Starting phenix.real_space_refine on Wed Sep 17 13:02:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdm_38281/09_2025/8xdm_38281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdm_38281/09_2025/8xdm_38281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xdm_38281/09_2025/8xdm_38281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdm_38281/09_2025/8xdm_38281.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdm_38281/09_2025/8xdm_38281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdm_38281/09_2025/8xdm_38281.cif" } resolution = 2.45 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 62 5.16 5 C 5517 2.51 5 N 1474 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8746 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.42, per 1000 atoms: 0.28 Number of scatterers: 8746 At special positions: 0 Unit cell: (89.88, 89.88, 136.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 6 15.00 Mg 3 11.99 O 1684 8.00 N 1474 7.00 C 5517 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 330.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 18 sheets defined 52.1% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.763A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.997A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.544A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 4.076A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.703A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.763A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.997A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.544A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 4.076A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.702A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.763A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.997A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.544A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.076A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.702A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.601A pdb=" N LEU A 16 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 13 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.600A pdb=" N LEU B 16 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 13 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.600A pdb=" N LEU C 16 " --> pdb=" O GLY C 13 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 13 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 461 hydrogen bonds defined for protein. 1161 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: 1.64 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2844 1.35 - 1.46: 2011 1.46 - 1.58: 3963 1.58 - 1.70: 9 1.70 - 1.81: 110 Bond restraints: 8937 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.405 -0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CG HIC B 73 " pdb=" CD2 HIC B 73 " ideal model delta sigma weight residual 1.369 1.413 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" CG HIC C 73 " pdb=" CD2 HIC C 73 " ideal model delta sigma weight residual 1.369 1.413 -0.044 2.00e-02 2.50e+03 4.77e+00 ... (remaining 8932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 11911 2.23 - 4.46: 178 4.46 - 6.69: 34 6.69 - 8.92: 6 8.92 - 11.15: 3 Bond angle restraints: 12132 Sorted by residual: angle pdb=" CG LYS A 84 " pdb=" CD LYS A 84 " pdb=" CE LYS A 84 " ideal model delta sigma weight residual 111.30 120.13 -8.83 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CG LYS C 84 " pdb=" CD LYS C 84 " pdb=" CE LYS C 84 " ideal model delta sigma weight residual 111.30 120.13 -8.83 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CG LYS B 84 " pdb=" CD LYS B 84 " pdb=" CE LYS B 84 " ideal model delta sigma weight residual 111.30 120.08 -8.78 2.30e+00 1.89e-01 1.46e+01 angle pdb=" CD LYS A 84 " pdb=" CE LYS A 84 " pdb=" NZ LYS A 84 " ideal model delta sigma weight residual 111.90 123.05 -11.15 3.20e+00 9.77e-02 1.21e+01 angle pdb=" CD LYS B 84 " pdb=" CE LYS B 84 " pdb=" NZ LYS B 84 " ideal model delta sigma weight residual 111.90 123.02 -11.12 3.20e+00 9.77e-02 1.21e+01 ... (remaining 12127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4648 17.77 - 35.54: 468 35.54 - 53.31: 191 53.31 - 71.08: 56 71.08 - 88.86: 9 Dihedral angle restraints: 5372 sinusoidal: 2168 harmonic: 3204 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -144.28 84.28 1 2.00e+01 2.50e-03 2.16e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 -144.27 84.27 1 2.00e+01 2.50e-03 2.16e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -144.24 84.23 1 2.00e+01 2.50e-03 2.16e+01 ... (remaining 5369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 729 0.025 - 0.051: 368 0.051 - 0.076: 107 0.076 - 0.101: 89 0.101 - 0.127: 56 Chirality restraints: 1349 