Starting phenix.real_space_refine on Thu Feb 5 01:01:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ddx_46783/02_2026/9ddx_46783.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ddx_46783/02_2026/9ddx_46783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ddx_46783/02_2026/9ddx_46783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ddx_46783/02_2026/9ddx_46783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ddx_46783/02_2026/9ddx_46783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ddx_46783/02_2026/9ddx_46783.map" } resolution = 2.55 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= 0.001 sd= 0.014 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 S 39 5.16 5 C 4863 2.51 5 N 1257 2.21 5 O 1599 1.98 5 H 6039 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13806 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 4494 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 303} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 4494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 4494 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 303} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'ATP': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'ATP': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Restraints were copied for chains: C Time building chain proxies: 3.94, per 1000 atoms: 0.29 Number of scatterers: 13806 At special positions: 0 Unit cell: (86.832, 90.072, 118.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 9 15.00 O 1599 8.00 N 1257 7.00 C 4863 6.00 H 6039 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 279 " distance=2.06 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " distance=2.06 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 279 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 133 " " NAG A 502 " - " ASN A 194 " " NAG B 501 " - " ASN B 133 " " NAG B 502 " - " ASN B 194 " " NAG C 501 " - " ASN C 133 " " NAG C 502 " - " ASN C 194 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 358.2 milliseconds 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1752 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 29.3% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 43 through 65 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 337 through 361 Processing helix chain 'B' and resid 44 through 65 Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 337 through 361 Processing helix chain 'C' and resid 44 through 65 Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 337 through 361 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 72 current: chain 'A' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 107 through 126 current: chain 'A' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 176 current: chain 'A' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 282 through 287 current: chain 'A' and resid 312 through 336 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 83 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 72 current: chain 'B' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 107 through 126 current: chain 'B' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 176 current: chain 'B' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 282 through 287 current: chain 'B' and resid 312 through 336 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 83 Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 72 current: chain 'C' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 107 through 126 current: chain 'C' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 168 through 176 current: chain 'C' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 282 through 287 current: chain 'C' and resid 312 through 336 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 83 Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 88 226 hydrogen bonds defined for protein. 