Starting phenix.real_space_refine on Sat May 2 18:07:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21dx_67603/05_2026/21dx_67603.cif Found real_map, /net/cci-nas-00/data/ceres_data/21dx_67603/05_2026/21dx_67603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21dx_67603/05_2026/21dx_67603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21dx_67603/05_2026/21dx_67603.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21dx_67603/05_2026/21dx_67603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21dx_67603/05_2026/21dx_67603.map" } resolution = 2.95 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= 0.018 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 54 5.16 5 C 4944 2.51 5 N 1287 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7764 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2515 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 33 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 Restraints were copied for chains: B, C Time building chain proxies: 1.65, per 1000 atoms: 0.21 Number of scatterers: 7764 At special positions: 0 Unit cell: (91.105, 89.187, 122.752, 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 54 16.00 P 9 15.00 O 1470 8.00 N 1287 7.00 C 4944 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 203 " - pdb=" SG CYS C 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 247 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS C 247 " - pdb=" SG CYS C 256 " 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 402 " - " ASN A 170 " " NAG A 403 " - " ASN A 194 " " NAG A 404 " - " ASN A 290 " " NAG B 402 " - " ASN B 170 " " NAG B 403 " - " ASN B 194 " " NAG B 404 " - " ASN B 290 " " NAG C 402 " - " ASN C 170 " " NAG C 403 " - " ASN C 194 " " NAG C 404 " - " ASN C 290 " Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 358.4 milliseconds 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 30.0% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 21 through 41 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.572A 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 Processing helix chain 'A' and resid 196 through 203 removed outlier: 4.043A pdb=" N THR A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 228 through 236 removed outlier: 3.828A pdb=" N ARG A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.681A pdb=" N CYS A 256 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.393A pdb=" N GLU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 271' Processing helix chain 'A' and resid 318 through 348 removed outlier: 3.670A pdb=" N LYS A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 41 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.572A pdb=" N TYR B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 80' Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 196 through 203 removed outlier: 4.043A pdb=" N THR B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 228 through 236 removed outlier: 3.827A pdb=" N ARG B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.681A pdb=" N CYS B 256 " --> pdb=" O TRP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 4.393A pdb=" N GLU B 270 " --> pdb=" O ASP B 266 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 271' Processing helix chain 'B' and resid 318 through 348 removed outlier: 3.671A pdb=" N LYS B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 41 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.572A pdb=" N TYR C 80 " --> pdb=" O ASP C 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 80' Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 196 through 203 removed outlier: 4.043A pdb=" N THR C 202 " --> pdb=" O ARG C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.828A pdb=" N ARG C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.681A pdb=" N CYS C 256 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.394A pdb=" N GLU C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'C' and resid 318 through 348 removed outlier: 3.671A pdb=" N LYS C 348 " --> pdb=" O LEU C 344 " (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 108 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 89 through 108 current: chain 'A' and resid 145 through 153 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 145 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 68 through 69 Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 