Sorted by residual: chirality pdb=" C3' ADP B 401 " pdb=" C2' ADP B 401 " pdb=" C4' ADP B 401 " pdb=" O3' ADP B 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.64 0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.64 0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL C 129 " pdb=" N VAL C 129 " pdb=" C VAL C 129 " pdb=" CB VAL C 129 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 1346 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 321 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO B 322 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 322 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 322 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 321 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 322 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 321 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO C 322 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " 0.018 5.00e-02 4.00e+02 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1463 2.77 - 3.30: 7868 3.30 - 3.84: 14641 3.84 - 4.37: 17524 4.37 - 4.90: 29911 Nonbonded interactions: 71407 Sorted by model distance: nonbonded pdb=" N GLU C 334 " pdb=" OE1 GLU C 334 " model vdw 2.238 3.120 nonbonded pdb=" N GLU B 334 " pdb=" OE1 GLU B 334 " model vdw 2.238 3.120 nonbonded pdb=" N GLU A 334 " pdb=" OE1 GLU A 334 " model vdw 2.238 3.120 nonbonded pdb=" OD2 ASP C 157 " pdb=" O3' ADP C 401 " model vdw 2.279 3.040 nonbonded pdb=" OD2 ASP B 157 " pdb=" O3' ADP B 401 " model vdw 2.279 3.040 ... (remaining 71402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 371 or resid 401 through 402)) selection = (chain 'B' and (resid 5 through 371 or resid 401 through 402)) 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: 8.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.330 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 0.058 8937 Z= 0.146 Angle : 0.674 11.151 12132 Z= 0.325 Chirality : 0.043 0.127 1349 Planarity : 0.004 0.033 1550 Dihedral : 17.956 88.856 3322 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 6.52 % Allowed : 15.40 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.26), residues: 1094 helix: 1.38 (0.26), residues: 444 sheet: 1.18 (0.35), residues: 210 loop : 0.98 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 312 TYR 0.007 0.001 TYR B 294 PHE 0.008 0.001 PHE A 255 TRP 0.012 0.001 TRP C 79 HIS 0.003 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8937) covalent geometry : angle 0.67371 (12132) hydrogen bonds : bond 0.19746 ( 455) hydrogen bonds : angle 6.14900 ( 1161) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 179 time to evaluate : 0.362 Fit side-chains REVERT: A 84 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7261 (tptm) REVERT: B 44 MET cc_start: 0.2209 (ttt) cc_final: 0.1987 (ttt) REVERT: B 47 MET cc_start: 0.4460 (ptt) cc_final: 0.3077 (tmm) REVERT: B 68 LYS cc_start: 0.6163 (OUTLIER) cc_final: 0.5912 (tptp) REVERT: B 72 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7072 (mt-10) REVERT: C 47 MET cc_start: 0.3158 (ptt) cc_final: 0.2913 (ptm) outliers start: 61 outliers final: 3 residues processed: 200 average time/residue: 0.7506 time to fit residues: 157.9118 Evaluate side-chains 133 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 271 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 162 ASN A 246 GLN B 297 ASN C 162 ASN C 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.149504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.132024 restraints weight = 8358.016| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.27 r_work: 0.3408 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8937 Z= 0.186 Angle : 0.727 7.331 12132 Z= 0.367 Chirality : 0.051 0.198 1349 Planarity : 0.005 0.058 1550 Dihedral : 8.239 87.906 1259 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.53 % Allowed : 18.40 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.26), residues: 1094 helix: 1.04 (0.25), residues: 455 sheet: 1.06 (0.36), residues: 205 loop : 0.91 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 177 TYR 0.012 0.002 TYR A 69 PHE 0.011 0.002 PHE A 262 TRP 0.016 0.003 TRP A 340 HIS 0.008 0.002 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8937) covalent geometry : angle 0.72715 (12132) hydrogen bonds : bond 0.05647 ( 455) hydrogen bonds : angle 4.85110 ( 1161) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.363 Fit side-chains REVERT: A 95 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7364 (mtt-85) REVERT: A 215 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7881 (mtpt) REVERT: A 359 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6750 (mmtm) REVERT: B 44 MET cc_start: 0.1796 (ttt) cc_final: 0.1488 (ttt) REVERT: B 47 MET cc_start: 