570 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6039 1.03 - 1.23: 75 1.23 - 1.43: 3249 1.43 - 1.62: 4449 1.62 - 1.82: 45 Bond restraints: 13857 Sorted by residual: bond pdb=" C4 ATP B 500 " pdb=" C5 ATP B 500 " ideal model delta sigma weight residual 1.388 1.477 -0.089 1.00e-02 1.00e+04 7.95e+01 bond pdb=" C4 ATP C 500 " pdb=" C5 ATP C 500 " ideal model delta sigma weight residual 1.388 1.477 -0.089 1.00e-02 1.00e+04 7.92e+01 bond pdb=" C4 ATP A 500 " pdb=" C5 ATP A 500 " ideal model delta sigma weight residual 1.388 1.477 -0.089 1.00e-02 1.00e+04 7.89e+01 bond pdb=" C5 ATP B 500 " pdb=" C6 ATP B 500 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.18e+01 bond pdb=" C5 ATP C 500 " pdb=" C6 ATP C 500 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.12e+01 ... (remaining 13852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 24360 3.92 - 7.84: 63 7.84 - 11.77: 9 11.77 - 15.69: 0 15.69 - 19.61: 3 Bond angle restraints: 24435 Sorted by residual: angle pdb=" PB ATP C 500 " pdb=" O3B ATP C 500 " pdb=" PG ATP C 500 " ideal model delta sigma weight residual 139.87 120.26 19.61 1.00e+00 1.00e+00 3.85e+02 angle pdb=" PB ATP B 500 " pdb=" O3B ATP B 500 " pdb=" PG ATP B 500 " ideal model delta sigma weight residual 139.87 120.26 19.61 1.00e+00 1.00e+00 3.84e+02 angle pdb=" PB ATP A 500 " pdb=" O3B ATP A 500 " pdb=" PG ATP A 500 " ideal model delta sigma weight residual 139.87 120.27 19.60 1.00e+00 1.00e+00 3.84e+02 angle pdb=" PA ATP A 500 " pdb=" O3A ATP A 500 " pdb=" PB ATP A 500 " ideal model delta sigma weight residual 136.83 125.42 11.41 1.00e+00 1.00e+00 1.30e+02 angle pdb=" PA ATP B 500 " pdb=" O3A ATP B 500 " pdb=" PB ATP B 500 " ideal model delta sigma weight residual 136.83 125.46 11.37 1.00e+00 1.00e+00 1.29e+02 ... (remaining 24430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 6154 17.68 - 35.36: 458 35.36 - 53.04: 186 53.04 - 70.72: 63 70.72 - 88.40: 15 Dihedral angle restraints: 6876 sinusoidal: 3648 harmonic: 3228 Sorted by residual: dihedral pdb=" CB CYS C 270 " pdb=" SG CYS C 270 " pdb=" SG CYS C 279 " pdb=" CB CYS C 279 " ideal model delta sinusoidal sigma weight residual 93.00 26.15 66.85 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS A 270 " pdb=" SG CYS A 270 " pdb=" SG CYS A 279 " pdb=" CB CYS A 279 " ideal model delta sinusoidal sigma weight residual 93.00 26.17 66.83 1 1.00e+01 1.00e-02 5.82e+01 dihedral pdb=" CB CYS B 270 " pdb=" SG CYS B 270 " pdb=" SG CYS B 279 " pdb=" CB CYS B 279 " ideal model delta sinusoidal sigma weight residual 93.00 26.20 66.80 1 1.00e+01 1.00e-02 5.82e+01 ... (remaining 6873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1150 0.122 - 0.244: 44 0.244 - 0.366: 3 0.366 - 0.487: 3 0.487 - 0.609: 3 Chirality restraints: 1203 Sorted by residual: chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 194 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.28e+00 chirality pdb=" C1 NAG C 502 " pdb=" ND2 ASN C 194 " pdb=" C2 NAG C 502 " pdb=" O5 NAG C 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.20e+00 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 194 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.20e+00 ... (remaining 1200 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 68 " -0.150 2.00e-02 2.50e+03 1.63e-01 3.98e+02 pdb=" CD GLN B 68 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN B 68 " 0.143 2.00e-02 2.50e+03 pdb=" NE2 GLN B 68 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN B 68 " 0.241 2.00e-02 2.50e+03 pdb="HE22 GLN B 68 " -0.241 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 68 " 0.150 2.00e-02 2.50e+03 1.63e-01 3.97e+02 pdb=" CD GLN A 68 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 68 " -0.143 2.00e-02 2.50e+03 pdb=" NE2 GLN A 68 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN A 68 " -0.240 2.00e-02 2.50e+03 pdb="HE22 GLN A 68 " 0.241 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 68 " -0.150 2.00e-02 2.50e+03 1.63e-01 3.96e+02 pdb=" CD GLN C 68 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN C 68 " 0.143 2.00e-02 2.50e+03 pdb=" NE2 GLN C 68 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN C 68 " 0.240 2.00e-02 2.50e+03 pdb="HE22 GLN C 68 " -0.241 2.00e-02 2.50e+03 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 992 2.21 - 2.81: 26473 2.81 - 3.40: 35282 3.40 - 4.00: 51344 4.00 - 4.60: 76208 Nonbonded interactions: 190299 Sorted by model distance: nonbonded pdb=" HH TYR B 235 " pdb="HD21 ASN B 280 " model vdw 1.611 2.100 nonbonded pdb=" HH TYR C 235 " pdb="HD21 ASN C 280 " model vdw 1.611 2.100 nonbonded pdb=" HH TYR A 235 " pdb="HD21 ASN A 280 " model vdw 1.611 2.100 nonbonded pdb=" HZ2 LYS C 305 " pdb=" O HOH C 508 " model vdw 1.666 2.450 nonbonded pdb="HD21 ASN C 267 " pdb=" O HOH C 506 " model vdw 1.666 2.450 ... (remaining 190294 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 361 or resid 501)) selection = (chain 'B' and (resid 43 through 361 or resid 502)) selection = (chain 'C' and (resid 43 through 361 or resid 502)) } 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: 10.