50 through 53 current: chain 'B' and resid 89 through 108 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 89 through 108 current: chain 'B' and resid 145 through 153 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 145 through 153 current: chain 'B' and resid 259 through 264 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 264 current: chain 'B' and resid 293 through 316 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 65 Processing sheet with id=AA6, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 50 through 53 current: chain 'C' and resid 89 through 108 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 89 through 108 current: chain 'C' and resid 145 through 153 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 145 through 153 current: chain 'C' and resid 259 through 264 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 264 current: chain 'C' and resid 293 through 316 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 57 through 65 Processing sheet with id=AA9, first strand: chain 'C' and resid 68 through 69 220 hydrogen bonds defined for protein. 588 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: 1.02 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2454 1.34 - 1.46: 1872 1.46 - 1.58: 3522 1.58 - 1.69: 15 1.69 - 1.81: 75 Bond restraints: 7938 Sorted by residual: bond pdb=" C1 NAG C 404 " pdb=" O5 NAG C 404 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG B 404 " pdb=" O5 NAG B 404 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG A 404 " pdb=" O5 NAG A 404 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C1 NAG B 403 " pdb=" O5 NAG B 403 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG C 402 " pdb=" O5 NAG C 402 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 7933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 10667 1.96 - 3.92: 114 3.92 - 5.88: 10 5.88 - 7.85: 6 7.85 - 9.81: 3 Bond angle restraints: 10800 Sorted by residual: angle pdb=" CG ARG B 198 " pdb=" CD ARG B 198 " pdb=" NE ARG B 198 " ideal model delta sigma weight residual 112.00 118.41 -6.41 2.20e+00 2.07e-01 8.48e+00 angle pdb=" CG ARG C 198 " pdb=" CD ARG C 198 " pdb=" NE ARG C 198 " ideal model delta sigma weight residual 112.00 118.40 -6.40 2.20e+00 2.07e-01 8.47e+00 angle pdb=" CG ARG A 198 " pdb=" CD ARG A 198 " pdb=" NE ARG A 198 " ideal model delta sigma weight residual 112.00 118.39 -6.39 2.20e+00 2.07e-01 8.43e+00 angle pdb=" CA LEU B 33 " pdb=" CB LEU B 33 " pdb=" CG LEU B 33 " ideal model delta sigma weight residual 116.30 126.11 -9.81 3.50e+00 8.16e-02 7.85e+00 angle pdb=" CA LEU C 33 " pdb=" CB LEU C 33 " pdb=" CG LEU C 33 " ideal model delta sigma weight residual 116.30 126.10 -9.80 3.50e+00 8.16e-02 7.84e+00 ... (remaining 10795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.95: 4467 23.95 - 47.89: 354 47.89 - 71.84: 66 71.84 - 95.78: 9 95.78 - 119.73: 9 Dihedral angle restraints: 4905 sinusoidal: 2076 harmonic: 2829 Sorted by residual: dihedral pdb=" C2 NAG C 404 " pdb=" C1 NAG C 404 " pdb=" O5 NAG C 404 " pdb=" C5 NAG C 404 " ideal model delta sinusoidal sigma weight residual -62.96 56.77 -119.73 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C2 NAG A 404 " pdb=" C1 NAG A 404 " pdb=" O5 NAG A 404 " pdb=" C5 NAG A 404 " ideal model delta sinusoidal sigma weight residual -62.96 56.76 -119.72 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C2 NAG B 404 " pdb=" C1 NAG B 404 " pdb=" O5 NAG B 404 " pdb=" C5 NAG B 404 " ideal model delta sinusoidal sigma weight residual -62.96 56.73 -119.69 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 4902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 817 0.033 - 0.067: 267 0.067 - 0.100: 88 0.100 - 0.133: 74 0.133 - 0.167: 5 Chirality restraints: 1251 Sorted by residual: chirality pdb=" C1 NAG A 404 " pdb=" ND2 ASN A 290 " pdb=" C2 NAG A 404 " pdb=" O5 NAG A 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 290 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" C1 NAG B 404 " pdb=" ND2 ASN B 290 " pdb=" C2 NAG B 404 " pdb=" O5 NAG B 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 1248 not shown) Planarity restraints: 1359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 185 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.09e+00 pdb=" C ASN A 185 " -0.018 2.00e-02 2.50e+03 pdb=" O ASN A 185 " 0.007 2.00e-02 2.50e+03 