Starting phenix.real_space_refine on Sat Aug 23 01:11:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ieq_35390/08_2025/8ieq_35390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ieq_35390/08_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_35390/08_2025/8ieq_35390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ieq_35390/08_2025/8ieq_35390.map" model { file = "/net/cci-nas-00/data/ceres_data/8ieq_35390/08_2025/8ieq_35390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ieq_35390/08_2025/8ieq_35390.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.38, per 1000 atoms: 0.27 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: 0.90 Conformation dependent library (CDL) restraints added in 330.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.23 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: 1.44 Time building geometry restraints manager: 1.12 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 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: 6.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.830 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.880 ------------------------------------------------------------------------------- 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 9085 Z= 0.350 Angle : 0.791 14.077 12328 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 75 TYR 0.010 0.001 TYR B 103 PHE 0.011 0.001 PHE A 308 TRP 0.080 0.003 TRP B 229 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00720 ( 9081) covalent geometry : angle 0.79171 (12320) SS BOND : bond 0.00140 ( 4) SS BOND : angle 0.31619 ( 8) hydrogen bonds : bond 0.12905 ( 766) hydrogen bonds : angle 5.09271 ( 2292) *********************** 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 : 0.334 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: 0.5187 time to fit residues: 73.0552 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 : 0.273 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.164603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117211 restraints weight = 8621.819| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.90 r_work: 0.3110 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9085 Z= 0.164 Angle : 0.558 6.969 12328 Z= 0.297 Chirality : 0.040 0.188 1514 Planarity : 0.005 0.072 1433 Dihedral : 11.288 87.544 1362 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.52 % Allowed : 6.07 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.49 (0.24), residues: 1100 helix: 3.05 (0.16), residues: 852 sheet: 2.99 (0.64), residues: 67 loop : -2.05 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 75 TYR 0.012 0.001 TYR D 103 PHE 0.013 0.002 PHE D 275 TRP 0.021 0.002 TRP B 229 HIS 0.003 0.000 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9081) covalent geometry : angle 0.55774 (12320) SS BOND : bond 0.00494 ( 4) SS BOND : angle 0.57385 ( 8) hydrogen bonds : bond 0.04920 ( 766) hydrogen bonds : angle 4.25722 ( 2292) *********************** 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 119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.327 Fit side-chains REVERT: A 81 LYS cc_start: 0.7915 (tttt) cc_final: 0.7390 (tppt) REVERT: A 98 THR cc_start: 0.7551 (m) cc_final: 0.7130 (p) REVERT: A 147 LYS cc_start: 0.7596 (mmmt) cc_final: 0.7296 (mmpt) REVERT: A 174 MET cc_start: 0.6754 (ttp) cc_final: 0.6227 (tpt) REVERT: A 181 MET cc_start: 0.7973 (mtp) cc_final: 0.7309 (mmp) REVERT: A 219 ARG cc_start: 0.7774 (mtp180) cc_final: 0.7243 (mtm110) REVERT: B 72 ILE cc_start: 0.8250 (mm) cc_final: 0.8024 (mt) REVERT: B 81 LYS cc_start: 0.7576 (tttt) cc_final: 0.7319 (ttmt) REVERT: B 123 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.6919 (ptp-170) REVERT: B 174 MET cc_start: 0.5560 (OUTLIER) cc_final: 0.4999 (tmm) REVERT: B 219 ARG cc_start: 0.7911 (ttt-90) cc_final: 0.7351 (ttp-110) REVERT: B 246 THR cc_start: 0.8606 (m) cc_final: 0.8122 (p) REVERT: B 275 PHE cc_start: 0.7640 (t80) cc_final: 0.6903 (t80) REVERT: B 328 MET cc_start: 0.4372 (mtp) cc_final: 0.3752 (mtp) REVERT: C 81 LYS cc_start: 0.7859 (ttmt) cc_final: 0.7037 (tptt) REVERT: C 98 