Starting phenix.real_space_refine on Thu Mar 13 12:46:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ieq_35390/03_2025/8ieq_35390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ieq_35390/03_2025/8ieq_35390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ieq_35390/03_2025/8ieq_35390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ieq_35390/03_2025/8ieq_35390.map" model { file = "/net/cci-nas-00/data/ceres_data/8ieq_35390/03_2025/8ieq_35390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ieq_35390/03_2025/8ieq_35390.cif" } resolution = 2.73 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= -0.004 sd= 0.189 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 4 5.49 5 S 71 5.16 5 C 5900 2.51 5 N 1399 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8900 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2135 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2230 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 1 Chain: "C" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2155 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2172 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 8, 'TRANS': 270} Chain breaks: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 6.10, per 1000 atoms: 0.69 Number of scatterers: 8900 At special positions: 0 Unit cell: (76.95, 91.53, 149.85, 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 71 16.00 P 4 15.00 O 1526 8.00 N 1399 7.00 C 5900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 974.2 milliseconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 78.7% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 46 through 74 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 84 through 105 removed outlier: 3.560A pdb=" N ILE A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 150 Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 161 through 187 removed outlier: 3.782A pdb=" N LEU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 246 removed outlier: 4.099A pdb=" N TRP A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 281 removed outlier: 3.558A pdb=" N ASN A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 327 Proline residue: A 310 - end of helix Processing helix chain 'B' and resid 46 through 74 Processing helix chain 'B' and resid 77 through 83 removed outlier: 3.692A pdb=" N SER B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 105 removed outlier: 3.664A pdb=" N VAL B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 149 Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 169 through 187 Processing helix chain 'B' and resid 220 through 246 removed outlier: 3.597A pdb=" N TRP B 224 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 281 Processing helix chain 'B' and resid 284 through 332 Proline residue: B 310 - end of helix Processing helix chain 'C' and resid 46 through 74 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 84 through 105 removed outlier: 3.671A pdb=" N ILE C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 150 Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 161 through 187 removed outlier: 3.599A pdb=" N LEU C 165 " --> pdb=" O LYS C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 246 removed outlier: 4.089A pdb=" N TRP C 224 " --> pdb=" O TYR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 281 Processing helix chain 'C' and resid 284 through 332 Proline residue: C 310 - end of helix Processing helix chain 'D' and resid 46 through 74 Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'D' and resid 84 through 105 removed outlier: 3.595A pdb=" N VAL D 90 " --> pdb=" O ASN D 86 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR D 103 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 149 Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 162 through 187 removed outlier: 3.558A pdb=" N ASP D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 246 removed outlier: 3.539A pdb=" N TRP D 224 " --> pdb=" O TYR D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 281 Processing helix chain 'D' and resid 284 through 332 Proline residue: D 310 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 216 removed outlier: 3.508A pdb=" N PHE A 215 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 195 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 215 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 206 through 216 removed outlier: 3.604A pdb=" N PHE C 215 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU C 195 " --> pdb=" O MET D 199 " (cutoff:3.500A) 766 hydrogen bonds defined for protein. 