0.5144 (ptt) cc_final: 0.3168 (tmm) REVERT: B 68 LYS cc_start: 0.8492 (mppt) cc_final: 0.8274 (mptp) REVERT: B 72 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: B 95 ARG cc_start: 0.7524 (ptp-110) cc_final: 0.6852 (mtt90) REVERT: B 314 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: B 354 GLN cc_start: 0.7542 (mp-120) cc_final: 0.7256 (pm20) REVERT: C 47 MET cc_start: 0.3727 (ptt) cc_final: 0.3398 (ptm) REVERT: C 59 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8508 (tp40) REVERT: C 68 LYS cc_start: 0.8363 (tppt) cc_final: 0.7601 (mppt) REVERT: C 100 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7899 (mt-10) REVERT: C 173 HIS cc_start: 0.6870 (p-80) cc_final: 0.6347 (m-70) REVERT: C 292 ASP cc_start: 0.8260 (m-30) cc_final: 0.8032 (m-30) REVERT: C 313 MET cc_start: 0.8900 (mmm) cc_final: 0.8623 (mmm) REVERT: C 353 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7812 (mm110) REVERT: C 354 GLN cc_start: 0.8110 (pt0) cc_final: 0.7887 (pm20) outliers start: 33 outliers final: 10 residues processed: 166 average time/residue: 0.7786 time to fit residues: 135.7691 Evaluate side-chains 149 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 0.0870 chunk 2 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 353 GLN B 162 ASN B 297 ASN B 353 GLN C 173 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128465 restraints weight = 8334.548| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.23 r_work: 0.3359 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8937 Z= 0.190 Angle : 0.727 7.364 12132 Z= 0.364 Chirality : 0.052 0.206 1349 Planarity : 0.006 0.069 1550 Dihedral : 8.039 88.668 1249 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.96 % Allowed : 17.65 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.25), residues: 1094 helix: 1.02 (0.25), residues: 455 sheet: 0.85 (0.35), residues: 208 loop : 0.88 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 256 TYR 0.010 0.002 TYR B 53 PHE 0.011 0.002 PHE A 262 TRP 0.016 0.003 TRP A 340 HIS 0.007 0.002 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8937) covalent geometry : angle 0.72672 (12132) hydrogen bonds : bond 0.05783 ( 455) hydrogen bonds : angle 4.78760 ( 1161) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8234 (pt) REVERT: A 68 LYS cc_start: 0.8499 (tppt) cc_final: 0.7928 (mppt) REVERT: A 95 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7574 (mtt-85) REVERT: A 215 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7824 (mtpt) REVERT: A 359 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6800 (mmtm) REVERT: B 64 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8508 (pt) REVERT: B 72 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: B 95 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6956 (mtm-85) REVERT: B 210 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8045 (ttm110) REVERT: B 314 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: B 334 GLU cc_start: 0.7494 (pm20) cc_final: 0.7049 (pm20) REVERT: B 354 GLN cc_start: 0.7620 (mp-120) cc_final: 0.7324 (pm20) REVERT: C 47 MET cc_start: 0.3651 (ptt) cc_final: 0.3348 (ptp) REVERT: C 95 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7457 (mtp85) REVERT: C 125 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: C 173 HIS cc_start: 0.6985 (p90) cc_final: 0.6436 (m-70) REVERT: C 292 ASP cc_start: 0.8274 (m-30) cc_final: 0.8026 (m-30) REVERT: C 313 MET cc_start: 0.8974 (mmm) cc_final: 0.8642 (mmm) REVERT: C 353 GLN cc_start: 0.8279 (mm-40) cc_final: 0.8031 (mm110) outliers start: 37 outliers final: 12 residues processed: 164 average time/residue: 0.7692 time to fit residues: 132.6117 Evaluate side-chains 147 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 77 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.0570 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 297 ASN C 59 GLN C 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.148026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130040 restraints weight = 8488.177| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.23 r_work: 0.3382 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8937 Z= 0.147 Angle : 0.656 6.846 12132 Z= 0.325 Chirality : 0.048 0.194 1349 Planarity : 0.005 0.047 1550 Dihedral : 7.656 86.852 1249 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.32 % Allowed : 18.40 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.25), residues: 1094 helix: 1.19 (0.25), residues: 455 sheet: 0.68 (0.36), residues: 202 loop : 0.89 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.008 0.001 TYR B 53 PHE 0.008 0.001 PHE A 255 TRP 0.013 0.002 TRP B 79 HIS 0.007 0.002 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8937) covalent geometry : angle 0.65601 (12132) hydrogen