THR cc_start: 0.8006 (m) cc_final: 0.7591 (p) REVERT: C 174 MET cc_start: 0.6918 (mmm) cc_final: 0.6690 (tpt) REVERT: C 187 ASP cc_start: 0.8501 (p0) cc_final: 0.8235 (p0) REVERT: C 199 MET cc_start: 0.7192 (ttt) cc_final: 0.5904 (mmt) REVERT: C 219 ARG cc_start: 0.8036 (mtp180) cc_final: 0.7417 (mtp-110) REVERT: C 328 MET cc_start: 0.5560 (mmm) cc_final: 0.4737 (ppp) REVERT: D 81 LYS cc_start: 0.8013 (tttt) cc_final: 0.7155 (ttpt) REVERT: D 190 GLN cc_start: 0.7670 (mt0) cc_final: 0.7081 (mm110) REVERT: D 235 LEU cc_start: 0.7766 (mm) cc_final: 0.7144 (tp) REVERT: D 328 MET cc_start: 0.3363 (mtm) cc_final: 0.2499 (pmt) outliers start: 15 outliers final: 9 residues processed: 112 average time/residue: 0.5646 time to fit residues: 67.5758 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 : 0.286 ------------------------------------------------------------------------------- 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 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 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 D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.161065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113657 restraints weight = 8637.798| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.87 r_work: 0.3077 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9085 Z= 0.166 Angle : 0.551 8.156 12328 Z= 0.293 Chirality : 0.040 0.225 1514 Planarity : 0.006 0.075 1433 Dihedral : 11.548 88.797 1360 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.53 % Allowed : 7.59 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.48 (0.24), residues: 1100 helix: 3.11 (0.15), residues: 855 sheet: 3.11 (0.78), residues: 42 loop : -1.84 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 75 TYR 0.011 0.001 TYR C 280 PHE 0.027 0.002 PHE B 215 TRP 0.008 0.001 TRP C 315 HIS 0.001 0.000 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9081) covalent geometry : angle 0.55146 (12320) SS BOND : bond 0.00384 ( 4) SS BOND : angle 0.56571 ( 8) hydrogen bonds : bond 0.04894 ( 766) hydrogen bonds : angle 4.14033 ( 2292) *********************** 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 : 0.407 Fit side-chains REVERT: A 81 LYS cc_start: 0.7977 (tttt) cc_final: 0.7421 (tppt) REVERT: A 98 THR cc_start: 0.7754 (m) cc_final: 0.7351 (p) REVERT: A 147 LYS cc_start: 0.7610 (mmmt) cc_final: 0.7313 (mmpt) REVERT: A 174 MET cc_start: 0.6800 (ttp) cc_final: 0.6300 (tpt) REVERT: A 181 MET cc_start: 0.7958 (mtp) cc_final: 0.7431 (tpt) REVERT: A 219 ARG cc_start: 0.7805 (mtp180) cc_final: 0.7184 (mtm-85) REVERT: B 81 LYS cc_start: 0.7592 (tttt) cc_final: 0.7331 (ttmt) REVERT: B 123 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.6919 (ptp-170) REVERT: B 174 MET cc_start: 0.5577 (OUTLIER) cc_final: 0.5025 (tmm) REVERT: B 219 ARG cc_start: 0.7875 (ttt-90) cc_final: 0.7355 (ttp-110) REVERT: B 222 ASP cc_start: 0.8837 (m-30) cc_final: 0.8592 (m-30) REVERT: B 246 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8289 (p) REVERT: B 275 PHE cc_start: 0.7742 (t80) cc_final: 0.6950 (t80) REVERT: C 98 THR cc_start: 0.8115 (m) cc_final: 0.7685 (p) REVERT: C 174 MET cc_start: 0.6879 (mmm) cc_final: 0.6584 (tpt) REVERT: C 187 ASP cc_start: 0.8490 (p0) cc_final: 0.8264 (p0) REVERT: C 199 MET cc_start: 0.7172 (ttt) cc_final: 0.5941 (mmt) REVERT: C 219 ARG cc_start: 0.8062 (mtp180) cc_final: 0.7467 (mtp-110) REVERT: C 328 MET cc_start: 0.5562 (mmm) cc_final: 0.4691 (ppp) REVERT: D 81 LYS cc_start: 0.7948 (tttt) cc_final: 0.7058 (ttpt) REVERT: D 190 GLN cc_start: 0.7723 (mt0) cc_final: 0.7114 (mm110) REVERT: D 235 LEU cc_start: 0.7811 (mm) cc_final: 0.7164 (tp) REVERT: D 328 MET cc_start: 0.3310 (mtm) cc_final: 0.2381 (pmt) outliers start: 25 outliers final: 10 residues processed: 120 average time/residue: 0.5813 time to fit residues: 74.5690 Evaluate side-chains 111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 66 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 10 optimal weight: 0.0270 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 255 ASN D 