 0.8470 (m-70) cc_final: 0.8001 (m90) REVERT: C 235 ILE cc_start: 0.9136 (mt) cc_final: 0.8864 (mt) REVERT: D 13 PHE cc_start: 0.8325 (m-80) cc_final: 0.7367 (t80) REVERT: D 49 LEU cc_start: 0.9621 (mt) cc_final: 0.9393 (mt) REVERT: D 50 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8691 (mm-30) REVERT: D 111 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8618 (mp) REVERT: D 129 ASN cc_start: 0.9265 (t0) cc_final: 0.9008 (t0) REVERT: D 146 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7892 (mp0) REVERT: D 149 ASP cc_start: 0.7978 (t70) cc_final: 0.7742 (t0) REVERT: D 217 ASN cc_start: 0.9127 (m-40) cc_final: 0.8685 (m-40) REVERT: D 242 PHE cc_start: 0.8357 (t80) cc_final: 0.7683 (m-80) outliers start: 45 outliers final: 33 residues processed: 232 average time/residue: 0.1928 time to fit residues: 60.1670 Evaluate side-chains 239 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 170 GLU 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 30 ILE 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 143 HIS 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 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 234 VAL 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: 9.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 56 optimal weight: 0.0000 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: 0.6980 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.118102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087517 restraints weight = 17025.932| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.75 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8216 Z= 0.191 Angle : 0.607 15.036 11068 Z= 0.308 Chirality : 0.037 0.127 1220 Planarity : 0.003 0.031 1288 Dihedral : 13.422 67.955 1388 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.46 % Allowed : 21.17 % 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: 3.99 (0.27), residues: 932 helix: 3.33 (0.17), residues: 764 sheet: None (None), residues: 0 loop : -0.98 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 227 HIS 0.005 0.001 HIS A 215 PHE 0.037 0.001 PHE D 13 TYR 0.010 0.001 TYR C 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 249 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.8401 (t80) cc_final: 0.8107 (t80) REVERT: A 50 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8862 (mm-30) REVERT: A 96 PHE cc_start: 0.9234 (t80) cc_final: 0.8882 (t80) REVERT: A 214 ASP cc_start: 0.7180 (t0) cc_final: 0.6679 (t0) REVERT: A 229 TYR cc_start: 0.9239 (t80) cc_final: 0.9038 (t80) REVERT: B 96 PHE cc_start: 0.9183 (t80) cc_final: 0.8721 (t80) REVERT: B 111 LEU cc_start: 0.8858 (mt) cc_final: 0.8579 (mp) REVERT: B 124 LYS cc_start: 0.8320 (mmmt) cc_final: 0.8103 (mmmt) REVERT: B 214 ASP cc_start: 0.7036 (t0) cc_final: 0.6449 (t0) REVERT: B 221 LEU cc_start: 0.9502 (mp) cc_final: 0.9259 (mp) REVERT: B 227 TRP cc_start: 0.8599 (m100) cc_final: 0.8274 (m-10) REVERT: C 4 PHE cc_start: 0.8664 (t80) cc_final: 0.8456 (t80) REVERT: C 50 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8798 (mm-30) REVERT: C 96 PHE cc_start: 0.9260 (t80) cc_final: 0.8899 (t80) REVERT: C 111 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8493 (mp) REVERT: C 124 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8311 (mmmt) REVERT: C 213 MET cc_start: 0.6687 (mmm) cc_final: 0.4417 (mmm) REVERT: C 214 ASP cc_start: 0.7034 (t0) cc_final: 0.6433 (t0) REVERT: C 215 HIS cc_start: 0.8406 (m-70) cc_final: 0.7845 (m90) REVERT: C 229 TYR cc_start: 0.9210 (t80) cc_final: 0.8943 (t80) REVERT: C 235 ILE cc_start: 0.9132 (mt) cc_final: 0.8879 (mt) REVERT: D 49 LEU cc_start: 0.9625 (mt) cc_final: 0.9415 (mt) REVERT: D 50 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8745 (mm-30) REVERT: D 111 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8540 (mp) REVERT: D 149 ASP cc_start: 0.7898 (t70) cc_final: 0.7659 (t0) REVERT: D 155 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8836 (mp) REVERT: D 216 GLU cc_start: 0.8505 (mp0) cc_final: 0.7953 (pm20) REVERT: D 217 ASN cc_start: 0.9000 (m-40) cc_final: 0.8476 (m-40) REVERT: D 221 LEU cc_start: 0.9492 (mt) cc_final: 0.9287 (mp) REVERT: D 242 PHE cc_start: 0.8330 (t80) cc_final: 0.7672 (m-80) outliers start: 35 outliers final: 28 residues processed: 239 average time/residue: 0.1995 time to fit residues: 63.7466 Evaluate side-chains 236 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 104 LEU Chi-restraints excluded: chain A residue 170 GLU 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 52 