bonds : bond 0.04789 ( 455) hydrogen bonds : angle 4.61965 ( 1161) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.411 Fit side-chains REVERT: A 64 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8172 (pt) REVERT: A 68 LYS cc_start: 0.8544 (tppt) cc_final: 0.8134 (mppt) REVERT: A 95 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7531 (mtt-85) REVERT: A 118 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8289 (mtpm) REVERT: A 215 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7750 (mtpt) REVERT: A 353 GLN cc_start: 0.8736 (mm110) cc_final: 0.8529 (mm110) REVERT: A 359 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6666 (mmtm) REVERT: B 64 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8538 (pt) REVERT: B 68 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8680 (mttp) REVERT: B 72 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: B 95 ARG cc_start: 0.7776 (ptp-110) cc_final: 0.7030 (mtm-85) REVERT: B 210 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8031 (ttm110) REVERT: B 314 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: B 334 GLU cc_start: 0.7565 (pm20) cc_final: 0.7110 (pm20) REVERT: B 354 GLN cc_start: 0.7603 (mp-120) cc_final: 0.7285 (pm20) REVERT: C 47 MET cc_start: 0.4125 (ptt) cc_final: 0.3736 (ptp) REVERT: C 95 ARG cc_start: 0.7683 (ptp-110) cc_final: 0.7408 (mtp85) REVERT: C 125 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: C 173 HIS cc_start: 0.6942 (p90) cc_final: 0.6424 (m-70) REVERT: C 292 ASP cc_start: 0.8204 (m-30) cc_final: 0.7971 (m-30) REVERT: C 313 MET cc_start: 0.8989 (mmm) cc_final: 0.8656 (mmm) REVERT: C 353 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7913 (mm110) outliers start: 31 outliers final: 14 residues processed: 158 average time/residue: 0.7704 time to fit residues: 128.1262 Evaluate side-chains 152 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 0.0370 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN C 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127074 restraints weight = 8349.181| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.21 r_work: 0.3341 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8937 Z= 0.214 Angle : 0.749 8.058 12132 Z= 0.377 Chirality : 0.052 0.209 1349 Planarity : 0.006 0.079 1550 Dihedral : 7.946 90.056 1248 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.28 % Allowed : 17.43 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.26), residues: 1094 helix: 1.08 (0.25), residues: 455 sheet: 0.64 (0.37), residues: 204 loop : 0.77 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 256 TYR 0.010 0.002 TYR B 53 PHE 0.012 0.002 PHE B 200 TRP 0.019 0.003 TRP A 340 HIS 0.008 0.002 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 8937) covalent geometry : angle 0.74941 (12132) hydrogen bonds : bond 0.06075 ( 455) hydrogen bonds : angle 4.82190 ( 1161) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8225 (pt) REVERT: A 68 LYS cc_start: 0.8593 (tppt) cc_final: 0.8040 (mppt) REVERT: A 95 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7642 (mtt-85) REVERT: A 125 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: A 215 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7852 (mtpt) REVERT: A 353 GLN cc_start: 0.8722 (mm110) cc_final: 0.8501 (mm110) REVERT: A 370 VAL cc_start: 0.8096 (m) cc_final: 0.7768 (p) REVERT: B 64 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8503 (pt) REVERT: B 68 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8689 (mttp) REVERT: B 72 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: B 95 ARG cc_start: 0.7837 (ptp-110) cc_final: 0.7180 (mtt90) REVERT: B 210 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8071 (ttm110) REVERT: B 314 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: B 334 GLU cc_start: 0.7587 (pm20) cc_final: 0.7101 (pm20) REVERT: B 354 GLN cc_start: 0.7602 (mp-120) cc_final: 0.7246 (pm20) REVERT: C 47 MET cc_start: 0.3874 (ptt) cc_final: 0.3390 (ptm) REVERT: C 95 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7472 (mtp85) REVERT: C 125 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: C 173 HIS cc_start: 0.7023 (p90) cc_final: 0.6459 (m-70) REVERT: C 292 ASP cc_start: 0.8294 (m-30) cc_final: 0.8055 (m-30) REVERT: C 313 MET cc_start: 0.9023 (mmm) cc_final: 0.8671 (mmm) REVERT: C 353 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7997 (mm110) outliers start: 40 outliers final: 18 residues processed: 157 average time/residue: 0.7886 time to fit residues: 130.0185 Evaluate side-chains 154 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.0870 chunk 104 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 63 optimal weight: 0.0770 chunk 31 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN C 