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.162978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115648 restraints weight = 8717.925| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.87 r_work: 0.3202 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9085 Z= 0.136 Angle : 0.506 6.734 12328 Z= 0.272 Chirality : 0.039 0.235 1514 Planarity : 0.005 0.075 1433 Dihedral : 11.455 86.339 1360 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.43 % Allowed : 8.70 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.68 (0.24), residues: 1100 helix: 3.27 (0.15), residues: 856 sheet: 3.15 (0.88), residues: 36 loop : -1.67 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 75 TYR 0.011 0.001 TYR A 280 PHE 0.026 0.001 PHE B 215 TRP 0.008 0.001 TRP C 315 HIS 0.001 0.000 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9081) covalent geometry : angle 0.50586 (12320) SS BOND : bond 0.00397 ( 4) SS BOND : angle 0.56849 ( 8) hydrogen bonds : bond 0.04489 ( 766) hydrogen bonds : angle 3.99302 ( 2292) *********************** 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 126 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7562 (tttt) cc_final: 0.6941 (tppt) REVERT: A 98 THR cc_start: 0.7073 (m) cc_final: 0.6607 (p) REVERT: A 147 LYS cc_start: 0.6792 (mmmt) cc_final: 0.6465 (mmpt) REVERT: A 174 MET cc_start: 0.6422 (ttp) cc_final: 0.5852 (tpt) REVERT: A 181 MET cc_start: 0.7285 (mtp) cc_final: 0.6731 (tpt) REVERT: A 219 ARG cc_start: 0.7471 (mtp180) cc_final: 0.6729 (mtm-85) REVERT: B 72 ILE cc_start: 0.7923 (mm) cc_final: 0.7708 (mt) REVERT: B 81 LYS cc_start: 0.7302 (tttt) cc_final: 0.6985 (ttmt) REVERT: B 123 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.6301 (ptp-170) REVERT: B 219 ARG cc_start: 0.7486 (ttt-90) cc_final: 0.6838 (ttp-110) REVERT: B 222 ASP cc_start: 0.8446 (m-30) cc_final: 0.8156 (m-30) REVERT: B 246 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7556 (p) REVERT: B 275 PHE cc_start: 0.7096 (t80) cc_final: 0.6315 (t80) REVERT: B 328 MET cc_start: 0.4432 (mtp) cc_final: 0.3862 (mtp) REVERT: C 81 LYS cc_start: 0.7402 (ttmt) cc_final: 0.6561 (tptt) REVERT: C 98 THR cc_start: 0.7512 (m) cc_final: 0.6964 (p) REVERT: C 117 GLU cc_start: 0.7871 (mp0) cc_final: 0.7665 (mp0) REVERT: C 174 MET cc_start: 0.6415 (mmm) cc_final: 0.6213 (tpt) REVERT: C 199 MET cc_start: 0.7028 (ttt) cc_final: 0.5861 (mmt) REVERT: C 219 ARG cc_start: 0.7730 (mtp180) cc_final: 0.7022 (mtp-110) REVERT: C 328 MET cc_start: 0.5528 (mmm) cc_final: 0.4698 (ppp) REVERT: D 81 LYS cc_start: 0.7631 (tttt) cc_final: 0.6538 (ttpt) REVERT: D 190 GLN cc_start: 0.7276 (mt0) cc_final: 0.6584 (mm110) REVERT: D 235 LEU cc_start: 0.7199 (mm) cc_final: 0.6420 (tp) REVERT: D 328 MET cc_start: 0.3277 (mtm) cc_final: 0.2428 (pmt) outliers start: 24 outliers final: 14 residues processed: 118 average time/residue: 0.5473 time to fit residues: 69.4840 Evaluate side-chains 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 197 VAL Chi-restraints excluded: chain B residue 246 THR 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 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 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 101 optimal weight: 0.0570 chunk 91 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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 D 255 ASN D 256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.164720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120069 restraints weight = 8638.655| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.71 r_work: 0.3134 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9085 Z= 0.127 Angle : 0.494 6.403 12328 Z= 0.265 Chirality : 0.039 0.240 1514 Planarity : 0.005 0.075 1433 Dihedral : 11.264 85.594 1360 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.73 % Allowed : 9.