2292 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: 3.02 Time building geometry restraints manager: 2.66 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: 1282 1.31 - 1.44: 2431 1.44 - 1.56: 5242 1.56 - 1.69: 24 1.69 - 1.81: 102 Bond restraints: 9081 Sorted by residual: bond pdb=" C39 PC1 B 601 " pdb=" C3A PC1 B 601 " ideal model delta sigma weight residual 1.524 1.324 0.200 2.00e-02 2.50e+03 9.99e+01 bond pdb=" C39 PC1 A 601 " pdb=" C3A PC1 A 601 " ideal model delta sigma weight residual 1.524 1.327 0.197 2.00e-02 2.50e+03 9.74e+01 bond pdb=" C39 PC1 C 601 " pdb=" C3A PC1 C 601 " ideal model delta sigma weight residual 1.524 1.327 0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" C39 PC1 D 601 " pdb=" C3A PC1 D 601 " ideal model delta sigma weight residual 1.524 1.327 0.197 2.00e-02 2.50e+03 9.69e+01 bond pdb=" C31 PC1 D 601 " pdb=" O31 PC1 D 601 " ideal model delta sigma weight residual 1.330 1.427 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 9076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 12164 2.82 - 5.63: 128 5.63 - 8.45: 24 8.45 - 11.26: 0 11.26 - 14.08: 4 Bond angle restraints: 12320 Sorted by residual: angle pdb=" O12 PC1 B 601 " pdb=" P PC1 B 601 " pdb=" O14 PC1 B 601 " ideal model delta sigma weight residual 123.67 109.59 14.08 3.00e+00 1.11e-01 2.20e+01 angle pdb=" O12 PC1 C 601 " pdb=" P PC1 C 601 " pdb=" O14 PC1 C 601 " ideal model delta sigma weight residual 123.67 109.62 14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" O12 PC1 D 601 " pdb=" P PC1 D 601 " pdb=" O14 PC1 D 601 " ideal model delta sigma weight residual 123.67 109.68 13.99 3.00e+00 1.11e-01 2.18e+01 angle pdb=" O12 PC1 A 601 " pdb=" P PC1 A 601 " pdb=" O14 PC1 A 601 " ideal model delta sigma weight residual 123.67 109.95 13.72 3.00e+00 1.11e-01 2.09e+01 angle pdb=" CB TRP B 229 " pdb=" CG TRP B 229 " pdb=" CD2 TRP B 229 " ideal model delta sigma weight residual 126.80 131.57 -4.77 1.40e+00 5.10e-01 1.16e+01 ... (remaining 12315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4889 17.93 - 35.87: 385 35.87 - 53.80: 78 53.80 - 71.74: 11 71.74 - 89.67: 12 Dihedral angle restraints: 5375 sinusoidal: 2148 harmonic: 3227 Sorted by residual: dihedral pdb=" CA ILE D 228 " pdb=" C ILE D 228 " pdb=" N TRP D 229 " pdb=" CA TRP D 229 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ILE B 228 " pdb=" C ILE B 228 " pdb=" N TRP B 229 " pdb=" CA TRP B 229 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ILE A 307 " pdb=" C ILE A 307 " pdb=" N PHE A 308 " pdb=" CA PHE A 308 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1168 0.044 - 0.088: 276 0.088 - 0.132: 64 0.132 - 0.176: 3 0.176 - 0.219: 3 Chirality restraints: 1514 Sorted by residual: chirality pdb=" CA TRP C 229 " pdb=" N TRP C 229 " pdb=" C TRP C 229 " pdb=" CB TRP C 229 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA TRP B 229 " pdb=" N TRP B 229 " pdb=" C TRP B 229 " pdb=" CB TRP B 229 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA TRP D 229 " pdb=" N TRP D 229 " pdb=" C TRP D 229 " pdb=" CB TRP D 229 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.77e-01 ... (remaining 1511 not shown) Planarity restraints: 1433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 229 " -0.028 2.00e-02 2.50e+03 2.95e-02 2.17e+01 pdb=" CG TRP B 229 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP B 229 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 229 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 229 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 229 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 229 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 229 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 229 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 229 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 229 " 0.026 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP D 229 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP D 229 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 229 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP D 229 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 229 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 229 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 229 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 229 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 229 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 229 " -0.024 2.00e-02 2.50e+03 2.56e-02 1.64e+01 pdb=" CG TRP C 229 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP C 229 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP C 229 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 229 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 229 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 229 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 229 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 229 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 229 " 0.004 2.00e-02 2.50e+03 ... (remaining 1430 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 201 2.71 - 3.26: 8745 3.26 - 3.80: 14261 3.80 - 4.35: 17246 4.35 - 4.90: 31039 Nonbonded interactions: 71492 Sorted by model distance: nonbonded pdb=" OG SER C 58 " pdb=" OH TYR C 103 " model vdw 2.159 3.040 nonbonded pdb=" O TYR D 146 " pdb=" OG1 THR D 150 " model vdw 2.167 3.040 nonbonded pdb=" OG1 THR C 202 " pdb=" OD1 ASP C 205 " model vdw 2.189 3.040 nonbonded pdb=" OG SER A 84 " pdb=" NH2 ARG A 144 " model vdw 2.227 3.120 nonbonded pdb=" OG SER B 