Starting phenix.real_space_refine on Sun Apr 5 03:31:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ux2_64570/04_2026/9ux2_64570_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ux2_64570/04_2026/9ux2_64570.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 { model { file = "/net/cci-nas-00/data/ceres_data/9ux2_64570/04_2026/9ux2_64570_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ux2_64570/04_2026/9ux2_64570_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ux2_64570/04_2026/9ux2_64570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ux2_64570/04_2026/9ux2_64570.map" } 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= -0.000 sd= 0.026 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 9 5.49 5 S 42 5.16 5 C 4880 2.51 5 N 1262 2.21 5 O 1447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7640 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2505 Classifications: {'peptide': 319} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 303} Chain: "B" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2472 Classifications: {'peptide': 317} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 301} Chain: "C" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2472 Classifications: {'peptide': 317} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 301} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "C" 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 Time building chain proxies: 1.74, per 1000 atoms: 0.23 Number of scatterers: 7640 At special positions: 0 Unit cell: (90.25, 87.4, 123.5, 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 42 16.00 P 9 15.00 O 1447 8.00 N 1262 7.00 C 4880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 153 " distance=2.02 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS A 256 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 176 " distance=2.02 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=2.03 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 Links applied NAG-ASN " NAG A 401 " - " ASN A 290 " " NAG A 402 " - " ASN A 170 " " NAG A 403 " - " ASN A 194 " " NAG B 501 " - " ASN B 133 " " NAG B 502 " - " ASN B 194 " " NAG C 502 " - " ASN C 133 " " NAG C 503 " - " ASN C 194 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 236.3 milliseconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 25.2% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 25 through 45 removed outlier: 3.671A pdb=" N VAL A 29 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.561A pdb=" N TYR A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 76 through 80' Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.769A pdb=" N ALA A 168 " --> pdb=" O MET A 165 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU A 169 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.539A pdb=" N ALA A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 removed outlier: 4.057A pdb=" N ARG A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.531A pdb=" N GLN A 255 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS A 256 " --> pdb=" O TRP A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.634A pdb=" N SER A 269 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 343 Processing helix chain 'B' and resid 43 through 62 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.735A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 191 through 194 removed outlier: 3.590A pdb=" N ASN B 194 " --> pdb=" O MET B 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 191 through 194' Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.560A pdb=" N LYS B 224 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 removed outlier: 3.805A pdb=" N GLU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 337 through 358 removed outlier: 3.909A pdb=" N THR B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 63 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.662A pdb=" N TYR C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 98' Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.699A pdb=" N CYS C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 337 through 358 removed outlier: 3.705A pdb=" N THR C 341 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C 355 " --> pdb=" O SER C 351 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 50 through 53 current: chain 'A' and resid 89 through 107 