pdb=" N PHE A 186 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 185 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.08e+00 pdb=" C ASN C 185 " -0.018 2.00e-02 2.50e+03 pdb=" O ASN C 185 " 0.007 2.00e-02 2.50e+03 pdb=" N PHE C 186 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 185 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.06e+00 pdb=" C ASN B 185 " -0.018 2.00e-02 2.50e+03 pdb=" O ASN B 185 " 0.007 2.00e-02 2.50e+03 pdb=" N PHE B 186 " 0.006 2.00e-02 2.50e+03 ... (remaining 1356 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2314 2.82 - 3.34: 6358 3.34 - 3.86: 12151 3.86 - 4.38: 13841 4.38 - 4.90: 24921 Nonbonded interactions: 59585 Sorted by model distance: nonbonded pdb=" O GLY A 66 " pdb=" OH TYR A 80 " model vdw 2.294 3.040 nonbonded pdb=" O GLY C 66 " pdb=" OH TYR C 80 " model vdw 2.295 3.040 nonbonded pdb=" O GLY B 66 " pdb=" OH TYR B 80 " model vdw 2.295 3.040 nonbonded pdb=" NH1 ARG B 180 " pdb=" OE2 GLU B 187 " model vdw 2.367 3.120 nonbonded pdb=" NH1 ARG C 180 " pdb=" OE2 GLU C 187 " model vdw 2.367 3.120 ... (remaining 59580 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.910 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.740 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 : 0.003 0.078 7962 Z= 0.149 Angle : 0.543 9.808 10857 Z= 0.266 Chirality : 0.044 0.167 1251 Planarity : 0.003 0.033 1350 Dihedral : 17.544 119.727 3048 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.62 % Allowed : 22.76 % Favored : 76.63 % 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: -0.03 (0.27), residues: 978 helix: 0.13 (0.32), residues: 270 sheet: 1.21 (0.29), residues: 327 loop : -1.22 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 198 TYR 0.004 0.001 TYR C 140 PHE 0.012 0.001 PHE C 301 TRP 0.004 0.001 TRP B 245 HIS 0.001 0.000 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7938) covalent geometry : angle 0.53957 (10800) SS BOND : bond 0.00162 ( 15) SS BOND : angle 0.54893 ( 30) hydrogen bonds : bond 0.13950 ( 220) hydrogen bonds : angle 5.22368 ( 588) link_NAG-ASN : bond 0.00461 ( 9) link_NAG-ASN : angle 1.37121 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.286 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 77 average time/residue: 0.4227 time to fit residues: 35.2070 Evaluate side-chains 64 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.100385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.065597 restraints weight = 12655.877| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.84 r_work: 0.2565 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2424 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7962 Z= 0.124 Angle : 0.556 9.931 10857 Z= 0.267 Chirality : 0.046 0.188 1251 Planarity : 0.003 0.021 1350 Dihedral : 11.474 87.005 1356 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.71 % Allowed : 19.31 % Favored : 77.98 % 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: 0.57 (0.27), residues: 978 helix: 0.89 (0.34), residues: 270 sheet: 1.52 (0.29), residues: 321 loop : -0.99 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 198 TYR 0.015 0.001 TYR B 37 PHE 0.010 0.001 PHE C 301 TRP 0.009 0.001 TRP B 245 HIS 0.001 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7938) covalent geometry : angle 0.54647 (10800) SS BOND : bond 0.00174 ( 15) SS BOND : angle 0.94035 ( 30) hydrogen bonds : bond 0.03544 ( 220) hydrogen bonds : angle 4.20313 ( 588) link_NAG-ASN : bond 0.00668 ( 9) link_NAG-ASN : angle 1.92587 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.335 Fit side-chains REVERT: A 185 ASN cc_start: 0.8934 (t0) cc_final: 0.8606 (t0) outliers start: 22 outliers final: 8 residues processed: 75 average time/residue: 0.3966 time to fit residues: 32.4043 Evaluate side-chains 74 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 288 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.099209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.064623 restraints weight = 12505.592| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 2.83 r_work: 0.2554 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2410 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7962 Z= 0.122 Angle : 0.555 8.281 10857 Z= 0.264 Chirality : 0.045 0.131 1251 Planarity : 0.003 0.021 1350 Dihedral : 9.484 63.977 1356 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.06 % Allowed : 