58 " pdb=" OH TYR B 103 " model vdw 2.246 3.040 ... (remaining 71487 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 through 110 or resid 115 through 152 or resid 161 throu \ gh 327 or resid 601)) selection = (chain 'B' and (resid 44 through 110 or resid 115 through 151 or (resid 152 and \ (name N or name CA or name C or name O or name CB )) or (resid 161 and (name N o \ r name CA or name C or name O or name CB )) or resid 162 through 327 or resid 60 \ 1)) selection = (chain 'C' and (resid 44 through 152 or resid 161 through 327 or resid 601)) selection = (chain 'D' and (resid 44 through 110 or resid 115 through 151 or (resid 152 thro \ ugh 161 and (name N or name CA or name C or name O or name CB )) or resid 162 th \ rough 327 or resid 601)) } 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: 3.520 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.750 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 : 0.007 0.200 9081 Z= 0.457 Angle : 0.792 14.077 12320 Z= 0.379 Chirality : 0.040 0.219 1514 Planarity : 0.005 0.077 1433 Dihedral : 14.175 89.673 3277 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 3.06 (0.25), residues: 1100 helix: 2.83 (0.16), residues: 846 sheet: 1.86 (0.65), residues: 72 loop : -2.15 (0.41), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP B 229 HIS 0.002 0.001 HIS A 214 PHE 0.011 0.001 PHE A 308 TYR 0.010 0.001 TYR B 103 ARG 0.003 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7129 (tttt) cc_final: 0.6697 (tppt) REVERT: A 96 CYS cc_start: 0.7326 (p) cc_final: 0.7075 (m) REVERT: A 174 MET cc_start: 0.6355 (ttp) cc_final: 0.5891 (tpt) REVERT: A 181 MET cc_start: 0.7052 (mtp) cc_final: 0.6577 (mmp) REVERT: A 219 ARG cc_start: 0.7127 (mtp180) cc_final: 0.6634 (mtm110) REVERT: A 222 ASP cc_start: 0.8359 (m-30) cc_final: 0.8128 (m-30) REVERT: B 72 ILE cc_start: 0.7994 (mm) cc_final: 0.7695 (mt) REVERT: B 246 THR cc_start: 0.8377 (m) cc_final: 0.7675 (p) REVERT: B 275 PHE cc_start: 0.6930 (t80) cc_final: 0.6438 (t80) REVERT: C 98 THR cc_start: 0.7428 (m) cc_final: 0.6897 (p) REVERT: C 187 ASP cc_start: 0.8382 (p0) cc_final: 0.8178 (p0) REVERT: C 199 MET cc_start: 0.7234 (ttt) cc_final: 0.6057 (mmt) REVERT: C 219 ARG cc_start: 0.7415 (mtp180) cc_final: 0.6914 (mtp-110) REVERT: C 222 ASP cc_start: 0.8482 (m-30) cc_final: 0.8179 (m-30) REVERT: C 275 PHE cc_start: 0.7295 (t80) cc_final: 0.7086 (t80) REVERT: C 328 MET cc_start: 0.5338 (mmm) cc_final: 0.4596 (ppp) REVERT: D 81 LYS cc_start: 0.7678 (tttt) cc_final: 0.6773 (ttpt) REVERT: D 82 MET cc_start: 0.7476 (ptt) cc_final: 0.7194 (ptp) REVERT: D 190 GLN cc_start: 0.7663 (mt0) cc_final: 0.6624 (mm110) REVERT: D 219 ARG cc_start: 0.7835 (ttp-170) cc_final: 0.7623 (ttp-110) REVERT: D 235 LEU cc_start: 0.7175 (mm) cc_final: 0.6474 (tp) outliers start: 0 outliers final: 1 residues processed: 131 average time/residue: 1.0434 time to fit residues: 147.3709 Evaluate side-chains 96 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 190 GLN C 190 GLN C 265 ASN D 86 ASN D 121 GLN D 255 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.164138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116783 restraints weight = 8527.723| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.89 r_work: 0.3104 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9081 Z= 0.259 Angle : 0.567 6.977 12320 Z= 0.301 Chirality : 0.041 0.189 1514 Planarity : 0.005 0.072 1433 Dihedral : 11.310 87.813 1362 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.62 % Allowed : 6.07 % Favored : 92.31 % 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: 3.47 (0.24), residues: 1100 helix: 3.04 (0.16), residues: 852 sheet: 3.07 (0.65), residues: 67 loop : -2.08 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 229 HIS 0.001 0.000 HIS D 214 PHE 0.013 0.002 PHE D 275 TYR 0.014 0.001 TYR D 103 ARG 0.004 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.992 Fit side-chains REVERT: A 81 LYS cc_start: 0.7929 (tttt) cc_final: 0.7406 (tppt) REVERT: A 98 THR cc_start: 0.7574 (m) cc_final: 0.7159 (p) REVERT: A 147 LYS cc_start: 0.7588 (mmmt) cc_final: 0.7281 (mmpt) REVERT: A 174 MET cc_start: 0.6766 (ttp) cc_final: 0.6238 (tpt) REVERT: A 181 MET cc_start: 0.7979 (mtp) cc_final: 0.7314 (mmp) REVERT: A 219 ARG cc_start: 0.7793 (mtp180) cc_final: 0.7261 (mtm110) REVERT: B 72 ILE cc_start: 0.8276 (mm) cc_final: 0.8058 (mt) REVERT: B 81 LYS cc_start: 0.7582 (tttt) cc_final: 0.7329 (ttmt) REVERT: B 123 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.6968 (ptp-170) REVERT: B 174 MET cc_start: 0.5512 (OUTLIER) cc_final: 0.4978 (tmm) REVERT: B 219 ARG cc_start: 0.7910 (ttt-90) cc_final: 0.7275 (ttp-110) REVERT: B 246 THR cc_start: 0.8645 (m) cc_final: 0.8178 (p) REVERT: B 275 PHE cc_start: 0.7657 (t80) cc_final: 0.6980 (t80) REVERT: B 328 MET cc_start: 0.4335 (mtp) cc_final: 0.3718 (mtp) REVERT: C 81 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7045 (tptt) REVERT: C 98 THR cc_start: 0.8026 (m) cc_final: 0.7611 (p) REVERT: C 174 MET cc_start: 0.6939 (mmm) cc_final: 0.6703 (tpt) REVERT: C 187 ASP cc_start: 0.8529 (p0) cc_final: 0.8249 (p0) REVERT: C 199 MET cc_start: 0.7164 (ttt) cc_final: 0.5912 (mmt) REVERT: C 219 ARG cc_start: 0.8050 (mtp180) cc_final: 0.7510 (mtp-110) REVERT: C 328 MET cc_start: 0.5529 (mmm) cc_final: 0.4722 (ppp) REVERT: D 81 LYS cc_start: 0.8024 (tttt) cc_final: 0.7165 (ttpt) REVERT: D 190 GLN cc_start: 0.7678 (mt0) cc_final: 0.7086 (mm110) REVERT: D 235 LEU cc_start: 0.7780 (mm) cc_final: 0.7160 (tp) REVERT: D 328 MET cc_start: 0.3233 (mtm) cc_final: 0.2406 (pmt) outliers start: 16 outliers final: 9 residues processed: 114 average time/residue: 1.1975 time to fit residues: 146.2981 Evaluate side-chains 111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 259 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 77 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.162118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114728 restraints weight = 8655.876| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.87 r_work: 0.3086 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9081 Z= 0.235 Angle : 0.543 8.230 12320 Z= 0.289 Chirality : 0.040 0.235 1514 Planarity : 0.006 0.075 1433 Dihedral : 11.497 88.443 1360 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.53 % Allowed : 7.79 % Favored : 89.68 % 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: 3.50 (0.24), residues: 1100 helix: 3.14 (0.15), residues: 854 sheet: 3.13 (0.78), residues: 42 loop : -1.86 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 229 HIS 0.001 0.000 HIS A 248 PHE 0.028 0.002 PHE B 215 TYR 0.011 0.001 TYR B 280 ARG 0.009 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.969 Fit side-chains REVERT: A 81 LYS cc_start: 0.8008 (tttt) cc_final: 0.7454 (tppt) REVERT: A 98 THR cc_start: 0.7746 (m) cc_final: 0.7365 (p) REVERT: A 147 LYS cc_start: 0.7644 (mmmt) cc_final: 0.7350 (mmpt) REVERT: A 174 MET cc_start: 0.6816 (ttp) cc_final: 0.6329 (tpt) REVERT: A 181 MET cc_start: 0.7988 (mtp) cc_final: 0.7469 (tpt) REVERT: A 219 ARG cc_start: 0.7810 (mtp180) cc_final: 0.7210 (mtm-85) REVERT: B 81 LYS cc_start: 0.7589 (tttt) cc_final: 0.7340 (ttmt) REVERT: B 123 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.6920 (ptp-170) REVERT: B 174 MET cc_start: 0.5537 (OUTLIER) cc_final: 0.4990 (tmm) REVERT: B 199 MET cc_start: 0.7210 (tpt) cc_final: 0.7004 (tmt) REVERT: B 219 ARG cc_start: 0.7887 (ttt-90) cc_final: 0.7375 (ttp-110) REVERT: B 222 ASP cc_start: 0.8838 (m-30) cc_final: 0.8587 (m-30) REVERT: B 246 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8289 (p) REVERT: B 275 PHE cc_start: 0.7727 (t80) cc_final: 0.6907 (t80) REVERT: B 328 MET cc_start: 0.4452 (mtp) cc_final: 0.3906 (mtp) REVERT: C 98 THR cc_start: 0.8079 (m) cc_final: 0.7664 (p) REVERT: C 174 MET cc_start: 0.6866 (mmm) cc_final: 0.6648 (tpt) REVERT: C 199 MET cc_start: 0.7167 (ttt) cc_final: 0.5915 (mmt) REVERT: C 219 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7473 (mtp-110) REVERT: C 328 MET cc_start: 0.5531 (mmm) cc_final: 0.4674 (ppp) REVERT: D 81 LYS cc_start: 0.7951 (tttt) cc_final: 0.7033 (ttpt) REVERT: D 190 GLN cc_start: 0.7731 (mt0) cc_final: 0.7117 (mm110) REVERT: D 235 LEU cc_start: 0.7856 (mm) cc_final: 0.7197 (tp) REVERT: D 328 MET cc_start: 0.3310 (mtm) cc_final: 0.2381 (pmt) outliers start: 25 outliers final: 8 residues processed: 118 average time/residue: 1.1344 time to fit residues: 143.4828 Evaluate side-chains 110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 259 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 53 optimal weight: 0.0050 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN C 255 ASN D 86 ASN D 121 GLN D 255 ASN D 304 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.162115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114740 restraints weight = 8670.024| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.86 r_work: 0.3230 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9081 Z= 0.214 Angle : 0.518 6.757 12320 Z= 0.278 Chirality : 0.039 0.229 1514 Planarity : 0.006 0.076 1433 Dihedral : 11.554 85.355 1360 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.63 % Allowed : 8.81 % Favored : 88.56 % 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: 3.61 (0.24), residues: 1100 helix: 3.22 (0.15), residues: 856 sheet: 3.13 (0.88), residues: 36 loop : -1.69 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 315 HIS 0.002 0.000 HIS C 73 PHE 0.027 0.001 PHE B 215 TYR 0.011 0.001 TYR D 103 ARG 0.005 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7621 (tttt) cc_final: 0.7033 (tppt) REVERT: A 98 THR cc_start: 0.7186 (m) cc_final: 0.6724 (p) REVERT: A 147 LYS cc_start: 0.6910 (mmmt) cc_final: 0.6591 (mmpt) REVERT: A 174 MET cc_start: 0.6418 (ttp) cc_final: 0.5850 (tpt) REVERT: A 181 MET cc_start: 0.7393 (mtp) cc_final: 0.6842 (tpt) REVERT: A 219 ARG cc_start: 0.7483 (mtp180) cc_final: 0.6764 (mtm-85) REVERT: B 72 ILE cc_start: 0.7991 (mm) cc_final: 0.7787 (mt) REVERT: B 81 LYS cc_start: 0.7376 (tttt) cc_final: 0.7060 (ttmt) REVERT: B 123 