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 89 through 107 current: chain 'A' and resid 149 through 153 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 149 through 153 current: chain 'A' and resid 259 through 264 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 264 current: chain 'A' and resid 293 through 316 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA5, first strand: chain 'B' and resid 68 through 71 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 71 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=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 83 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 281 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 281 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 88 181 hydrogen bonds defined for protein. 483 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: 1.14 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2274 1.33 - 1.46: 1799 1.46 - 1.58: 3687 1.58 - 1.70: 15 1.70 - 1.83: 53 Bond restraints: 7828 Sorted by residual: bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.63e+01 bond pdb=" C4 ATP B 503 " pdb=" C5 ATP B 503 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.36e+01 bond pdb=" C ASP A 340 " pdb=" N ILE A 341 " ideal model delta sigma weight residual 1.334 1.237 0.098 1.26e-02 6.30e+03 6.01e+01 bond pdb=" C4 ATP A 404 " pdb=" C5 ATP A 404 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.62e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.83e+01 ... (remaining 7823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 10526 3.58 - 7.16: 92 7.16 - 10.74: 18 10.74 - 14.32: 2 14.32 - 17.90: 5 Bond angle restraints: 10643 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 121.97 17.90 1.00e+00 1.00e+00 3.20e+02 angle pdb=" PB ATP A 404 " pdb=" O3B ATP A 404 " pdb=" PG ATP A 404 " ideal model delta sigma weight residual 139.87 122.28 17.59 1.00e+00 1.00e+00 3.09e+02 angle pdb=" PB ATP B 503 " pdb=" O3B ATP B 503 " pdb=" PG ATP B 503 " ideal model delta sigma weight residual 139.87 122.31 17.56 1.00e+00 1.00e+00 3.08e+02 angle pdb=" PA ATP B 503 " pdb=" O3A ATP B 503 " pdb=" PB ATP B 503 " ideal model delta sigma weight residual 136.83 119.65 17.18 1.00e+00 1.00e+00 2.95e+02 angle pdb=" PA ATP A 404 " pdb=" O3A ATP A 404 " pdb=" PB ATP A 404 " ideal model delta sigma weight residual 136.83 122.37 14.46 1.00e+00 1.00e+00 2.09e+02 ... (remaining 10638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4366 17.57 - 35.14: 334 35.14 - 52.71: 66 52.71 - 70.28: 16 70.28 - 87.85: 8 Dihedral angle restraints: 4790 sinusoidal: 2054 harmonic: 2736 Sorted by residual: dihedral pdb=" CB CYS A 122 " pdb=" SG CYS A 122 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual 93.00 161.78 -68.78 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " pdb=" SG CYS A 256 " pdb=" CB CYS A 256 " ideal model delta sinusoidal sigma weight residual 93.00 157.98 -64.98 1 1.00e+01 1.00e-02 5.54e+01 dihedral pdb=" CB CYS B 136 " pdb=" SG CYS B 136 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual 93.00 51.63 41.37 1 1.00e+01 1.00e-02 2.40e+01 ... (remaining 4787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 855 0.047 - 0.094: 259 0.094 - 0.141: 88 0.141 - 0.188: 4 0.188 - 0.236: 3 Chirality restraints: 1209 Sorted by residual: chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 133 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL A 337 " pdb=" N VAL A 337 " pdb=" C VAL A 337 " pdb=" CB VAL A 337 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB VAL A 337 " pdb=" CA VAL A 337 " pdb=" CG1 VAL A 337 " pdb=" CG2 VAL A 337 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 1206 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 403 " 0.310 2.00e-02 2.50e+03 2.61e-01 8.50e+02 pdb=" C7 NAG A 403 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 403 " 0.190 2.00e-02 2.50e+03 pdb=" N2 NAG A 403 " -0.448 2.00e-02 2.50e+03 pdb=" O7 NAG A 403 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " 0.307 2.00e-02 2.50e+03 2.60e-01 8.44e+02 pdb=" C7 NAG C 502 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " -0.450 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 401 " -0.291 2.00e-02 2.50e+03 2.48e-01 7.66e+02 pdb=" C7 NAG A 401 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A 401 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG A 401 " 0.428 2.00e-02 2.50e+03 