19.07 % Favored : 76.88 % 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: 0.78 (0.28), residues: 978 helix: 1.13 (0.34), residues: 270 sheet: 1.59 (0.29), residues: 321 loop : -0.88 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 198 TYR 0.011 0.001 TYR B 37 PHE 0.010 0.001 PHE C 301 TRP 0.006 0.001 TRP B 245 HIS 0.001 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7938) covalent geometry : angle 0.52897 (10800) SS BOND : bond 0.00193 ( 15) SS BOND : angle 1.00203 ( 30) hydrogen bonds : bond 0.03512 ( 220) hydrogen bonds : angle 4.12159 ( 588) link_NAG-ASN : bond 0.00426 ( 9) link_NAG-ASN : angle 3.29481 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.198 Fit side-chains REVERT: A 185 ASN cc_start: 0.9006 (t0) cc_final: 0.8644 (t0) outliers start: 33 outliers final: 14 residues processed: 88 average time/residue: 0.3489 time to fit residues: 33.2281 Evaluate side-chains 80 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 19 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.099192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.064403 restraints weight = 12740.832| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 2.86 r_work: 0.2549 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2407 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7962 Z= 0.113 Angle : 0.525 8.119 10857 Z= 0.258 Chirality : 0.044 0.131 1251 Planarity : 0.003 0.023 1350 Dihedral : 8.868 61.567 1356 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.32 % Allowed : 20.54 % Favored : 76.14 % 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: 0.83 (0.28), residues: 978 helix: 1.17 (0.35), residues: 270 sheet: 1.59 (0.29), residues: 321 loop : -0.82 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 198 TYR 0.008 0.001 TYR B 37 PHE 0.009 0.001 PHE C 301 TRP 0.006 0.001 TRP B 245 HIS 0.001 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7938) covalent geometry : angle 0.51064 (10800) SS BOND : bond 0.00196 ( 15) SS BOND : angle 0.98499 ( 30) hydrogen bonds : bond 0.03365 ( 220) hydrogen bonds : angle 4.05720 ( 588) link_NAG-ASN : bond 0.00450 ( 9) link_NAG-ASN : angle 2.32873 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.260 Fit side-chains REVERT: A 185 ASN cc_start: 0.9050 (t0) cc_final: 0.8676 (t0) outliers start: 27 outliers final: 14 residues processed: 85 average time/residue: 0.4607 time to fit residues: 42.0789 Evaluate side-chains 81 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 43 optimal weight: 0.8980 chunk 88 optimal weight: 0.0030 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 72 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.102049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.069732 restraints weight = 12723.418| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.40 r_work: 0.2668 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7962 Z= 0.093 Angle : 0.499 8.713 10857 Z= 0.246 Chirality : 0.044 0.130 1251 Planarity : 0.003 0.020 1350 Dihedral : 8.344 62.890 1356 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.34 % Allowed : 21.65 % Favored : 76.01 % 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: 1.15 (0.28), residues: 978 helix: 1.67 (0.36), residues: 252 sheet: 1.67 (0.29), residues: 321 loop : -0.59 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 198 TYR 0.006 0.001 TYR B 37 PHE 0.006 0.001 PHE C 301 TRP 0.004 0.000 TRP B 245 HIS 0.001 0.000 HIS B 45 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 7938) covalent geometry : angle 0.49032 (10800) SS BOND : bond 0.00182 ( 15) SS BOND : angle 0.84401 ( 30) hydrogen bonds : bond 0.03079 ( 220) hydrogen bonds : angle 3.95540 ( 588) link_NAG-ASN : bond 0.00439 ( 9) link_NAG-ASN : angle 1.82972 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.294 Fit side-chains REVERT: A 185 ASN cc_start: 0.9051 (t0) cc_final: 0.8640 (t0) outliers start: 19 outliers final: 14 residues processed: 79 average time/residue: 0.4084 time to fit residues: 34.9198 Evaluate side-chains 81 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 95 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.0370 overall best weight: 1.2262 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.098023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.063225 restraints weight = 12679.756| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.85 r_work: 0.2524 