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.140 Find NCS groups from input model: 0.190 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:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 0.089 7839 Z= 0.504 Angle : 1.010 19.610 10695 Z= 0.744 Chirality : 0.067 0.609 1203 Planarity : 0.010 0.136 1323 Dihedral : 15.591 88.398 2943 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: -1.27 (0.26), residues: 951 helix: -2.32 (0.29), residues: 243 sheet: -0.13 (0.26), residues: 336 loop : -0.18 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 287 TYR 0.021 0.002 TYR C 299 PHE 0.010 0.001 PHE A 61 TRP 0.012 0.002 TRP C 361 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00712 ( 7818) covalent geometry : angle 0.98633 (10647) SS BOND : bond 0.01455 ( 15) SS BOND : angle 2.93228 ( 30) hydrogen bonds : bond 0.18987 ( 226) hydrogen bonds : angle 9.54566 ( 570) link_NAG-ASN : bond 0.00263 ( 6) link_NAG-ASN : angle 4.02702 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.8390 (p) cc_final: 0.7912 (m) REVERT: B 64 GLN cc_start: 0.8049 (mm110) cc_final: 0.7820 (mm-40) REVERT: B 96 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6869 (tm-30) REVERT: B 149 MET cc_start: 0.8332 (mmp) cc_final: 0.7512 (mmp) REVERT: B 191 MET cc_start: 0.8112 (mtm) cc_final: 0.7889 (mtt) REVERT: C 64 GLN cc_start: 0.8076 (mm110) cc_final: 0.7806 (mm-40) REVERT: C 119 SER cc_start: 0.8654 (m) cc_final: 0.8411 (p) REVERT: C 149 MET cc_start: 0.8267 (mmp) cc_final: 0.7839 (mmp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.9063 time to fit residues: 187.4885 Evaluate side-chains 171 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 280 ASN B 68 GLN B 280 ASN C 68 GLN C 280 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.114661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098698 restraints weight = 29180.631| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.17 r_work: 0.3269 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7839 Z= 0.219 Angle : 0.560 5.402 10695 Z= 0.304 Chirality : 0.049 0.324 1203 Planarity : 0.006 0.062 1323 Dihedral : 11.490 83.421 1260 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.74 % Allowed : 10.46 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: -0.87 (0.26), residues: 951 helix: -1.29 (0.33), residues: 246 sheet: -0.15 (0.27), residues: 342 loop : -0.19 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 315 TYR 0.017 0.002 TYR B 98 PHE 0.011 0.002 PHE C 208 TRP 0.011 0.002 TRP C 268 HIS 0.005 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 7818) covalent geometry : angle 0.54204 (10647) SS BOND : bond 0.00480 ( 15) SS BOND : angle 1.66907 ( 30) hydrogen bonds : bond 0.04761 ( 226) hydrogen bonds : angle 6.01433 ( 570) link_NAG-ASN : bond 0.01065 ( 6) link_NAG-ASN : angle 2.75755 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.8133 (p) cc_final: 0.7919 (m) REVERT: B 282 LYS cc_start: 0.8857 (tptm) cc_final: 0.8643 (tmtm) REVERT: B 286 ARG cc_start: 0.8149 (ptm-80) cc_final: 0.7898 (ptm-80) REVERT: C 96 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6866 (tm-30) REVERT: C 170 CYS cc_start: 0.6603 (m) cc_final: 0.6314 (m) outliers start: 6 outliers final: 1 residues processed: 187 average time/residue: 1.0395 time to fit residues: 205.7052 Evaluate side-chains 176 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 201 ASN C 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097308 restraints weight = 29422.796| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.17 r_work: 0.3248 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7839 Z= 0.216 Angle : 0.527 5.229 10695 Z= 0.283 Chirality : 0.048 0.254 1203 Planarity : 0.005 0.054 1323 Dihedral : 10.361 86.299 1260 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.11 % Allowed : 11.81 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: -0.68 (0.26), residues: 951 helix: -0.88 (0.34), residues: 246 sheet: -0.08 (0.27), residues: 324 loop : -0.24 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 130 TYR 0.018 0.002 TYR B 98 PHE 0.011 0.001 PHE B 