pdb=" O7 NAG A 401 " -0.033 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 48 2.50 - 3.10: 5486 3.10 - 3.70: 10653 3.70 - 4.30: 15812 4.30 - 4.90: 27015 Nonbonded interactions: 59014 Sorted by model distance: nonbonded pdb=" NZ LYS A 242 " pdb=" OE2 GLU C 75 " model vdw 1.897 3.120 nonbonded pdb=" O LYS A 271 " pdb=" OD2 ASP C 217 " model vdw 1.927 3.040 nonbonded pdb=" NE2 GLN A 50 " pdb=" OD2 ASP A 250 " model vdw 2.224 3.120 nonbonded pdb=" OH TYR B 222 " pdb=" OD1 ASP B 233 " model vdw 2.238 3.040 nonbonded pdb=" SD MET B 191 " pdb=" CD2 LEU C 147 " model vdw 2.240 3.820 ... (remaining 59009 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 'B' and (resid 42 through 358 or resid 502)) selection = (chain 'C' and (resid 42 through 358 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: 4.110 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.620 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:7.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 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 0.098 7850 Z= 0.439 Angle : 0.991 17.899 10694 Z= 0.693 Chirality : 0.050 0.236 1209 Planarity : 0.015 0.261 1323 Dihedral : 13.248 87.851 3001 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.47 (0.24), residues: 947 helix: -2.36 (0.31), residues: 185 sheet: -0.09 (0.27), residues: 323 loop : -2.54 (0.24), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 73 TYR 0.013 0.001 TYR C 235 PHE 0.014 0.001 PHE A 301 TRP 0.019 0.002 TRP C 58 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00714 ( 7828) covalent geometry : angle 0.98296 (10643) SS BOND : bond 0.00488 ( 15) SS BOND : angle 2.12368 ( 30) hydrogen bonds : bond 0.18283 ( 181) hydrogen bonds : angle 7.24669 ( 483) link_NAG-ASN : bond 0.00309 ( 7) link_NAG-ASN : angle 2.01129 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8284 (mmt-90) cc_final: 0.8009 (mmt-90) REVERT: B 164 GLN cc_start: 0.8759 (pm20) cc_final: 0.8480 (pp30) REVERT: C 58 TRP cc_start: 0.7846 (t60) cc_final: 0.7344 (t60) REVERT: C 132 HIS cc_start: 0.8451 (t70) cc_final: 0.8223 (t-90) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.5914 time to fit residues: 51.2100 Evaluate side-chains 57 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 312 ASN B 132 HIS B 152 ASN B 201 ASN B 204 HIS B 229 HIS C 118 HIS C 132 HIS C 152 ASN C 201 ASN C 204 HIS C 344 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.060925 restraints weight = 17368.960| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.49 r_work: 0.2802 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7850 Z= 0.154 Angle : 0.658 7.722 10694 Z= 0.341 Chirality : 0.049 0.238 1209 Planarity : 0.004 0.051 1323 Dihedral : 10.065 87.618 1281 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.82 % Allowed : 9.25 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.55 (0.25), residues: 947 helix: -1.15 (0.33), residues: 204 sheet: 0.21 (0.27), residues: 336 loop : -2.03 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 198 TYR 0.032 0.001 TYR C 55 PHE 0.011 0.001 PHE C 252 TRP 0.008 0.001 TRP C 58 HIS 0.002 0.000 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 7828) covalent geometry : angle 0.64671 (10643) SS BOND : bond 0.00425 ( 15) SS BOND : angle 1.70730 ( 30) hydrogen bonds : bond 0.05007 ( 181) hydrogen bonds : angle 5.47991 ( 483) link_NAG-ASN : bond 0.00414 ( 7) link_NAG-ASN : angle 2.09662 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.223 Fit side-chains REVERT: A 43 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: A 52 ARG cc_start: 0.8812 (mmt-90) cc_final: 0.8338 (mpt180) REVERT: B 64 GLN cc_start: 0.8847 (pp30) cc_final: 0.8594 (pp30) REVERT: B 164 GLN cc_start: 0.8824 (pm20) cc_final: 0.8327 (pp30) REVERT: C 64 GLN cc_start: 0.9136 (mt0) cc_final: 0.8812 (pm20) REVERT: C 90 HIS cc_start: 0.8853 (m90) cc_final: 0.7807 (m90) REVERT: C 152 ASN cc_start: 0.8826 (m-40) cc_final: 0.8542 (m110) outliers start: 15 outliers final: 4 residues processed: 77 average time/residue: 0.4882 time to fit residues: 40.2277 Evaluate side-chains 62 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 13 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.089856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.062618 restraints weight = 17258.044| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.37 r_work: 0.2809 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7850 