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.90 (0.24), residues: 1100 helix: 3.33 (0.15), residues: 859 sheet: 3.37 (0.72), residues: 48 loop : -1.58 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 75 TYR 0.011 0.001 TYR A 280 PHE 0.028 0.001 PHE B 215 TRP 0.008 0.001 TRP C 315 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9081) covalent geometry : angle 0.49381 (12320) SS BOND : bond 0.00276 ( 4) SS BOND : angle 0.48145 ( 8) hydrogen bonds : bond 0.04319 ( 766) hydrogen bonds : angle 3.90473 ( 2292) *********************** 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 133 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7779 (tttt) cc_final: 0.7151 (tppt) REVERT: A 98 THR cc_start: 0.7445 (m) cc_final: 0.7002 (p) REVERT: A 147 LYS cc_start: 0.7314 (mmmt) cc_final: 0.7007 (mmpt) REVERT: A 174 MET cc_start: 0.6684 (ttp) cc_final: 0.6140 (tpt) REVERT: A 181 MET cc_start: 0.7708 (mtp) cc_final: 0.7200 (tpt) REVERT: A 219 ARG cc_start: 0.7613 (mtp180) cc_final: 0.6948 (mtm-85) REVERT: B 72 ILE cc_start: 0.8166 (mm) cc_final: 0.7961 (mt) REVERT: B 81 LYS cc_start: 0.7405 (tttt) cc_final: 0.7116 (ttmt) REVERT: B 123 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.6578 (ptp-170) REVERT: B 219 ARG cc_start: 0.7694 (ttt-90) cc_final: 0.7106 (ttp-110) REVERT: B 222 ASP cc_start: 0.8610 (m-30) cc_final: 0.8343 (m-30) REVERT: B 246 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7907 (p) REVERT: B 275 PHE cc_start: 0.7475 (t80) cc_final: 0.6664 (t80) REVERT: B 328 MET cc_start: 0.4521 (mtp) cc_final: 0.3994 (mtp) REVERT: C 81 LYS cc_start: 0.7629 (ttmt) cc_final: 0.6809 (tptt) REVERT: C 98 THR cc_start: 0.7849 (m) cc_final: 0.7369 (p) REVERT: C 174 MET cc_start: 0.6597 (mmm) cc_final: 0.6375 (tpt) REVERT: C 187 ASP cc_start: 0.8360 (p0) cc_final: 0.8135 (p0) REVERT: C 199 MET cc_start: 0.7121 (ttt) cc_final: 0.5918 (mmt) REVERT: C 219 ARG cc_start: 0.7834 (mtp180) cc_final: 0.7180 (mtp-110) REVERT: C 328 MET cc_start: 0.5544 (mmm) cc_final: 0.4715 (ppp) REVERT: D 81 LYS cc_start: 0.7734 (tttt) cc_final: 0.6673 (ttpt) REVERT: D 190 GLN cc_start: 0.7569 (mt0) cc_final: 0.6939 (mm110) REVERT: D 235 LEU cc_start: 0.7595 (mm) cc_final: 0.6868 (tp) REVERT: D 328 MET cc_start: 0.3392 (mtm) cc_final: 0.2538 (pmt) outliers start: 27 outliers final: 15 residues processed: 122 average time/residue: 0.5362 time to fit residues: 70.2261 Evaluate side-chains 121 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU 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 197 VAL Chi-restraints excluded: chain B residue 246 THR 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 65 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 304 ASN D 121 GLN D 255 ASN D 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.160694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116172 restraints weight = 8756.308| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.71 r_work: 0.3082 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9085 Z= 0.166 Angle : 0.543 6.531 12328 Z= 0.289 Chirality : 0.041 0.287 1514 Planarity : 0.006 0.078 1433 Dihedral : 11.563 89.487 1360 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.94 % Allowed : 9.41 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.67 (0.24), residues: 1100 helix: 3.18 (0.15), residues: 857 sheet: 3.59 (0.72), residues: 48 loop : -1.75 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 75 TYR 0.013 0.001 TYR B 280 PHE 0.031 0.002 PHE B 215 TRP 0.008 0.001 TRP C 315 HIS 0.002 0.000 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9081) covalent geometry : angle 0.54279 (12320) SS BOND : bond 0.00385 ( 4) SS BOND : angle 0.65840 ( 8) hydrogen bonds : bond 0.04820 ( 766) hydrogen bonds : angle 3.99942 ( 2292) *********************** 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 132 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7827 (tttt) cc_final: 0.7240 (tppt) REVERT: A 98 THR cc_start: 0.7633 (m) cc_final: 0.7206 (p) REVERT: A 147 LYS cc_start: 0.7379 (mmmt) cc_final: 0.7169 (mmpt) REVERT: A 174 MET cc_start: 0.6757 (ttp) cc_final: 0.6243 (tpt) REVERT: A 181 MET cc_start: 0.7815 (mtp) cc_final: 0.7260 (tpt) REVERT: A 219 ARG cc_start: 0.7672 (mtp180) cc_final: 0.7034 (mtm-85) REVERT: A 228 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7550 (mp) REVERT: B 81 LYS cc_start: 0.7518 (tttt) cc_final: 0.7194 (ttmt) REVERT: B 123 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.6810 (ptp-170) REVERT: B 222 ASP cc_start: 0.8805 (m-30) cc_final: 0.8514 (m-30) REVERT: B 235 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7296 (mm) REVERT: B 246 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8176 (p) REVERT: B 275 PHE cc_start: 0.7604 (t80) cc_final: 0.6754 (t80) REVERT: B 328 MET cc_start: 0.4589 (mtp) cc_final: 0.4063 (mtp) REVERT: C 98 THR cc_start: 0.8029 (m) cc_final: 0.7594 (p) REVERT: C 199 MET cc_start: 0.7199 (ttt) cc_final: 0.6565 (mtp) REVERT: C 219 ARG cc_start: 0.7899 (mtp180) cc_final: 0.7297 (mtp-110) REVERT: C 282 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7559 (t70) REVERT: C 328 MET cc_start: 0.5468 (mmm) cc_final: 0.4624 (ppp) REVERT: D 81 LYS cc_start: 0.7821 (tttt) cc_final: 0.6842 (ttpt) REVERT: D 190 GLN cc_start: 0.7592 (mt0) cc_final: 0.6984 (mm110) REVERT: D 235 LEU cc_start: 0.7777 (mm) cc_final: 0.7026 (tp) REVERT: D 328 MET cc_start: 0.3280 (mtm) cc_final: 0.2706 (ppp) outliers start: 29 outliers final: 13 residues processed: 121 average time/residue: 0.5783 time to fit residues: 74.7695 Evaluate side-chains 118 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU 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 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 181 MET Chi-restraints excluded: chain D residue 192 LEU 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 15 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 314 GLN D 86 ASN D 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.160196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.115615 restraints weight = 8745.125| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.70 r_work: 0.3097 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9085 Z= 0.155 Angle : 0.529 6.861 12328 Z= 0.284 Chirality : 0.040 0.278 1514 Planarity : 0.006 0.077 1433 Dihedral : 11.191 86.611 1360 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.83 % Allowed : 9.72 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.70 (0.24), residues: 1100 helix: 3.19 (0.15), residues: 858 sheet: 3.63 (0.76), residues: 46 loop : -1.69 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 75 TYR 0.012 0.001 TYR C 280 PHE 0.028 0.002 PHE B 215 TRP 0.008 0.001 TRP C 315 HIS 0.001 0.000 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9081) covalent geometry : angle 0.52918 (12320) SS BOND : bond 0.00342 ( 4) SS BOND : angle 0.56095 ( 8) hydrogen bonds : bond 0.04647 ( 766) hydrogen bonds : angle 3.94578 ( 2292) *********************** 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 130 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7856 (tttt) cc_final: 0.7242 (tppt) REVERT: A 98 THR cc_start: 0.7606 (m) cc_final: 0.7175 (p) REVERT: A 147 LYS cc_start: 0.7444 (mmmt) cc_final: 0.7222 (mmpt) REVERT: A 174 MET cc_start: 0.6819 (ttp) cc_final: 0.6285 (tpt) REVERT: A 181 MET cc_start: 0.7817 (mtp) cc_final: 0.7262 (tpt) REVERT: A 219 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7125 (mtm110) REVERT: A 228 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7509 (mp) REVERT: B 81 LYS cc_start: 0.7503 (tttt) cc_final: 0.7175 (ttmt) REVERT: B 123 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.6795 (ptp-170) REVERT: B 219 ARG cc_start: 0.7794 (ttt180) cc_final: 0.7070 (ttp-110) REVERT: B 222 ASP cc_start: 0.8786 (m-30) cc_final: 0.8490 (m-30) REVERT: B 235 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7289 (mm) REVERT: B 246 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8121 (p) REVERT: B 275 PHE cc_start: 0.7588 (t80) cc_final: 0.6802 (t80) REVERT: B 328 MET cc_start: 0.4581 (mtp) cc_final: 0.4049 (mtp) REVERT: C 81 LYS cc_start: 0.7777 (ttmt) cc_final: 0.6944 (tptt) REVERT: C 98 THR cc_start: 0.7993 (m) cc_final: 0.7556 (p) REVERT: C 187 ASP cc_start: 0.8408 (p0) cc_final: 0.8207 (p0) REVERT: C 199 MET cc_start: 0.7181 (ttt) cc_final: 0.6481 (mtp) REVERT: C 219 ARG cc_start: 0.7881 (mtp180) cc_final: 0.7280 (mtp-110) REVERT: C 282 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.7547 (t70) REVERT: C 328 MET cc_start: 0.5469 (mmm) cc_final: 0.4627 (ppp) REVERT: D 81 LYS cc_start: 0.7783 (tttt) cc_final: 0.6798 (ttpt) REVERT: D 190 GLN cc_start: 0.7576 (mt0) cc_final: 0.6924 (mm110) REVERT: D 195 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6868 (pt) REVERT: D 235 LEU cc_start: 0.7818 (mm) cc_final: 0.7060 (tp) REVERT: D 328 MET cc_start: 0.3305 (mtm) cc_final: 0.2722 (ppp) outliers start: 28 outliers final: 15 residues processed: 121 average time/residue: 0.5571 time to fit residues: 72.2031 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 : 0.358 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 60 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 D 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.161424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117117 restraints weight = 8700.156| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.70 r_work: 0.3112 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9085 Z= 0.134 Angle : 0.502 6.474 12328 Z= 0.271 Chirality : 0.039 0.258 1514 Planarity : 0.005 0.075 1433 Dihedral : 10.876 87.464 1360 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.33 % Allowed : 10.22 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.85 (0.24), residues: 1100 helix: 3.29 (0.15), residues: 858 sheet: 3.69 (0.76), residues: 46 loop : -1.57 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 75 TYR 0.011 0.001 TYR A 280 PHE 0.028 0.001 PHE B 215 TRP 0.008 0.001 TRP C 315 HIS 0.001 0.000 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9081) covalent geometry : angle 0.50164 (12320) SS BOND : bond 0.00343 ( 4) SS BOND : angle 0.53389 ( 8) hydrogen bonds : bond 0.04393 ( 766) hydrogen bonds : angle 3.86016 ( 2292) *********************** 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 125 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7846 (tttt) cc_final: 0.7206 (tppt) REVERT: A 98 THR cc_start: 0.7551 (m) cc_final: 0.7119 (p) REVERT: A 147 LYS cc_start: 0.7420 (mmmt) cc_final: 0.7205 (mmpt) REVERT: A 174 MET cc_start: 0.6810 (ttp) cc_final: 0.6347 (tpt) REVERT: A 181 MET cc_start: 0.7802 (mtp) cc_final: 0.7270 (tpt) REVERT: A 199 MET cc_start: 0.7702 (ttt) cc_final: 0.7159 (ttp) REVERT: A 219 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7085 (mtm110) REVERT: A 228 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7417 (mp) REVERT: B 81 LYS cc_start: 0.7381 (tttt) cc_final: 0.7078 (ttmt) REVERT: B 123 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.6645 (ptp-170) REVERT: B 199 MET cc_start: 0.7074 (tpt) cc_final: 0.6660 (tmt) REVERT: B 219 ARG cc_start: 0.7765 (ttt180) cc_final: 0.7050 (ttp-110) REVERT: B 222 ASP cc_start: 0.8785 (m-30) cc_final: 0.8498 (m-30) REVERT: B 235 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7273 (mm) REVERT: B 246 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8091 (p) REVERT: B 275 PHE cc_start: 0.7523 (t80) cc_final: 0.6738 (t80) REVERT: B 328 MET cc_start: 0.4657 (mtp) cc_final: 0.4107 (mtp) REVERT: C 81 LYS cc_start: 0.7711 (ttmt) cc_final: 0.6892 (tptt) REVERT: C 98 THR cc_start: 0.7924 (m) cc_final: 0.7495 (p) REVERT: C 187 ASP cc_start: 0.8339 (p0) cc_final: 0.8119 (p0) REVERT: C 199 MET cc_start: 0.7214 (ttt) cc_final: 0.6573 (mtp) REVERT: C 219 ARG cc_start: 0.7818 (mtp180) cc_final: 0.7196 (mtp-110) REVERT: C 282 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7543 (t70) REVERT: C 328 MET cc_start: 0.5475 (mmm) cc_final: 0.4679 (ppp) REVERT: D 81 LYS cc_start: 0.7718 (tttt) cc_final: 0.6654 (ttpt) REVERT: D 181 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7623 (ttp) REVERT: D 190 GLN cc_start: 0.7559 (mt0) cc_final: 0.6943 (mm110) REVERT: D 235 LEU cc_start: 0.7699 (mm) cc_final: 0.6986 (tp) REVERT: D 328 MET cc_start: 0.3446 (mtm) cc_final: 0.2838 (ppp) outliers start: 23 outliers final: 15 residues processed: 116 average time/residue: 0.5680 time to fit residues: 70.5807 Evaluate side-chains 120 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 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 181 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.160363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115855 restraints weight = 8745.223| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.70 r_work: 0.3094 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9085 Z= 0.146 Angle : 0.529 10.388 12328 Z= 0.280 Chirality : 0.040 0.276 1514 Planarity : 0.006 0.076 1433 Dihedral : 10.890 88.636 1360 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.94 % Allowed : 9.