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2381 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7962 Z= 0.148 Angle : 0.542 8.654 10857 Z= 0.270 Chirality : 0.045 0.134 1251 Planarity : 0.003 0.021 1350 Dihedral : 8.844 60.767 1356 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.32 % Allowed : 21.16 % Favored : 75.52 % 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: 0.87 (0.28), residues: 978 helix: 1.20 (0.35), residues: 270 sheet: 1.72 (0.29), residues: 315 loop : -0.86 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 198 TYR 0.007 0.001 TYR A 286 PHE 0.011 0.001 PHE C 301 TRP 0.008 0.001 TRP B 245 HIS 0.002 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 7938) covalent geometry : angle 0.53159 (10800) SS BOND : bond 0.00221 ( 15) SS BOND : angle 1.15635 ( 30) hydrogen bonds : bond 0.03604 ( 220) hydrogen bonds : angle 4.13276 ( 588) link_NAG-ASN : bond 0.00455 ( 9) link_NAG-ASN : angle 1.94760 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.228 Fit side-chains REVERT: A 185 ASN cc_start: 0.9069 (t0) cc_final: 0.8691 (t0) outliers start: 27 outliers final: 17 residues processed: 84 average time/residue: 0.4613 time to fit residues: 41.6722 Evaluate side-chains 83 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.098882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.064186 restraints weight = 12631.039| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.85 r_work: 0.2549 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2406 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7962 Z= 0.111 Angle : 0.517 9.063 10857 Z= 0.256 Chirality : 0.044 0.137 1251 Planarity : 0.003 0.027 1350 Dihedral : 8.462 63.022 1356 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.71 % Allowed : 22.26 % Favored : 75.03 % 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: 0.91 (0.28), residues: 978 helix: 1.19 (0.35), residues: 270 sheet: 1.64 (0.29), residues: 321 loop : -0.74 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 198 TYR 0.006 0.001 TYR A 286 PHE 0.008 0.001 PHE C 301 TRP 0.005 0.001 TRP B 245 HIS 0.001 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7938) covalent geometry : angle 0.50849 (10800) SS BOND : bond 0.00192 ( 15) SS BOND : angle 0.97895 ( 30) hydrogen bonds : bond 0.03286 ( 220) hydrogen bonds : angle 4.00256 ( 588) link_NAG-ASN : bond 0.00439 ( 9) link_NAG-ASN : angle 1.67943 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.344 Fit side-chains REVERT: A 185 ASN cc_start: 0.9073 (t0) cc_final: 0.8696 (t0) REVERT: B 52 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7283 (mtp-110) outliers start: 22 outliers final: 18 residues processed: 78 average time/residue: 0.4426 time to fit residues: 37.1897 Evaluate side-chains 86 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 22 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.102095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.069417 restraints weight = 12708.694| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.41 r_work: 0.2665 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7962 Z= 0.091 Angle : 0.501 9.237 10857 Z= 0.247 Chirality : 0.044 0.139 1251 Planarity : 0.003 0.030 1350 Dihedral : 7.885 65.945 1356 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.71 % Allowed : 22.26 % Favored : 75.03 % 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: 1.21 (0.28), residues: 978 helix: 1.65 (0.36), residues: 252 sheet: 1.73 (0.29), residues: 321 loop : -0.53 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 198 TYR 0.005 0.001 TYR A 286 PHE 0.006 0.001 PHE C 301 TRP 0.004 0.000 TRP B 245 HIS 0.001 0.000 HIS B 45 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7938) covalent geometry : angle 0.49486 (10800) SS BOND : bond 0.00180 ( 15) SS BOND : angle 0.83332 ( 30) hydrogen bonds : bond 0.03034 ( 220) hydrogen bonds : angle 3.90581 ( 588) link_NAG-ASN : bond 0.00445 ( 9) link_NAG-ASN : angle 1.47265 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.286 Fit side-chains REVERT: A 185 ASN cc_start: 0.9042 (t0) cc_final: 0.8622 (t0) outliers start: 22 outliers final: 15 residues processed: 80 average time/residue: 0.4205 time to fit residues: 36.4130 Evaluate side-chains 83 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 58 optimal weight: 0.0010 chunk 90 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 