252 TRP 0.011 0.002 TRP C 268 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 7818) covalent geometry : angle 0.51245 (10647) SS BOND : bond 0.00493 ( 15) SS BOND : angle 1.47028 ( 30) hydrogen bonds : bond 0.04293 ( 226) hydrogen bonds : angle 5.91630 ( 570) link_NAG-ASN : bond 0.00429 ( 6) link_NAG-ASN : angle 2.51248 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.8156 (p) cc_final: 0.7943 (m) REVERT: B 286 ARG cc_start: 0.8263 (ptm-80) cc_final: 0.7974 (ptm-80) REVERT: C 96 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6952 (tm-30) REVERT: C 280 ASN cc_start: 0.8563 (m-40) cc_final: 0.8347 (m-40) outliers start: 9 outliers final: 4 residues processed: 190 average time/residue: 1.1731 time to fit residues: 234.3144 Evaluate side-chains 185 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 86 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.097850 restraints weight = 29511.010| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.16 r_work: 0.3252 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7839 Z= 0.180 Angle : 0.494 5.135 10695 Z= 0.266 Chirality : 0.047 0.232 1203 Planarity : 0.005 0.048 1323 Dihedral : 10.099 84.804 1260 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.35 % Allowed : 13.16 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: -0.39 (0.27), residues: 951 helix: -0.29 (0.37), residues: 228 sheet: -0.20 (0.27), residues: 324 loop : -0.06 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 287 TYR 0.014 0.002 TYR B 98 PHE 0.011 0.001 PHE B 252 TRP 0.009 0.001 TRP C 268 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 7818) covalent geometry : angle 0.48046 (10647) SS BOND : bond 0.00379 ( 15) SS BOND : angle 1.32249 ( 30) hydrogen bonds : bond 0.03920 ( 226) hydrogen bonds : angle 5.76946 ( 570) link_NAG-ASN : bond 0.00468 ( 6) link_NAG-ASN : angle 2.32033 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.8150 (p) cc_final: 0.7922 (m) REVERT: B 286 ARG cc_start: 0.8256 (ptm-80) cc_final: 0.7971 (ptm-80) REVERT: C 96 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6961 (tm-30) REVERT: C 115 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7597 (mt-10) outliers start: 11 outliers final: 7 residues processed: 191 average time/residue: 1.1888 time to fit residues: 238.6095 Evaluate side-chains 189 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 88 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 82 optimal weight: 0.9980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.098349 restraints weight = 29456.772| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.16 r_work: 0.3259 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7839 Z= 0.147 Angle : 0.472 5.023 10695 Z= 0.254 Chirality : 0.046 0.217 1203 Planarity : 0.004 0.044 1323 Dihedral : 9.652 77.291 1260 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.11 % Allowed : 14.02 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: -0.21 (0.27), residues: 951 helix: -0.04 (0.38), residues: 228 sheet: -0.19 (0.27), residues: 321 loop : 0.08 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 287 TYR 0.013 0.001 TYR B 98 PHE 0.010 0.001 PHE B 252 TRP 0.009 0.001 TRP C 58 HIS 0.003 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7818) covalent geometry : angle 0.46077 (10647) SS BOND : bond 0.00368 ( 15) SS BOND : angle 1.20043 ( 30) hydrogen bonds : bond 0.03612 ( 226) hydrogen bonds : angle 5.62449 ( 570) link_NAG-ASN : bond 0.00478 ( 6) link_NAG-ASN : angle 2.08855 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.8122 (p) cc_final: 0.7879 (m) REVERT: B 286 ARG cc_start: 0.8228 (ptm-80) cc_final: 0.7942 (ptm-80) REVERT: C 115 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7597 (mt-10) outliers start: 9 outliers final: 7 residues processed: 186 average time/residue: 1.1324 time to fit residues: 222.0561 Evaluate side-chains 189 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 88 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.112896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.097108 restraints weight = 29397.581| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.15 r_work: 0.3242 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7839 Z= 0.229 Angle : 0.512 5.238 10695 Z= 0.275 Chirality : 0.048 0.233 1203 Planarity : 0.005 0.043 1323 Dihedral : 10.095 77.212 1260 