Z= 0.137 Angle : 0.675 11.819 10694 Z= 0.335 Chirality : 0.050 0.321 1209 Planarity : 0.004 0.057 1323 Dihedral : 9.763 88.547 1281 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.58 % Allowed : 11.68 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.99 (0.26), residues: 947 helix: -0.44 (0.36), residues: 210 sheet: 0.57 (0.27), residues: 328 loop : -1.83 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 198 TYR 0.031 0.001 TYR C 55 PHE 0.027 0.001 PHE C 56 TRP 0.017 0.001 TRP C 58 HIS 0.005 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7828) covalent geometry : angle 0.64981 (10643) SS BOND : bond 0.00478 ( 15) SS BOND : angle 1.96131 ( 30) hydrogen bonds : bond 0.04284 ( 181) hydrogen bonds : angle 5.06772 ( 483) link_NAG-ASN : bond 0.00439 ( 7) link_NAG-ASN : angle 3.55900 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8864 (mmt-90) cc_final: 0.8605 (mpt180) REVERT: A 166 MET cc_start: 0.8774 (mmm) cc_final: 0.8534 (mmm) REVERT: A 201 LYS cc_start: 0.9111 (mttp) cc_final: 0.8810 (mmtp) REVERT: A 231 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8591 (mtmt) REVERT: B 64 GLN cc_start: 0.9108 (pp30) cc_final: 0.8830 (pp30) REVERT: B 164 GLN cc_start: 0.8818 (pm20) cc_final: 0.8295 (pp30) REVERT: C 64 GLN cc_start: 0.9112 (mt0) cc_final: 0.8735 (mp10) REVERT: C 68 GLN cc_start: 0.8543 (mt0) cc_final: 0.8198 (mt0) REVERT: C 152 ASN cc_start: 0.8879 (m-40) cc_final: 0.8650 (m110) REVERT: C 191 MET cc_start: 0.8743 (mpt) cc_final: 0.8469 (mpt) outliers start: 13 outliers final: 5 residues processed: 73 average time/residue: 0.5208 time to fit residues: 40.3922 Evaluate side-chains 62 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain C residue 61 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 0.0570 chunk 3 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.090404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.061988 restraints weight = 17523.711| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.50 r_work: 0.2837 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7850 Z= 0.134 Angle : 0.652 9.901 10694 Z= 0.324 Chirality : 0.049 0.278 1209 Planarity : 0.004 0.057 1323 Dihedral : 9.326 87.039 1281 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.19 % Allowed : 12.53 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.69 (0.27), residues: 947 helix: -0.10 (0.38), residues: 210 sheet: 0.77 (0.28), residues: 328 loop : -1.70 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.030 0.001 TYR C 55 PHE 0.026 0.001 PHE C 56 TRP 0.014 0.001 TRP C 58 HIS 0.005 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7828) covalent geometry : angle 0.63198 (10643) SS BOND : bond 0.00415 ( 15) SS BOND : angle 1.78725 ( 30) hydrogen bonds : bond 0.03974 ( 181) hydrogen bonds : angle 4.89255 ( 483) link_NAG-ASN : bond 0.00400 ( 7) link_NAG-ASN : angle 3.05515 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8916 (mmt-90) cc_final: 0.8559 (mpt180) REVERT: A 166 MET cc_start: 0.8841 (mmm) cc_final: 0.8531 (mmm) REVERT: A 201 LYS cc_start: 0.9093 (mttp) cc_final: 0.8792 (mmtp) REVERT: B 64 GLN cc_start: 0.9208 (pp30) cc_final: 0.8965 (pp30) REVERT: B 164 GLN cc_start: 0.8741 (pm20) cc_final: 0.8212 (pp30) REVERT: C 64 GLN cc_start: 0.9100 (mt0) cc_final: 0.8726 (mp10) REVERT: C 68 GLN cc_start: 0.8528 (mt0) cc_final: 0.8224 (mt0) REVERT: C 152 ASN cc_start: 0.8933 (m-40) cc_final: 0.8628 (m110) REVERT: C 164 GLN cc_start: 0.8872 (pm20) cc_final: 0.8625 (pm20) REVERT: C 191 MET cc_start: 0.8663 (mpt) cc_final: 0.8381 (mpt) outliers start: 18 outliers final: 7 residues processed: 74 average time/residue: 0.4828 time to fit residues: 38.2860 Evaluate side-chains 63 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 352 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 50 optimal weight: 0.0170 chunk 27 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.090474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.062654 restraints weight = 17477.484| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.47 r_work: 0.2837 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7850 Z= 0.127 Angle : 0.644 10.618 10694 Z= 0.320 Chirality : 0.050 0.331 1209 Planarity : 0.004 0.057 1323 Dihedral : 9.000 83.858 1281 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.07 % Allowed : 13.99 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.51 (0.27), residues: 947 helix: 0.03 (0.38), residues: 210 sheet: 0.89 (0.28), residues: 328 loop : -1.59 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.027 0.001 TYR C 55 PHE 0.027 0.001 PHE C 56 TRP 0.011 0.001 TRP C 58 HIS 0.005 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7828) covalent geometry : angle 0.62445 (10643) SS BOND : bond 0.00389 ( 15) SS BOND : angle 1.70956 ( 30) hydrogen bonds : bond 0.03791 ( 181) hydrogen bonds : angle 4.82033 ( 483) link_NAG-ASN : bond 0.00347 ( 7) link_NAG-ASN : angle 3.10820 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8973 (mmt-90) cc_final: 0.8556 (mpt180) REVERT: A 166 MET cc_start: 0.8838 (mmm) cc_final: 0.8531 (mmm) REVERT: A 201 LYS cc_start: 0.9060 (mttp) cc_final: 0.8784 (mmtp) REVERT: A 231 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8527 (mtmt) REVERT: B 64 GLN cc_start: 0.9152 (pp30) cc_final: 0.8805 (pp30) REVERT: B 164 GLN cc_start: 0.8720 (pm20) cc_final: 0.8305 (pp30) REVERT: C 64 GLN cc_start: 0.9102 (mt0) cc_final: 0.8706 (mp10) REVERT: C 68 GLN cc_start: 0.8532 (mt0) cc_final: 0.8180 (mt0) REVERT: C 149 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8981 (tpt) REVERT: C 152 ASN cc_start: 0.8877 (m-40) cc_final: 0.8584 (m110) REVERT: C 164 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8640 (pm20) REVERT: C 191 MET cc_start: 0.8643 (mpt) cc_final: 0.8332 (mpt) outliers start: 17 outliers final: 6 residues processed: 70 average time/residue: 0.4824 time to fit residues: 36.1460 Evaluate side-chains 64 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 164 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.089582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.061477 restraints weight = 17537.656| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.48 r_work: 0.2815 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7850 Z= 0.160 Angle : 0.655 9.501 10694 Z= 0.326 Chirality : 0.049 0.327 1209 Planarity : 0.004 0.057 1323 Dihedral : 8.925 77.016 1281 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.19 % Allowed : 14.11 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 947 helix: 0.17 (0.39), residues: 210 sheet: 0.92 (0.28), residues: 328 loop : -1.50 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 286 TYR 0.025 0.001 TYR C 55 PHE 0.027 0.001 PHE C 56 TRP 0.011 0.001 TRP C 58 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7828) covalent geometry : angle 0.63379 (10643) SS BOND : bond 0.00467 ( 15) SS BOND : angle 1.89853 ( 30) hydrogen bonds : bond 0.03829 ( 181) hydrogen bonds : angle 4.80670 ( 483) link_NAG-ASN : bond 0.00308 ( 7) link_NAG-ASN : angle 3.13957 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8988 (mmt-90) cc_final: 0.8581 (mpt180) REVERT: A 166 MET cc_start: 0.8854 (mmm) cc_final: 0.8583 (mmm) REVERT: B 64 GLN cc_start: 0.9213 (pp30) cc_final: 0.8916 (pp30) REVERT: B 164 GLN cc_start: 0.8727 (pm20) cc_final: 0.8217 (pp30) REVERT: C 64 GLN cc_start: 0.9077 (mt0) cc_final: 0.8750 (pm20) REVERT: C 68 GLN cc_start: 0.8552 (mt0) cc_final: 0.8263 (mt0) REVERT: C 149 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.9050 (tpt) REVERT: C 152 ASN cc_start: 0.8886 (m-40) cc_final: 0.8591 (m110) REVERT: C 164 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8647 (pm20) REVERT: C 191 MET cc_start: 0.8666 (mpt) cc_final: 0.8316 (mpt) outliers start: 18 outliers final: 5 residues processed: 72 average time/residue: 0.4557 time to fit residues: 35.1730 Evaluate side-chains 62 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 164 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 60 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 0.0020 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.090851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.062773 restraints weight = 17444.950| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.49 r_work: 0.2844 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7850 Z= 0.118 Angle : 0.639 10.520 10694 Z= 0.316 Chirality : 0.049 0.334 1209 Planarity : 0.004 0.057 1323 Dihedral : 8.622 72.838 1281 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.58 % Allowed : 14.60 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.27), residues: 947 helix: 0.23 (0.39), residues: 210 sheet: 1.03 (0.28), residues: 328 loop : -1.43 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.026 0.001 TYR C 