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.6381 (ptp-170) REVERT: B 199 MET cc_start: 0.7221 (tpt) cc_final: 0.6776 (tmt) REVERT: B 219 ARG cc_start: 0.7539 (ttt-90) cc_final: 0.6896 (ttp-110) REVERT: B 222 ASP cc_start: 0.8578 (m-30) cc_final: 0.8245 (m-30) REVERT: B 246 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7698 (p) REVERT: B 275 PHE cc_start: 0.7215 (t80) cc_final: 0.6405 (t80) REVERT: B 328 MET cc_start: 0.4498 (mtp) cc_final: 0.3955 (mtp) REVERT: C 81 LYS cc_start: 0.7586 (ttmt) cc_final: 0.6741 (tptt) REVERT: C 98 THR cc_start: 0.7590 (m) cc_final: 0.7048 (p) REVERT: C 174 MET cc_start: 0.6496 (mmm) cc_final: 0.6289 (tpt) REVERT: C 187 ASP cc_start: 0.8388 (p0) cc_final: 0.8146 (p0) REVERT: C 199 MET cc_start: 0.7054 (ttt) cc_final: 0.5868 (mmt) REVERT: C 219 ARG cc_start: 0.7781 (mtp180) cc_final: 0.7090 (mtp-110) REVERT: C 328 MET cc_start: 0.5495 (mmm) cc_final: 0.4687 (ppp) REVERT: D 81 LYS cc_start: 0.7689 (tttt) cc_final: 0.6682 (ttpt) REVERT: D 190 GLN cc_start: 0.7357 (mt0) cc_final: 0.6659 (mm110) REVERT: D 235 LEU cc_start: 0.7369 (mm) cc_final: 0.6600 (tp) REVERT: D 328 MET cc_start: 0.3315 (mtm) cc_final: 0.2456 (pmt) outliers start: 26 outliers final: 13 residues processed: 118 average time/residue: 1.1251 time to fit residues: 142.7652 Evaluate side-chains 115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 259 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 256 GLN B 304 ASN D 121 GLN D 255 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.159696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.113823 restraints weight = 8624.514| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.76 r_work: 0.3078 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9081 Z= 0.246 Angle : 0.542 6.825 12320 Z= 0.288 Chirality : 0.040 0.279 1514 Planarity : 0.006 0.077 1433 Dihedral : 11.643 89.409 1360 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.44 % Allowed : 8.81 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.24), residues: 1100 helix: 3.14 (0.15), residues: 857 sheet: 3.59 (0.73), residues: 46 loop : -1.74 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 315 HIS 0.001 0.000 HIS C 73 PHE 0.028 0.002 PHE B 215 TYR 0.012 0.001 TYR B 280 ARG 0.007 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7749 (tttt) cc_final: 0.7157 (tppt) REVERT: A 98 THR cc_start: 0.7525 (m) cc_final: 0.7048 (p) REVERT: A 147 LYS cc_start: 0.7202 (mmmt) cc_final: 0.6983 (mmpt) REVERT: A 174 MET cc_start: 0.6676 (ttp) cc_final: 0.6108 (tpt) REVERT: A 181 MET cc_start: 0.7697 (mtp) cc_final: 0.7136 (tpt) REVERT: A 199 MET cc_start: 0.7705 (ttt) cc_final: 0.7198 (ttp) REVERT: A 219 ARG cc_start: 0.7586 (mtp180) cc_final: 0.6919 (mtm-85) REVERT: A 228 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7448 (mp) REVERT: B 81 LYS cc_start: 0.7497 (tttt) cc_final: 0.7164 (ttmt) REVERT: B 123 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.6697 (ptp-170) REVERT: B 199 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6664 (tpp) REVERT: B 222 ASP cc_start: 0.8766 (m-30) cc_final: 0.8471 (m-30) REVERT: B 246 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8059 (p) REVERT: B 275 PHE cc_start: 0.7533 (t80) cc_final: 0.6687 (t80) REVERT: B 328 MET cc_start: 0.4428 (mtp) cc_final: 0.3898 (mtp) REVERT: C 75 ARG cc_start: 0.7535 (ttm110) cc_final: 0.7333 (ttp80) REVERT: C 81 LYS cc_start: 0.7685 (ttmt) cc_final: 0.6877 (tptt) REVERT: C 98 THR cc_start: 0.7872 (m) cc_final: 0.7385 (p) REVERT: C 199 MET cc_start: 0.7137 (ttt) cc_final: 0.5973 (mmt) REVERT: C 219 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7302 (mtp-110) REVERT: C 328 MET cc_start: 0.5499 (mmm) cc_final: 0.4662 (ppp) REVERT: D 81 LYS cc_start: 0.7822 (tttt) cc_final: 0.6830 (ttpt) REVERT: D 190 GLN cc_start: 0.7543 (mt0) cc_final: 0.6852 (mm110) REVERT: D 235 LEU cc_start: 0.7667 (mm) cc_final: 0.6894 (tp) REVERT: D 328 MET cc_start: 0.3317 (mtm) cc_final: 0.2752 (ppp) outliers start: 34 outliers final: 13 residues processed: 122 average time/residue: 1.4497 time to fit residues: 190.1932 Evaluate side-chains 115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 259 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 33 optimal weight: 0.0980 chunk 81 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 314 GLN D 86 ASN D 121 GLN D 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118696 restraints weight = 8627.712| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.71 r_work: 0.3195 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9081 Z= 0.204 Angle : 0.512 6.933 12320 Z= 0.275 Chirality : 0.039 0.272 1514 Planarity : 0.005 0.076 1433 Dihedral : 11.384 87.922 1360 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.24 % Allowed : 8.81 % Favored : 87.96 % 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: 3.75 (0.24), residues: 1100 helix: 3.22 (0.15), residues: 858 sheet: 3.77 (0.73), residues: 46 loop : -1.63 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 315 HIS 0.001 0.000 HIS C 73 PHE 0.028 0.001 