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.148998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131237 restraints weight = 8461.329| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.23 r_work: 0.3396 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8937 Z= 0.120 Angle : 0.617 7.321 12132 Z= 0.302 Chirality : 0.046 0.179 1349 Planarity : 0.004 0.041 1550 Dihedral : 7.411 86.834 1248 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.32 % Allowed : 18.93 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.26), residues: 1094 helix: 1.31 (0.25), residues: 455 sheet: 0.62 (0.36), residues: 206 loop : 0.94 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 335 TYR 0.007 0.001 TYR B 294 PHE 0.008 0.001 PHE A 255 TRP 0.013 0.002 TRP C 79 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8937) covalent geometry : angle 0.61673 (12132) hydrogen bonds : bond 0.04133 ( 455) hydrogen bonds : angle 4.51803 ( 1161) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8132 (pt) REVERT: A 68 LYS cc_start: 0.8553 (tppt) cc_final: 0.8118 (mppt) REVERT: A 95 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7539 (mtt-85) REVERT: A 118 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8276 (mtpm) REVERT: A 125 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: A 353 GLN cc_start: 0.8698 (mm110) cc_final: 0.8495 (mm110) REVERT: A 370 VAL cc_start: 0.7981 (m) cc_final: 0.7689 (p) REVERT: B 57 GLU cc_start: 0.7983 (tt0) cc_final: 0.7777 (mt-10) REVERT: B 72 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: B 95 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7070 (mtt90) REVERT: B 118 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8464 (tmtt) REVERT: B 210 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8014 (ttm110) REVERT: B 334 GLU cc_start: 0.7609 (pm20) cc_final: 0.7116 (pm20) REVERT: B 354 GLN cc_start: 0.7588 (mp-120) cc_final: 0.7279 (pm20) REVERT: C 47 MET cc_start: 0.3784 (ptt) cc_final: 0.1501 (ppp) REVERT: C 68 LYS cc_start: 0.8631 (tppt) cc_final: 0.8078 (mppt) REVERT: C 95 ARG cc_start: 0.7796 (ptp-110) cc_final: 0.7474 (mtp85) REVERT: C 173 HIS cc_start: 0.6904 (p90) cc_final: 0.6426 (m-70) REVERT: C 292 ASP cc_start: 0.8183 (m-30) cc_final: 0.7943 (m-30) REVERT: C 313 MET cc_start: 0.9012 (mmm) cc_final: 0.8671 (mmm) REVERT: C 353 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7984 (mm110) outliers start: 31 outliers final: 14 residues processed: 154 average time/residue: 0.7930 time to fit residues: 128.2632 Evaluate side-chains 152 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN C 225 ASN C 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128041 restraints weight = 8483.135| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.19 r_work: 0.3352 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8937 Z= 0.155 Angle : 0.668 8.283 12132 Z= 0.331 Chirality : 0.049 0.191 1349 Planarity : 0.005 0.053 1550 Dihedral : 7.569 88.779 1248 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.85 % Allowed : 17.86 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.26), residues: 1094 helix: 1.27 (0.25), residues: 455 sheet: 0.67 (0.37), residues: 204 loop : 0.88 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 177 TYR 0.008 0.001 TYR B 279 PHE 0.009 0.002 PHE A 262 TRP 0.013 0.002 TRP A 340 HIS 0.006 0.002 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8937) covalent geometry : angle 0.66807 (12132) hydrogen bonds : bond 0.04972 ( 455) hydrogen bonds : angle 4.64106 ( 1161) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8181 (pt) REVERT: A 68 LYS cc_start: 0.8536 (tppt) cc_final: 0.8138 (mppt) REVERT: A 95 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7617 (mtt-85) REVERT: A 118 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8301 (mtpm) REVERT: A 125 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: A 215 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7766 (mtpt) REVERT: A 353 GLN cc_start: 0.8703 (mm110) cc_final: 0.8496 (mm110) REVERT: A 370 VAL cc_start: 0.8016 (m) cc_final: 0.7704 (p) REVERT: B 47 MET cc_start: 0.5419 (ptt) cc_final: 0.4742 (mtt) REVERT: B 57 GLU cc_start: 0.8007 (tt0) cc_final: 0.7803 (mt-10) REVERT: B 64 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8525 (pt) REVERT: B 95 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7112 (mtm-85) REVERT: B 210 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8070 (ttm110) REVERT: B 314 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: B 334 GLU cc_start: 0.7621 (pm20) cc_final: 0.7147 (pm20) REVERT: B 354 GLN cc_start: 0.7538 (mp-120) cc_final: 0.7261 (pm20) REVERT: C 95 ARG cc_start: 0.7824 (ptp-110) cc_final: 0.7505 (mtp85) REVERT: C 173 HIS cc_start: 0.6957 (p90) cc_final: 