55 PHE 0.028 0.001 PHE C 56 TRP 0.012 0.001 TRP B 58 HIS 0.003 0.000 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7828) covalent geometry : angle 0.62046 (10643) SS BOND : bond 0.00309 ( 15) SS BOND : angle 1.62046 ( 30) hydrogen bonds : bond 0.03468 ( 181) hydrogen bonds : angle 4.63997 ( 483) link_NAG-ASN : bond 0.00344 ( 7) link_NAG-ASN : angle 2.99817 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8931 (mmt-90) cc_final: 0.8573 (mpt180) REVERT: A 166 MET cc_start: 0.8850 (mmm) cc_final: 0.8597 (mmm) REVERT: B 64 GLN cc_start: 0.9180 (pp30) cc_final: 0.8891 (pp30) REVERT: B 164 GLN cc_start: 0.8686 (pm20) cc_final: 0.8261 (pp30) REVERT: C 64 GLN cc_start: 0.9091 (mt0) cc_final: 0.8752 (pm20) REVERT: C 68 GLN cc_start: 0.8548 (mt0) cc_final: 0.8195 (mt0) REVERT: C 152 ASN cc_start: 0.8871 (m-40) cc_final: 0.8583 (m110) REVERT: C 164 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8627 (pm20) REVERT: C 191 MET cc_start: 0.8651 (mpt) cc_final: 0.8265 (mpt) REVERT: C 349 LEU cc_start: 0.8648 (mm) cc_final: 0.8356 (tt) outliers start: 13 outliers final: 7 residues processed: 70 average time/residue: 0.5456 time to fit residues: 40.5507 Evaluate side-chains 67 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 164 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 32 optimal weight: 0.0270 chunk 71 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.091773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.063754 restraints weight = 17455.140| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.49 r_work: 0.2866 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7850 Z= 0.110 Angle : 0.654 11.248 10694 Z= 0.319 Chirality : 0.049 0.344 1209 Planarity : 0.004 0.055 1323 Dihedral : 8.329 72.640 1281 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.46 % Allowed : 14.84 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 947 helix: 0.25 (0.39), residues: 210 sheet: 1.15 (0.28), residues: 326 loop : -1.36 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 198 TYR 0.026 0.001 TYR C 55 PHE 0.028 0.001 PHE C 56 TRP 0.011 0.001 TRP B 58 HIS 0.002 0.000 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7828) covalent geometry : angle 0.63803 (10643) SS BOND : bond 0.00296 ( 15) SS BOND : angle 1.45510 ( 30) hydrogen bonds : bond 0.03279 ( 181) hydrogen bonds : angle 4.55339 ( 483) link_NAG-ASN : bond 0.00370 ( 7) link_NAG-ASN : angle 2.89133 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8925 (mmt-90) cc_final: 0.8573 (mpt180) REVERT: A 166 MET cc_start: 0.8863 (mmm) cc_final: 0.8590 (mmm) REVERT: A 201 LYS cc_start: 0.9016 (mttp) cc_final: 0.8784 (mmtp) REVERT: B 64 GLN cc_start: 0.9183 (pp30) cc_final: 0.8920 (pp30) REVERT: B 164 GLN cc_start: 0.8622 (pm20) cc_final: 0.8187 (pp30) REVERT: C 64 GLN cc_start: 0.9087 (mt0) cc_final: 0.8731 (pm20) REVERT: C 68 GLN cc_start: 0.8611 (mt0) cc_final: 0.8274 (mt0) REVERT: C 152 ASN cc_start: 0.8849 (m-40) cc_final: 0.8564 (m110) REVERT: C 164 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8638 (pm20) REVERT: C 191 MET cc_start: 0.8645 (mpt) cc_final: 0.8241 (mpt) REVERT: C 349 LEU cc_start: 0.8604 (mm) cc_final: 0.8330 (tt) outliers start: 12 outliers final: 8 residues processed: 73 average time/residue: 0.5338 time to fit residues: 41.4354 Evaluate side-chains 68 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 164 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 9 optimal weight: 0.0470 chunk 64 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.063067 restraints weight = 17497.748| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.47 r_work: 0.2852 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7850 Z= 0.123 Angle : 0.675 11.689 10694 Z= 0.325 Chirality : 0.050 0.373 1209 Planarity : 0.004 0.055 1323 Dihedral : 8.300 73.406 1281 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.58 % Allowed : 15.21 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.09 (0.27), residues: 947 helix: 0.32 (0.39), residues: 210 sheet: 1.17 (0.28), residues: 326 loop : -1.31 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.028 0.001 TYR C 55 PHE 0.007 0.001 PHE C 252 TRP 0.011 0.001 TRP B 58 HIS 0.002 0.000 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7828) covalent geometry : angle 0.65863 (10643) SS BOND : bond 0.00347 ( 15) SS BOND : angle 1.62316 ( 30) hydrogen bonds : bond 0.03318 ( 