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.79 (0.24), residues: 1100 helix: 3.25 (0.15), residues: 858 sheet: 3.69 (0.76), residues: 46 loop : -1.61 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 75 TYR 0.012 0.001 TYR C 280 PHE 0.023 0.001 PHE B 215 TRP 0.009 0.001 TRP B 54 HIS 0.002 0.000 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9081) covalent geometry : angle 0.52876 (12320) SS BOND : bond 0.00392 ( 4) SS BOND : angle 0.54934 ( 8) hydrogen bonds : bond 0.04557 ( 766) hydrogen bonds : angle 3.89321 ( 2292) *********************** 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 130 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7870 (tttt) cc_final: 0.7248 (tppt) REVERT: A 98 THR cc_start: 0.7619 (m) cc_final: 0.7188 (p) REVERT: A 147 LYS cc_start: 0.7434 (mmmt) cc_final: 0.7213 (mmpt) REVERT: A 174 MET cc_start: 0.6811 (ttp) cc_final: 0.6294 (tpt) REVERT: A 181 MET cc_start: 0.7786 (mtp) cc_final: 0.7235 (tpt) REVERT: A 199 MET cc_start: 0.7773 (ttt) cc_final: 0.7166 (ttp) REVERT: A 219 ARG cc_start: 0.7629 (mtp180) cc_final: 0.7123 (mtm110) REVERT: A 228 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7468 (mp) REVERT: B 81 LYS cc_start: 0.7491 (tttt) cc_final: 0.7159 (ttmt) REVERT: B 123 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.6768 (ptp-170) REVERT: B 219 ARG cc_start: 0.7774 (ttt180) cc_final: 0.7048 (ttp-110) REVERT: B 222 ASP cc_start: 0.8796 (m-30) cc_final: 0.8485 (m-30) REVERT: B 235 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7285 (mm) REVERT: B 246 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8118 (p) REVERT: B 275 PHE cc_start: 0.7563 (t80) cc_final: 0.6773 (t80) REVERT: B 328 MET cc_start: 0.4547 (mtp) cc_final: 0.3999 (mtp) REVERT: C 81 LYS cc_start: 0.7772 (ttmt) cc_final: 0.6934 (tptt) REVERT: C 98 THR cc_start: 0.7958 (m) cc_final: 0.7539 (p) REVERT: C 199 MET cc_start: 0.7154 (ttt) cc_final: 0.6437 (mtp) REVERT: C 219 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7191 (mtp-110) REVERT: C 282 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7529 (t70) REVERT: C 328 MET cc_start: 0.5479 (mmm) cc_final: 0.4676 (ppp) REVERT: D 81 LYS cc_start: 0.7756 (tttt) cc_final: 0.6690 (ttpt) REVERT: D 181 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7628 (ttp) REVERT: D 190 GLN cc_start: 0.7560 (mt0) cc_final: 0.6943 (mm110) REVERT: D 195 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6845 (pt) REVERT: D 235 LEU cc_start: 0.7787 (mm) cc_final: 0.7031 (tp) REVERT: D 328 MET cc_start: 0.3417 (mtm) cc_final: 0.2813 (ppp) outliers start: 29 outliers final: 16 residues processed: 121 average time/residue: 0.5488 time to fit residues: 71.3078 Evaluate side-chains 124 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 228 ILE Chi-restraints excluded: chain A residue 261 MET 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 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 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 46 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN D 86 ASN D 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.161986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117493 restraints weight = 8678.242| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.71 r_work: 0.3084 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9085 Z= 0.155 Angle : 0.541 9.512 12328 Z= 0.287 Chirality : 0.040 0.285 1514 Planarity : 0.006 0.077 1433 Dihedral : 10.778 81.152 1360 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.63 % Allowed : 10.