PHE B 215 TYR 0.011 0.001 TYR C 280 ARG 0.005 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7898 (tttt) cc_final: 0.7313 (tppt) REVERT: A 98 THR cc_start: 0.7625 (m) cc_final: 0.7208 (p) REVERT: A 147 LYS cc_start: 0.7387 (mmmt) cc_final: 0.7162 (mmpt) REVERT: A 174 MET cc_start: 0.6755 (ttp) cc_final: 0.6263 (tpt) REVERT: A 181 MET cc_start: 0.7859 (mtp) cc_final: 0.7333 (tpt) REVERT: A 219 ARG cc_start: 0.7582 (mtp180) cc_final: 0.7117 (mtm110) REVERT: A 228 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7543 (mp) REVERT: B 81 LYS cc_start: 0.7467 (tttt) cc_final: 0.7165 (ttmt) REVERT: B 123 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.6818 (ptp-170) REVERT: B 199 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6850 (tmt) REVERT: B 222 ASP cc_start: 0.8796 (m-30) cc_final: 0.8495 (m-30) REVERT: B 235 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7321 (mm) REVERT: B 246 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8129 (p) REVERT: B 275 PHE cc_start: 0.7580 (t80) cc_final: 0.6715 (t80) REVERT: B 328 MET cc_start: 0.4729 (mtp) cc_final: 0.4145 (mtp) REVERT: C 81 LYS cc_start: 0.7824 (ttmt) cc_final: 0.7023 (tptt) REVERT: C 98 THR cc_start: 0.7979 (m) cc_final: 0.7554 (p) REVERT: C 187 ASP cc_start: 0.8365 (p0) cc_final: 0.8158 (p0) REVERT: C 199 MET cc_start: 0.7299 (ttt) cc_final: 0.6161 (mmt) REVERT: C 219 ARG cc_start: 0.7883 (mtp180) cc_final: 0.7312 (mtp-110) REVERT: C 328 MET cc_start: 0.5503 (mmm) cc_final: 0.4667 (ppp) REVERT: D 81 LYS cc_start: 0.7768 (tttt) cc_final: 0.6742 (ttpt) REVERT: D 190 GLN cc_start: 0.7649 (mt0) cc_final: 0.6980 (mm110) REVERT: D 235 LEU cc_start: 0.7819 (mm) cc_final: 0.7080 (tp) REVERT: D 328 MET cc_start: 0.3488 (mtm) cc_final: 0.2882 (ppp) outliers start: 32 outliers final: 15 residues processed: 120 average time/residue: 1.0955 time to fit residues: 141.6771 Evaluate side-chains 119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 259 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN D 86 ASN D 121 GLN D 255 ASN D 256 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.161766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.117367 restraints weight = 8677.393| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.70 r_work: 0.3105 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9081 Z= 0.204 Angle : 0.512 7.016 12320 Z= 0.274 Chirality : 0.039 0.281 1514 Planarity : 0.005 0.077 1433 Dihedral : 10.945 87.921 1360 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.83 % Allowed : 9.82 % Favored : 87.35 % 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: 3.78 (0.24), residues: 1100 helix: 3.24 (0.15), residues: 858 sheet: 3.70 (0.75), residues: 44 loop : -1.55 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 315 HIS 0.001 0.000 HIS C 73 PHE 0.028 0.001 PHE B 215 TYR 0.012 0.001 TYR C 280 ARG 0.003 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7858 (tttt) cc_final: 0.7218 (tppt) REVERT: A 98 THR cc_start: 0.7609 (m) cc_final: 0.7178 (p) REVERT: A 147 LYS cc_start: 0.7382 (mmmt) cc_final: 0.7160 (mmpt) REVERT: A 174 MET cc_start: 0.6750 (ttp) cc_final: 0.6275 (tpt) REVERT: A 181 MET cc_start: 0.7801 (mtp) cc_final: 0.7258 (tpt) REVERT: A 199 MET cc_start: 0.7784 (ttt) cc_final: 0.7202 (ttp) REVERT: A 219 ARG cc_start: 0.7627 (mtp180) cc_final: 0.7132 (mtm110) REVERT: A 228 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7471 (mp) REVERT: B 81 LYS cc_start: 0.7469 (tttt) cc_final: 0.7140 (ttmt) REVERT: B 123 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.6754 (ptp-170) REVERT: B 199 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6710 (tmt) REVERT: B 219 ARG cc_start: 0.7775 (ttt180) cc_final: 0.7054 (ttp-110) REVERT: B 222 ASP cc_start: 0.8791 (m-30) cc_final: 0.8482 (m-30) REVERT: B 235 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7289 (mm) REVERT: B 246 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8106 (p) REVERT: B 275 PHE cc_start: 0.7540 (t80) cc_final: 0.6756 (t80) REVERT: B 328 MET cc_start: 0.4475 (mtp) cc_final: 0.3914 (mtp) REVERT: C 81 LYS cc_start: 0.7777 (ttmt) cc_final: 0.6955 (tptt) REVERT: C 98 THR cc_start: 0.7943 (m) cc_final: 0.7513 (p) REVERT: C 199 MET cc_start: 0.7173 (ttt) cc_final: 0.6458 (mtp) REVERT: C 219 ARG cc_start: 0.7881 (mtp180) cc_final: 0.7270 (mtp-110) REVERT: C 282 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7536 (t70) REVERT: C 328 MET cc_start: 0.5441 (mmm) cc_final: 0.4659 (ppp) REVERT: D 81 LYS cc_start: 0.7788 (tttt) cc_final: 0.6731 (ttpt) REVERT: D 190 GLN cc_start: 0.7559 (mt0) cc_final: 0.6931 (mm110) REVERT: D 195 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6878 (pt) REVERT: D 235 LEU cc_start: 0.7769 (mm) cc_final: 0.7016 (tp) REVERT: D 328 MET cc_start: 0.3392 (mtm) cc_final: 0.2789 (ppp) outliers start: 28 outliers final: 14 residues processed: 122 average time/residue: 1.0733 time to fit residues: 141.4118 Evaluate side-chains 121 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 259 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN C 164 GLN D 86 ASN D 121 GLN D 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.163867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120215 restraints weight = 8756.745| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.77 r_work: 0.3094 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9081 Z= 0.215 Angle : 0.530 10.800 12320 Z= 0.281 Chirality : 0.040 0.288 1514 Planarity : 0.006 0.077 1433 Dihedral : 10.931 89.199 1360 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.83 % Allowed : 10.02 % Favored : 87.15 % 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: 3.76 (0.24), residues: 1100 helix: 3.22 (0.15), residues: 859 sheet: 3.72 (0.75), residues: 44 loop : -1.55 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 54 HIS 0.001 0.000 HIS C 73 PHE 0.028 0.001 PHE B 215 TYR 0.012 0.001 TYR B 280 ARG 0.004 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7835 (tttt) cc_final: 0.7214 (tppt) REVERT: A 98 THR cc_start: 0.7588 (m) cc_final: 0.7144 (p) REVERT: A 147 LYS cc_start: 0.7342 (mmmt) cc_final: 0.7126 (mmpt) REVERT: A 174 MET cc_start: 0.6835 (ttp) cc_final: 0.6314 (tpt) REVERT: A 181 MET cc_start: 0.7742 (mtp) cc_final: 0.7183 (tpt) REVERT: A 199 MET cc_start: 0.7856 (ttt) cc_final: 0.7233 (ttp) REVERT: A 219 ARG cc_start: 0.7595 (mtp180) cc_final: 0.7081 (mtm110) REVERT: A 228 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7425 (mp) REVERT: B 81 LYS cc_start: 0.7453 (tttt) cc_final: 0.7120 (ttmt) REVERT: B 123 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.6735 (ptp-170) REVERT: B 199 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6507 (tpp) REVERT: B 219 ARG cc_start: 0.7764 (ttt180) cc_final: 0.7008 (ttp-110) REVERT: B 222 ASP cc_start: 0.8779 (m-30) cc_final: 0.8469 (m-30) REVERT: B 235 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7244 (mm) REVERT: B 246 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8094 (p) REVERT: B 275 PHE cc_start: 0.7520 (t80) cc_final: 0.6719 (t80) REVERT: C 81 LYS cc_start: 0.7674 (ttmt) cc_final: 0.6850 (tptt) REVERT: C 98 THR cc_start: 0.7893 (m) cc_final: 0.7458 (p) REVERT: C 187 ASP cc_start: 0.8277 (p0) cc_final: 0.8061 (p0) REVERT: C 199 MET cc_start: 0.7176 (ttt) cc_final: 0.6457 (mtp) REVERT: C 219 ARG cc_start: 0.7831 (mtp180) cc_final: 0.7185 (mtp-110) REVERT: C 282 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7509 (t70) REVERT: C 328 MET cc_start: 0.5489 (mmm) cc_final: 0.4684 (ppp) REVERT: D 81 LYS cc_start: 0.7719 (tttt) cc_final: 0.6637 (ttpt) REVERT: D 181 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7552 (ttp) REVERT: D 190 GLN cc_start: 0.7529 (mt0) cc_final: 0.6846 (mm110) REVERT: D 195 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6874 (pt) REVERT: D 235 LEU cc_start: 0.7760 (mm) cc_final: 0.6987 (tp) REVERT: D 328 MET cc_start: 0.3445 (mtm) cc_final: 0.2822 (ppp) outliers start: 28 outliers final: 15 residues processed: 119 average time/residue: 1.0805 time to fit residues: 138.3965 Evaluate side-chains 122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 259 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 90 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 77 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 61 optimal weight: 0.0670 chunk 29 optimal weight: 0.9980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN D 86 ASN D 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118842 restraints weight = 8661.686| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.25 r_work: 0.3221 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9081 Z= 0.156 Angle : 0.491 9.727 12320 Z= 0.262 Chirality : 0.038 0.257 1514 Planarity : 0.005 0.075 1433 Dihedral : 10.538 88.513 1360 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.23 % Allowed : 10.73 % Favored : 87.04 % 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: 4.01 (0.24), residues: 1100 helix: 3.39 (0.15), residues: 859 sheet: 3.77 (0.75), residues: 44 loop : -1.40 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 315 HIS 0.002 0.000 HIS C 214 PHE 0.023 0.001 PHE B 215 TYR 0.011 0.001 TYR C 280 ARG 0.004 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7916 (tttt) cc_final: 0.7297 (tppt) REVERT: A 98 THR cc_start: 0.7578 (m) cc_final: 0.7127 (p) REVERT: A 147 LYS cc_start: 0.7368 (mmmt) cc_final: 0.7060 (mmpt) REVERT: A 174 MET cc_start: 0.6731 (ttp) cc_final: 0.6274 (tpt) REVERT: A 181 MET cc_start: 0.7823 (mtp) cc_final: 0.7301 (tpt) REVERT: A 199 MET cc_start: 0.7860 (ttt) cc_final: 0.7260 (ttp) REVERT: A 219 ARG cc_start: 0.7547 (mtp180) cc_final: 0.7075 (mtm110) REVERT: B 81 LYS cc_start: 0.7396 (tttt) cc_final: 0.7112 (ttmt) REVERT: B 199 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6736 (tmt) REVERT: B 219 ARG cc_start: 0.7753 (ttt180) cc_final: 0.7078 (ttp-110) REVERT: B 222 ASP cc_start: 0.8673 (m-30) cc_final: 0.8409 (m-30) REVERT: B 235 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7267 (mm) REVERT: B 246 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.7964 (p) REVERT: B 275 PHE cc_start: 0.7530 (t80) cc_final: 0.6730 (t80) REVERT: B 328 MET cc_start: 0.4569 (mtp) cc_final: 0.3953 (mtp) REVERT: C 81 LYS cc_start: 0.7762 (ttmt) cc_final: 0.6940 (tptt) REVERT: C 98 THR cc_start: 0.7919 (m) cc_final: 0.7486 (p) REVERT: C 199 MET cc_start: 0.7206 (ttt) cc_final: 0.6504 (mtp) REVERT: C 219 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7201 (mtp-110) REVERT: C 282 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7552 (t-90) REVERT: C 328 MET cc_start: 0.5485 (mmm) cc_final: 0.4682 (ppp) REVERT: D 81 LYS cc_start: 0.7688 (tttt) cc_final: 0.6670 (ttpt) REVERT: D 181 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7584 (ttp) REVERT: D 190 GLN cc_start: 0.7558 (mt0) cc_final: 0.6936 (mm110) REVERT: D 195 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6955 (pt) REVERT: D 235 LEU cc_start: 0.7680 (mm) cc_final: 0.6965 (tp) REVERT: D 328 MET cc_start: 0.3576 (mtm) cc_final: 0.2968 (ppp) outliers start: 22 outliers final: 15 residues processed: 115 average time/residue: 1.0537 time to fit residues: 131.0915 Evaluate side-chains 121 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 259 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 99 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 190 GLN D 121 GLN D 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.163431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119043 restraints weight = 8693.447| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.71 r_work: 0.3213 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9081 Z= 0.196 Angle : 0.528 13.713 12320 Z= 0.275 Chirality : 0.039 0.279 1514 Planarity : 0.005 0.076 1433 Dihedral : 10.475 87.955 1360 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.43 % Allowed : 10.83 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.24), residues: 1100 helix: 3.34 (0.15), residues: 859 sheet: 3.76 (0.76), residues: 44 loop : -1.41 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 54 HIS 0.001 0.000 HIS A 214 PHE 0.021 0.001 PHE C 275 TYR 0.011 0.001 TYR C 280 ARG 0.004 0.000 ARG C 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7913 (tttt) cc_final: 0.7298 (tppt) REVERT: A 98 THR cc_start: 0.7652 (m) cc_final: 0.7223 (p) REVERT: A 147 LYS cc_start: 0.7407 (mmmt) cc_final: 0.7097 (mmpt) REVERT: A 174 MET cc_start: 0.6768 (ttp) cc_final: 0.6356 (tpt) REVERT: A 181 MET cc_start: 0.7825 (mtp) cc_final: 0.7297 (tpt) REVERT: A 199 MET cc_start: 0.7856 (ttt) cc_final: 0.7291 (ttp) REVERT: A 219 ARG cc_start: 0.7572 (mtp180) cc_final: 0.6998 (mtm-85) REVERT: B 81 LYS cc_start: 0.7436 (tttt) cc_final: 0.7140 (ttmt) REVERT: B 199 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6695 (tmt) REVERT: B 222 ASP cc_start: 0.8735 (m-30) cc_final: 0.8449 (m-30) REVERT: B 235 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7265 (mm) REVERT: B 246 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8085 (p) REVERT: B 275 PHE cc_start: 0.7539 (t80) cc_final: 0.6749 (t80) REVERT: B 328 MET cc_start: 0.4603 (mtp) cc_final: 0.3974 (mtp) REVERT: C 81 LYS cc_start: 0.7767 (ttmt) cc_final: 0.6940 (tptt) REVERT: C 98 THR cc_start: 0.7967 (m) cc_final: 0.7553 (p) REVERT: C 199 MET cc_start: 0.7208 (ttt) cc_final: 0.6537 (mtp) REVERT: C 219 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7187 (mtp-110) REVERT: C 282 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7578 (t70) REVERT: C 328 MET cc_start: 0.5494 (mmm) cc_final: 0.4683 (ppp) REVERT: D 81 LYS cc_start: 0.7726 (tttt) cc_final: 0.6702 (ttpt) REVERT: D 181 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7591 (ttp) REVERT: D 190 GLN cc_start: 0.7599 (mt0) cc_final: 0.6959 (mm110) REVERT: D 195 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6972 (pt) REVERT: D 235 LEU cc_start: 0.7723 (mm) cc_final: 0.7040 (tp) REVERT: D 328 MET cc_start: 0.3594 (mtm) cc_final: 0.2977 (ppp) outliers start: 24 outliers final: 15 residues processed: 115 average time/residue: 1.0807 time to fit residues: 134.0239 Evaluate side-chains 119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 259 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.159670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114793 restraints weight = 8803.703| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.74 r_work: 0.3097 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9081 Z= 0.214 Angle : 0.546 13.267 12320 Z= 0.282 Chirality : 0.040 0.288 1514 Planarity : 0.006 0.077 1433 Dihedral : 10.473 84.093 1360 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.53 % Allowed : 10.83 % Favored : 86.64 % 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: 3.89 (0.24), residues: 1100 helix: 3.30 (0.15), residues: 859 sheet: 3.95 (0.71), residues: 46 loop : -1.54 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 54 HIS 0.001 0.000 HIS C 73 PHE 0.021 0.001 PHE C 275 TYR 0.012 0.001 TYR C 280 ARG 0.003 0.000 ARG C 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6605.48 seconds wall clock time: 115 minutes 53.02 seconds (6953.02 seconds total)