181) hydrogen bonds : angle 4.54574 ( 483) link_NAG-ASN : bond 0.00322 ( 7) link_NAG-ASN : angle 2.87901 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8942 (mmt-90) cc_final: 0.8400 (mmt180) REVERT: A 166 MET cc_start: 0.8882 (mmm) cc_final: 0.8593 (mmm) REVERT: A 201 LYS cc_start: 0.9014 (mttp) cc_final: 0.8628 (mmtm) REVERT: B 64 GLN cc_start: 0.9193 (pp30) cc_final: 0.8886 (pp30) REVERT: B 164 GLN cc_start: 0.8623 (pm20) cc_final: 0.8179 (pp30) REVERT: C 64 GLN cc_start: 0.9106 (mt0) cc_final: 0.8734 (pm20) REVERT: C 152 ASN cc_start: 0.8872 (m-40) cc_final: 0.8608 (m110) REVERT: C 164 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8621 (pm20) REVERT: C 191 MET cc_start: 0.8665 (mpt) cc_final: 0.8240 (mpt) REVERT: C 349 LEU cc_start: 0.8652 (mm) cc_final: 0.8384 (tt) outliers start: 13 outliers final: 8 residues processed: 68 average time/residue: 0.5258 time to fit residues: 38.2406 Evaluate side-chains 66 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 164 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 42 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.091476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.063457 restraints weight = 17278.171| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.47 r_work: 0.2858 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7850 Z= 0.121 Angle : 0.684 13.755 10694 Z= 0.328 Chirality : 0.050 0.404 1209 Planarity : 0.004 0.055 1323 Dihedral : 8.229 74.989 1281 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.70 % Allowed : 15.09 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.02 (0.27), residues: 947 helix: 0.33 (0.39), residues: 210 sheet: 1.22 (0.28), residues: 326 loop : -1.24 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 198 TYR 0.027 0.001 TYR C 59 PHE 0.007 0.001 PHE C 252 TRP 0.012 0.001 TRP A 253 HIS 0.002 0.000 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7828) covalent geometry : angle 0.66908 (10643) SS BOND : bond 0.00321 ( 15) SS BOND : angle 1.57287 ( 30) hydrogen bonds : bond 0.03248 ( 181) hydrogen bonds : angle 4.50873 ( 483) link_NAG-ASN : bond 0.00326 ( 7) link_NAG-ASN : angle 2.79010 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8951 (mmt-90) cc_final: 0.8420 (mmt180) REVERT: A 166 MET cc_start: 0.8887 (mmm) cc_final: 0.8599 (mmm) REVERT: A 201 LYS cc_start: 0.8952 (mttp) cc_final: 0.8676 (mmtp) REVERT: B 64 GLN cc_start: 0.9202 (pp30) cc_final: 0.8928 (pp30) REVERT: B 164 GLN cc_start: 0.8589 (pm20) cc_final: 0.8105 (pp30) REVERT: C 64 GLN cc_start: 0.9091 (mt0) cc_final: 0.8746 (pm20) REVERT: C 149 MET cc_start: 0.9253 (mmt) cc_final: 0.9010 (tpt) REVERT: C 152 ASN cc_start: 0.8868 (m-40) cc_final: 0.8574 (m110) REVERT: C 164 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8637 (pm20) REVERT: C 191 MET cc_start: 0.8688 (mpt) cc_final: 0.8216 (mpt) REVERT: C 349 LEU cc_start: 0.8662 (mm) cc_final: 0.8413 (tt) outliers start: 14 outliers final: 8 residues processed: 67 average time/residue: 0.4872 time to fit residues: 35.1447 Evaluate side-chains 67 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 164 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 92 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.091251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.063411 restraints weight = 17372.461| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.47 r_work: 0.2853 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7850 Z= 0.126 Angle : 0.685 13.682 10694 Z= 0.329 Chirality : 0.050 0.402 1209 Planarity : 0.004 0.055 1323 Dihedral : 8.213 75.459 1281 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.09 % Allowed : 15.69 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.01 (0.27), residues: 947 helix: 0.35 (0.39), residues: 210 sheet: 1.21 (0.28), residues: 328 loop : -1.21 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 198 TYR 0.028 0.001 TYR C 55 PHE 0.007 0.001 PHE B 243 TRP 0.014 0.001 TRP A 253 HIS 0.002 0.000 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7828) covalent geometry : angle 0.67052 (10643) SS BOND : bond 0.00251 ( 15) SS BOND : angle 1.61622 ( 30) hydrogen bonds : bond 0.03285 ( 181) hydrogen bonds : angle 4.49401 ( 483) link_NAG-ASN : bond 0.00313 ( 7) link_NAG-ASN : angle 2.74729 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2535.36 seconds wall clock time: 44 minutes 2.15 seconds (2642.15 seconds total)