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.73 (0.24), residues: 1100 helix: 3.21 (0.15), residues: 859 sheet: 3.60 (0.75), residues: 46 loop : -1.64 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 75 TYR 0.012 0.001 TYR C 280 PHE 0.021 0.001 PHE C 275 TRP 0.012 0.001 TRP B 54 HIS 0.001 0.000 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9081) covalent geometry : angle 0.54101 (12320) SS BOND : bond 0.00397 ( 4) SS BOND : angle 0.55456 ( 8) hydrogen bonds : bond 0.04653 ( 766) hydrogen bonds : angle 3.92837 ( 2292) ********************** 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 126 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7809 (tttt) cc_final: 0.7189 (tppt) REVERT: A 98 THR cc_start: 0.7611 (m) cc_final: 0.7167 (p) REVERT: A 147 LYS cc_start: 0.7434 (mmmt) cc_final: 0.7211 (mmpt) REVERT: A 174 MET cc_start: 0.6792 (ttp) cc_final: 0.6287 (tpt) REVERT: A 181 MET cc_start: 0.7766 (mtp) cc_final: 0.7208 (tpt) REVERT: A 199 MET cc_start: 0.7698 (ttt) cc_final: 0.7188 (ttp) REVERT: A 219 ARG cc_start: 0.7624 (mtp180) cc_final: 0.7010 (mtm-85) REVERT: A 228 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7474 (mp) REVERT: B 81 LYS cc_start: 0.7476 (tttt) cc_final: 0.7137 (ttmt) REVERT: B 123 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.6734 (ptp-170) REVERT: B 222 ASP cc_start: 0.8777 (m-30) cc_final: 0.8472 (m-30) REVERT: B 235 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7257 (mm) REVERT: B 246 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8119 (p) REVERT: B 275 PHE cc_start: 0.7562 (t80) cc_final: 0.6751 (t80) REVERT: B 328 MET cc_start: 0.4608 (mtp) cc_final: 0.4042 (mtp) REVERT: C 98 THR cc_start: 0.7942 (m) cc_final: 0.7510 (p) REVERT: C 199 MET cc_start: 0.7168 (ttt) cc_final: 0.6447 (mtp) REVERT: C 219 ARG cc_start: 0.7859 (mtp180) cc_final: 0.7205 (mtp-110) REVERT: C 282 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.7523 (t70) REVERT: C 328 MET cc_start: 0.5489 (mmm) cc_final: 0.4676 (ppp) REVERT: D 81 LYS cc_start: 0.7757 (tttt) cc_final: 0.6754 (ttpt) REVERT: D 181 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7574 (ttp) REVERT: D 190 GLN cc_start: 0.7550 (mt0) cc_final: 0.6899 (mm110) REVERT: D 195 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6901 (pt) REVERT: D 219 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7805 (ttp-170) REVERT: D 235 LEU cc_start: 0.7793 (mm) cc_final: 0.7027 (tp) REVERT: D 328 MET cc_start: 0.3442 (mtm) cc_final: 0.2824 (ppp) outliers start: 26 outliers final: 16 residues processed: 117 average time/residue: 0.5498 time to fit residues: 69.0937 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 : 0.335 ------------------------------------------------------------------------------- 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 228 ILE Chi-restraints excluded: chain A residue 261 MET 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 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 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 11 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.161435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116978 restraints weight = 8575.584| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.70 r_work: 0.3086 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9085 Z= 0.163 Angle : 0.553 10.138 12328 Z= 0.292 Chirality : 0.041 0.288 1514 Planarity : 0.006 0.077 1433 Dihedral : 10.721 79.033 1360 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.33 % Allowed : 10.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.24), residues: 1100 helix: 3.16 (0.15), residues: 858 sheet: 3.59 (0.75), residues: 46 loop : -1.64 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 75 TYR 0.013 0.001 TYR B 280 PHE 0.021 0.002 PHE C 275 TRP 0.014 0.001 TRP B 54 HIS 0.001 0.000 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9081) covalent geometry : angle 0.55332 (12320) SS BOND : bond 0.00400 ( 4) SS BOND : angle 0.54030 ( 8) hydrogen bonds : bond 0.04729 ( 766) hydrogen bonds : angle 3.95154 ( 2292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3326.84 seconds wall clock time: 57 minutes 43.71 seconds (3463.71 seconds total)