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 LEU 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 143 HIS 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 111 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 155 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS D 129 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 = 0.3678 r_free = 0.3678 target = 0.114830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.083468 restraints weight = 17044.926| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.67 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8216 Z= 0.283 Angle : 0.720 15.819 11068 Z= 0.366 Chirality : 0.038 0.156 1220 Planarity : 0.004 0.031 1288 Dihedral : 13.621 67.403 1388 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.46 % Allowed : 22.45 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.90 (0.27), residues: 932 helix: 3.23 (0.17), residues: 764 sheet: None (None), residues: 0 loop : -0.83 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 227 HIS 0.008 0.001 HIS A 215 PHE 0.047 0.002 PHE B 13 TYR 0.009 0.001 TYR D 229 ARG 0.007 0.001 ARG C 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 240 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.8438 (t80) cc_final: 0.8024 (t80) REVERT: A 96 PHE cc_start: 0.9239 (t80) cc_final: 0.8945 (t80) REVERT: A 214 ASP cc_start: 0.7298 (t0) cc_final: 0.6804 (t0) REVERT: B 96 PHE cc_start: 0.9242 (t80) cc_final: 0.8772 (t80) REVERT: B 111 LEU cc_start: 0.8872 (mt) cc_final: 0.8603 (mp) REVERT: B 124 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8297 (mmmt) REVERT: B 214 ASP cc_start: 0.7637 (t0) cc_final: 0.6982 (t0) REVERT: B 215 HIS cc_start: 0.8492 (m170) cc_final: 0.8130 (m-70) REVERT: B 227 TRP cc_start: 0.8692 (m100) cc_final: 0.8457 (m100) REVERT: B 229 TYR cc_start: 0.9312 (t80) cc_final: 0.9038 (t80) REVERT: C 96 PHE cc_start: 0.9306 (t80) cc_final: 0.8978 (t80) REVERT: C 111 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8608 (mp) REVERT: C 124 LYS cc_start: 0.8682 (mmmt) cc_final: 0.8419 (mmmt) REVERT: C 211 ASP cc_start: 0.8410 (t0) cc_final: 0.8097 (t0) REVERT: C 214 ASP cc_start: 0.7634 (t0) cc_final: 0.7210 (t0) REVERT: C 215 HIS cc_start: 0.8314 (m-70) cc_final: 0.7944 (m90) REVERT: C 229 TYR cc_start: 0.9382 (t80) cc_final: 0.9182 (t80) REVERT: C 235 ILE cc_start: 0.9096 (mt) cc_final: 0.8831 (mt) REVERT: D 49 LEU cc_start: 0.9644 (mt) cc_final: 0.9441 (mt) REVERT: D 50 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8871 (mm-30) REVERT: D 111 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8599 (mp) REVERT: D 146 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7892 (mp0) REVERT: D 149 ASP cc_start: 0.8065 (t70) cc_final: 0.7811 (t0) REVERT: D 216 GLU cc_start: 0.8525 (mp0) cc_final: 0.8047 (pm20) REVERT: D 217 ASN cc_start: 0.9357 (m-40) cc_final: 0.8696 (m-40) REVERT: D 221 LEU cc_start: 0.9509 (mt) cc_final: 0.9292 (mp) REVERT: D 242 PHE cc_start: 0.8293 (t80) cc_final: 0.7649 (m-80) outliers start: 35 outliers final: 29 residues processed: 227 average time/residue: 0.1919 time to fit residues: 58.9006 Evaluate side-chains 228 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 52 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 30 ILE 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 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 143 HIS Chi-restraints excluded: chain C residue 194 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 111 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 155 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 69 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3723 r_free = 0.3723 target = 0.118432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.087578 restraints weight = 16722.517| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.71 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8216 Z= 0.207 Angle : 0.728 16.244 11068 Z= 0.358 Chirality : 0.038 0.163 1220 Planarity : 0.003 0.032 1288 Dihedral : 13.165 63.219 1388 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.21 % Allowed : 23.09 % 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: 3.97 (0.27), residues: 932 helix: 3.24 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.72 (0.53), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 227 HIS 0.006 0.001 HIS D 215 PHE 0.036 0.001 PHE A 242 TYR 0.008 0.001 TYR D 229 ARG 0.007 0.001 ARG D 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3394.20 seconds wall clock time: 60 minutes 9.47 seconds (3609.47 seconds total)