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.23 % Allowed : 14.02 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: -0.33 (0.27), residues: 951 helix: -0.18 (0.37), residues: 228 sheet: -0.24 (0.27), residues: 321 loop : 0.02 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 287 TYR 0.017 0.002 TYR A 235 PHE 0.014 0.001 PHE B 252 TRP 0.011 0.002 TRP C 268 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 7818) covalent geometry : angle 0.49928 (10647) SS BOND : bond 0.00467 ( 15) SS BOND : angle 1.41199 ( 30) hydrogen bonds : bond 0.04066 ( 226) hydrogen bonds : angle 5.78356 ( 570) link_NAG-ASN : bond 0.00461 ( 6) link_NAG-ASN : angle 2.27220 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.8172 (p) cc_final: 0.7921 (m) REVERT: C 96 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7014 (tm-30) outliers start: 10 outliers final: 8 residues processed: 197 average time/residue: 1.2163 time to fit residues: 251.4207 Evaluate side-chains 198 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.112677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.096797 restraints weight = 29466.929| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.16 r_work: 0.3238 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7839 Z= 0.219 Angle : 0.514 5.232 10695 Z= 0.275 Chirality : 0.048 0.226 1203 Planarity : 0.005 0.041 1323 Dihedral : 10.154 80.304 1260 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.72 % Allowed : 14.51 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: -0.35 (0.27), residues: 951 helix: -0.17 (0.37), residues: 228 sheet: -0.30 (0.27), residues: 321 loop : 0.03 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 287 TYR 0.015 0.002 TYR A 235 PHE 0.014 0.001 PHE B 252 TRP 0.011 0.002 TRP C 268 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 7818) covalent geometry : angle 0.50048 (10647) SS BOND : bond 0.00426 ( 15) SS BOND : angle 1.44670 ( 30) hydrogen bonds : bond 0.04039 ( 226) hydrogen bonds : angle 5.76039 ( 570) link_NAG-ASN : bond 0.00434 ( 6) link_NAG-ASN : angle 2.35991 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.8193 (p) cc_final: 0.7941 (m) REVERT: C 96 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7036 (tm-30) outliers start: 14 outliers final: 12 residues processed: 199 average time/residue: 1.3166 time to fit residues: 274.9386 Evaluate side-chains 204 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 343 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 26 optimal weight: 0.9990 chunk 89 optimal weight: 0.0570 chunk 42 optimal weight: 0.0050 chunk 77 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.4312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.113562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.097829 restraints weight = 29218.724| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.14 r_work: 0.3252 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7839 Z= 0.153 Angle : 0.483 5.045 10695 Z= 0.259 Chirality : 0.046 0.212 1203 Planarity : 0.004 0.040 1323 Dihedral : 9.834 80.741 1260 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.72 % Allowed : 14.64 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: -0.25 (0.27), residues: 951 helix: -0.00 (0.38), residues: 228 sheet: -0.35 (0.27), residues: 321 loop : 0.15 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 287 TYR 0.013 0.001 TYR A 235 PHE 0.010 0.001 PHE B 252 TRP 0.009 0.001 TRP C 268 HIS 0.003 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 7818) covalent geometry : angle 0.47079 (10647) SS BOND : bond 0.00326 ( 15) SS BOND : angle 1.31373 ( 30) hydrogen bonds : bond 0.03674 ( 226) hydrogen bonds : angle 5.64330 ( 570) link_NAG-ASN : bond 0.00481 ( 6) link_NAG-ASN : angle 2.17620 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.8174 (p) cc_final: 0.7896 (m) REVERT: B 191 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7833 (mtt) REVERT: C 96 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6961 (tm-30) outliers start: 14 outliers final: 11 residues processed: 197 average time/residue: 1.3151 time to fit residues: 271.6787 Evaluate side-chains 199 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 37 optimal weight: 0.0270 chunk 84 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 chunk 69 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.113997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098279 