0.6445 (m-70) REVERT: C 210 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7669 (ttm110) REVERT: C 292 ASP cc_start: 0.8195 (m-30) cc_final: 0.7960 (m-30) REVERT: C 313 MET cc_start: 0.9037 (mmm) cc_final: 0.8743 (mmm) REVERT: C 353 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7976 (mm110) outliers start: 36 outliers final: 21 residues processed: 152 average time/residue: 0.7365 time to fit residues: 117.6194 Evaluate side-chains 157 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 0.0670 chunk 81 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN C 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128142 restraints weight = 8481.608| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.12 r_work: 0.3354 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8937 Z= 0.161 Angle : 0.679 8.584 12132 Z= 0.336 Chirality : 0.049 0.193 1349 Planarity : 0.005 0.057 1550 Dihedral : 7.215 88.841 1245 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.85 % Allowed : 17.65 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.26), residues: 1094 helix: 1.27 (0.25), residues: 455 sheet: 0.64 (0.36), residues: 208 loop : 0.89 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 210 TYR 0.008 0.001 TYR B 279 PHE 0.009 0.002 PHE A 262 TRP 0.014 0.002 TRP A 340 HIS 0.006 0.002 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8937) covalent geometry : angle 0.67879 (12132) hydrogen bonds : bond 0.05067 ( 455) hydrogen bonds : angle 4.65591 ( 1161) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8189 (pt) REVERT: A 68 LYS cc_start: 0.8543 (tppt) cc_final: 0.8166 (mppt) REVERT: A 95 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7543 (mtt-85) REVERT: A 118 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8319 (mtpm) REVERT: A 125 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: A 215 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7781 (mtpt) REVERT: A 370 VAL cc_start: 0.8031 (m) cc_final: 0.7764 (p) REVERT: B 47 MET cc_start: 0.5427 (OUTLIER) cc_final: 0.4941 (mtt) REVERT: B 64 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8532 (pt) REVERT: B 95 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7186 (mtt90) REVERT: B 210 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8082 (ttm110) REVERT: B 314 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: B 334 GLU cc_start: 0.7571 (pm20) cc_final: 0.7128 (pm20) REVERT: B 354 GLN cc_start: 0.7539 (mp-120) cc_final: 0.7169 (pm20) REVERT: C 95 ARG cc_start: 0.7834 (ptp-110) cc_final: 0.7508 (mtp85) REVERT: C 173 HIS cc_start: 0.6966 (p90) cc_final: 0.6456 (m-70) REVERT: C 210 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7680 (ttm110) REVERT: C 292 ASP cc_start: 0.8195 (m-30) cc_final: 0.7968 (m-30) REVERT: C 313 MET cc_start: 0.9039 (mmm) cc_final: 0.8733 (mmm) REVERT: C 353 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7968 (mm110) outliers start: 36 outliers final: 22 residues processed: 150 average time/residue: 0.7277 time to fit residues: 114.8204 Evaluate side-chains 154 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 67 optimal weight: 0.0170 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN C 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.146100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128404 restraints weight = 8433.775| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.17 r_work: 0.3354 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8937 Z= 0.149 Angle : 0.661 8.517 12132 Z= 0.326 Chirality : 0.048 0.185 1349 Planarity : 0.005 0.050 1550 Dihedral : 7.136 88.473 1245 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.06 % Allowed : 17.54 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.26), residues: 1094 helix: 1.32 (0.25), residues: 455 sheet: 0.65 (0.36), residues: 208 loop : 0.91 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.008 0.001 TYR B 279 PHE 0.008 0.002 PHE A 255 TRP 0.014 0.002 TRP C 79 HIS 0.006 0.002 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8937) covalent geometry : angle 0.66053 (12132) hydrogen bonds : bond 0.04794 ( 455) hydrogen bonds : angle 4.60686 ( 1161) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8198 (pt) REVERT: A 68 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8150 (mppt) REVERT: A 95 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7518 (mtt-85) REVERT: A 118 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8303 (mtpm) REVERT: A 125 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.6261 (mp0) REVERT: A 215 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7751 (mtpt) REVERT: A 370 VAL cc_start: 0.8007 (m) cc_final: 0.7740 (p) REVERT: B 47 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.5027 (mtt) REVERT: B 