0.0270 overall best weight: 0.3444 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.103169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.070169 restraints weight = 12659.332| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.49 r_work: 0.2686 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7962 Z= 0.086 Angle : 0.500 9.406 10857 Z= 0.247 Chirality : 0.044 0.143 1251 Planarity : 0.003 0.053 1350 Dihedral : 7.330 70.948 1356 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.21 % Allowed : 22.51 % Favored : 75.28 % 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: 1.33 (0.28), residues: 978 helix: 1.73 (0.35), residues: 252 sheet: 1.90 (0.29), residues: 318 loop : -0.52 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 198 TYR 0.005 0.001 TYR B 286 PHE 0.005 0.001 PHE C 301 TRP 0.004 0.000 TRP B 245 HIS 0.001 0.000 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 7938) covalent geometry : angle 0.49533 (10800) SS BOND : bond 0.00168 ( 15) SS BOND : angle 0.75387 ( 30) hydrogen bonds : bond 0.02885 ( 220) hydrogen bonds : angle 3.82101 ( 588) link_NAG-ASN : bond 0.00450 ( 9) link_NAG-ASN : angle 1.33635 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.313 Fit side-chains REVERT: A 185 ASN cc_start: 0.9047 (t0) cc_final: 0.8638 (t0) REVERT: B 45 HIS cc_start: 0.8703 (t-90) cc_final: 0.8220 (t-90) outliers start: 18 outliers final: 10 residues processed: 78 average time/residue: 0.4546 time to fit residues: 38.4209 Evaluate side-chains 79 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.098654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.065701 restraints weight = 13016.837| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.53 r_work: 0.2588 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7962 Z= 0.167 Angle : 0.572 9.035 10857 Z= 0.286 Chirality : 0.046 0.144 1251 Planarity : 0.004 0.058 1350 Dihedral : 8.654 62.756 1356 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.97 % Allowed : 22.88 % Favored : 75.15 % 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: 0.90 (0.28), residues: 978 helix: 1.15 (0.35), residues: 270 sheet: 1.79 (0.29), residues: 315 loop : -0.83 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 198 TYR 0.008 0.001 TYR C 80 PHE 0.013 0.001 PHE C 301 TRP 0.008 0.001 TRP B 245 HIS 0.002 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 7938) covalent geometry : angle 0.56232 (10800) SS BOND : bond 0.00212 ( 15) SS BOND : angle 1.23854 ( 30) hydrogen bonds : bond 0.03688 ( 220) hydrogen bonds : angle 4.14701 ( 588) link_NAG-ASN : bond 0.00481 ( 9) link_NAG-ASN : angle 1.77692 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.367 Fit side-chains REVERT: A 185 ASN cc_start: 0.9076 (t0) cc_final: 0.8659 (t0) REVERT: B 45 HIS cc_start: 0.8646 (t-90) cc_final: 0.8118 (t-90) REVERT: B 52 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7264 (mtp-110) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.4826 time to fit residues: 39.0529 Evaluate side-chains 80 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 288 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.0670 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.099479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.066693 restraints weight = 12935.957| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.52 r_work: 0.2608 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7962 Z= 0.129 Angle : 0.542 9.273 10857 Z= 0.270 Chirality : 0.045 0.143 1251 Planarity : 0.004 0.055 1350 Dihedral : 8.416 65.624 1356 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.72 % Allowed : 23.25 % Favored : 75.03 % 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: 0.92 (0.28), residues: 978 helix: 1.16 (0.35), residues: 270 sheet: 1.65 (0.29), residues: 321 loop : -0.70 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 198 TYR 0.007 0.001 TYR C 80 PHE 0.010 0.001 PHE C 301 TRP 0.006 0.001 TRP B 245 HIS 0.001 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7938) covalent geometry : angle 0.53413 (10800) SS BOND : bond 0.00198 ( 15) SS BOND : angle 1.07615 ( 30) hydrogen bonds : bond 0.03407 ( 220) hydrogen bonds : angle 4.02764 ( 588) link_NAG-ASN : bond 0.00436 ( 9) link_NAG-ASN : angle 1.61596 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2559.48 seconds wall clock time: 44 minutes 19.31 seconds (2659.31 seconds total)