restraints weight = 29416.569| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.14 r_work: 0.3256 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7839 Z= 0.126 Angle : 0.469 4.957 10695 Z= 0.250 Chirality : 0.046 0.204 1203 Planarity : 0.004 0.040 1323 Dihedral : 9.518 80.841 1260 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.85 % Allowed : 14.88 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: -0.15 (0.27), residues: 951 helix: 0.14 (0.39), residues: 228 sheet: -0.36 (0.27), residues: 321 loop : 0.23 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 287 TYR 0.011 0.001 TYR C 235 PHE 0.008 0.001 PHE B 252 TRP 0.008 0.001 TRP C 268 HIS 0.002 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7818) covalent geometry : angle 0.45801 (10647) SS BOND : bond 0.00282 ( 15) SS BOND : angle 1.21029 ( 30) hydrogen bonds : bond 0.03437 ( 226) hydrogen bonds : angle 5.54230 ( 570) link_NAG-ASN : bond 0.00485 ( 6) link_NAG-ASN : angle 2.02535 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.8128 (p) cc_final: 0.7873 (m) REVERT: B 191 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7847 (mtt) REVERT: C 96 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6978 (tm-30) outliers start: 15 outliers final: 11 residues processed: 195 average time/residue: 1.2807 time to fit residues: 261.9941 Evaluate side-chains 199 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.096734 restraints weight = 29456.786| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.15 r_work: 0.3239 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 7839 Z= 0.234 Angle : 0.521 5.266 10695 Z= 0.277 Chirality : 0.048 0.226 1203 Planarity : 0.005 0.039 1323 Dihedral : 10.013 83.192 1260 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.48 % Allowed : 15.13 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: -0.22 (0.27), residues: 951 helix: -0.12 (0.38), residues: 228 sheet: -0.25 (0.27), residues: 330 loop : 0.20 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 287 TYR 0.016 0.002 TYR A 235 PHE 0.015 0.001 PHE B 252 TRP 0.011 0.002 TRP C 268 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 7818) covalent geometry : angle 0.50684 (10647) SS BOND : bond 0.00481 ( 15) SS BOND : angle 1.56696 ( 30) hydrogen bonds : bond 0.03961 ( 226) hydrogen bonds : angle 5.72455 ( 570) link_NAG-ASN : bond 0.00433 ( 6) link_NAG-ASN : angle 2.25097 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.8175 (p) cc_final: 0.7927 (m) REVERT: B 191 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7858 (mtt) REVERT: C 96 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7080 (tm-30) outliers start: 12 outliers final: 12 residues processed: 196 average time/residue: 1.3645 time to fit residues: 280.2561 Evaluate side-chains 198 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 15 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.0570 chunk 73 optimal weight: 0.0770 chunk 85 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 54 optimal weight: 0.0980 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.114814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099078 restraints weight = 29296.255| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.14 r_work: 0.3270 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7839 Z= 0.101 Angle : 0.461 4.829 10695 Z= 0.246 Chirality : 0.046 0.279 1203 Planarity : 0.004 0.040 1323 Dihedral : 9.329 81.493 1260 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.74 % Allowed : 16.48 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 are not related in a simple way. whole: 0.26 (0.28), residues: 951 helix: 0.67 (0.41), residues: 210 sheet: -0.29 (0.27), residues: 330 loop : 0.57 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 287 TYR 0.010 0.001 TYR A 98 PHE 0.006 0.001 PHE A 208 TRP 0.010 0.001 TRP A 268 HIS 0.001 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7818) covalent geometry : angle 0.44875 (10647) SS BOND : bond 0.00230 ( 15) SS BOND : angle 1.25114 ( 30) hydrogen bonds : bond 0.03205 ( 226) hydrogen bonds : angle 5.45444 ( 570) link_NAG-ASN : bond 0.00592 ( 6) link_NAG-ASN : angle 2.17067 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6383.44 seconds wall clock time: 108 minutes 38.29 seconds (6518.29 seconds total)