64 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8536 (pt) REVERT: B 95 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7148 (mtt90) REVERT: B 210 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8061 (ttm110) REVERT: B 314 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: B 334 GLU cc_start: 0.7595 (pm20) cc_final: 0.7132 (pm20) REVERT: B 354 GLN cc_start: 0.7528 (mp-120) cc_final: 0.7201 (pm20) REVERT: C 95 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7488 (mtp85) REVERT: C 173 HIS cc_start: 0.6942 (p90) cc_final: 0.6417 (m-70) REVERT: C 210 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7651 (ttm110) REVERT: C 292 ASP cc_start: 0.8176 (m-30) cc_final: 0.7941 (m-30) REVERT: C 313 MET cc_start: 0.9039 (mmm) cc_final: 0.8753 (mmm) REVERT: C 353 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7975 (mm110) outliers start: 38 outliers final: 23 residues processed: 151 average time/residue: 0.7650 time to fit residues: 121.4100 Evaluate side-chains 159 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN C 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128433 restraints weight = 8392.297| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.17 r_work: 0.3352 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8937 Z= 0.152 Angle : 0.668 8.341 12132 Z= 0.330 Chirality : 0.048 0.187 1349 Planarity : 0.005 0.051 1550 Dihedral : 7.155 88.536 1245 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.74 % Allowed : 18.07 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.26), residues: 1094 helix: 1.30 (0.25), residues: 455 sheet: 0.64 (0.36), residues: 208 loop : 0.88 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 210 TYR 0.008 0.001 TYR B 279 PHE 0.008 0.002 PHE A 255 TRP 0.013 0.002 TRP C 79 HIS 0.006 0.002 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8937) covalent geometry : angle 0.66763 (12132) hydrogen bonds : bond 0.04909 ( 455) hydrogen bonds : angle 4.62430 ( 1161) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8200 (pt) REVERT: A 68 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8154 (mppt) REVERT: A 95 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7515 (mtt-85) REVERT: A 118 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8300 (mtpm) REVERT: A 125 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.6262 (mp0) REVERT: A 215 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7755 (mtpt) REVERT: A 370 VAL cc_start: 0.8017 (m) cc_final: 0.7749 (p) REVERT: B 47 MET cc_start: 0.5453 (OUTLIER) cc_final: 0.5140 (mtt) REVERT: B 64 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8519 (pt) REVERT: B 95 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7160 (mtt90) REVERT: B 210 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8064 (ttm110) REVERT: B 314 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: B 334 GLU cc_start: 0.7617 (pm20) cc_final: 0.7149 (pm20) REVERT: B 354 GLN cc_start: 0.7495 (mp-120) cc_final: 0.7116 (pm20) REVERT: C 95 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7501 (mtp85) REVERT: C 173 HIS cc_start: 0.6942 (p90) cc_final: 0.6421 (m-70) REVERT: C 210 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7660 (ttm110) REVERT: C 292 ASP cc_start: 0.8198 (m-30) cc_final: 0.7969 (m-30) REVERT: C 313 MET cc_start: 0.9039 (mmm) cc_final: 0.8745 (mmm) REVERT: C 326 LYS cc_start: 0.8344 (tmtt) cc_final: 0.8094 (tptp) REVERT: C 353 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7975 (mm110) outliers start: 35 outliers final: 21 residues processed: 146 average time/residue: 0.7138 time to fit residues: 109.5594 Evaluate side-chains 157 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 297 ASN C 225 ASN C 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125445 restraints weight = 8361.053| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.22 r_work: 0.3320 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 8937 Z= 0.295 Angle : 0.858 9.591 12132 Z= 0.435 Chirality : 0.057 0.237 1349 Planarity : 0.007 0.098 1550 Dihedral : 7.674 93.851 1245 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.17 % Allowed : 17.65 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.26), residues: 1094 helix: 0.93 (0.25), residues: 455 sheet: 0.46 (0.36), residues: 208 loop : 0.71 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 256 TYR 0.011 0.002 TYR B 279 PHE 0.014 0.003 PHE A 262 TRP 0.025 0.004 TRP A 340 HIS 0.009 0.003 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00711 ( 8937) covalent geometry : angle 0.85812 (12132) hydrogen bonds : bond 0.07142 ( 455) hydrogen bonds : angle 4.97855 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4258.56 seconds wall clock time: 73 minutes 15.81 seconds (4395.81 seconds total)