Starting phenix.real_space_refine on Sat Jul 26 18:46:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdm_38281/07_2025/8xdm_38281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdm_38281/07_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_38281/07_2025/8xdm_38281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdm_38281/07_2025/8xdm_38281.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdm_38281/07_2025/8xdm_38281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdm_38281/07_2025/8xdm_38281.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.10, per 1000 atoms: 0.93 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: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.30 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: 2.75 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 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: 11.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 26.410 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP C 79 HIS 0.003 0.001 HIS C 40 PHE 0.008 0.001 PHE A 255 TYR 0.007 0.001 TYR B 294 ARG 0.002 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.19746 ( 455) hydrogen bonds : angle 6.14900 ( 1161) covalent geometry : bond 0.00302 ( 8937) covalent geometry : angle 0.67371 (12132) *********************** 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 : 0.950 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: 1.4922 time to fit residues: 314.4019 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 : 0.943 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 28 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 246 GLN B 297 ASN C 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.152212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134165 restraints weight = 8422.674| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.23 r_work: 0.3436 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8937 Z= 0.147 Angle : 0.663 6.552 12132 Z= 0.330 Chirality : 0.048 0.171 1349 Planarity : 0.005 0.038 1550 Dihedral : 7.968 85.746 1259 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.78 % Allowed : 18.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1094 helix: 1.19 (0.25), residues: 454 sheet: 1.15 (0.36), residues: 205 loop : 1.06 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 340 HIS 0.006 0.002 HIS A 40 PHE 0.009 0.002 PHE A 262 TYR 0.011 0.001 TYR A 69 ARG 0.003 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 455) hydrogen bonds : angle 4.73165 ( 1161) covalent geometry : bond 0.00325 ( 8937) covalent geometry : angle 0.66250 (12132) *********************** 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 176 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.196 Fit side-chains REVERT: A 64 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8084 (pt) REVERT: A 95 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7322 (mtt-85) REVERT: A 359 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6567 (mmtm) REVERT: B 44 MET cc_start: 0.1739 (ttt) cc_final: 0.1437 (ttt) REVERT: B 47 MET cc_start: 0.5058 (ptt) cc_final: 0.3150 (tmm) REVERT: B 68 LYS cc_start: 0.8354 (mppt) cc_final: 0.8138 (mmtp) REVERT: B 72 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: B 95 ARG cc_start: 0.7432 (ptp-110) cc_final: 0.6617 (mtt90) REVERT: B 354 GLN cc_start: 0.7582 (mp-120) cc_final: 0.7262 (pm20) REVERT: C 47 MET cc_start: 0.3699 (ptt) cc_final: 0.3362 (ptm) REVERT: C 68 LYS cc_start: 0.8252 (tppt) cc_final: 0.7388 (mppt) REVERT: C 100 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7864 (mt-10) REVERT: C 173 HIS cc_start: 0.6812 (p-80) cc_final: 0.6381 (m-70) REVERT: C 292 ASP cc_start: 0.8236 (m-30) cc_final: 0.8007 (m-30) REVERT: C 313 MET cc_start: 0.8854 (mmm) cc_final: 0.8583 (mmm) REVERT: C 326 LYS cc_start: 0.7745 (tmmt) cc_final: 0.7519 (tmtm) REVERT: C 353 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7675 (mm110) REVERT: C 354 GLN cc_start: 0.8016 (pt0) cc_final: 0.7762 (pm20) outliers start: 26 outliers final: 9 residues processed: 166 average time/residue: 1.9705 time to fit residues: 343.8787 Evaluate side-chains 147 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE 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 314 GLN 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 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 13 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 297 ASN A 353 GLN B 162 ASN B 297 ASN B 353 GLN C 59 GLN C 162 ASN C 173 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127794 restraints weight = 8413.594| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.21 r_work: 0.3353 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8937 Z= 0.216 Angle : 0.761 7.593 12132 Z= 0.383 Chirality : 0.053 0.210 1349 Planarity : 0.006 0.075 1550 Dihedral : 8.163 88.383 1249 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.96 % Allowed : 17.43 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1094 helix: 0.95 (0.25), residues: 455 sheet: 0.86 (0.35), residues: 208 loop : 0.88 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 340 HIS 0.008 0.003 HIS A 40 PHE 0.014 0.002 PHE A 262 TYR 0.011 0.002 TYR B 53 ARG 0.004 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.06205 ( 455) hydrogen bonds : angle 4.84507 ( 1161) covalent geometry : bond 0.00506 ( 8937) covalent geometry : angle 0.76056 (12132) *********************** 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 173 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.015 Fit side-chains REVERT: A 64 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8172 (pt) REVERT: A 68 LYS cc_start: 0.8457 (tppt) cc_final: 0.7976 (mppt) REVERT: A 95 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7575 (mtt-85) REVERT: A 215 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7866 (mtpt) REVERT: A 359 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6809 (mmtm) REVERT: B 64 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8501 (pt) REVERT: B 72 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: B 95 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6990 (mtm-85) REVERT: B 210 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8020 (ttm110) REVERT: B 314 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: B 334 GLU cc_start: 0.7509 (pm20) cc_final: 0.7080 (pm20) REVERT: B 354 GLN cc_start: 0.7606 (mp-120) cc_final: 0.7296 (pm20) REVERT: C 47 MET cc_start: 0.3633 (ptt) cc_final: 0.3347 (ptp) REVERT: C 95 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7379 (mtp85) REVERT: C 173 HIS cc_start: 0.6952 (p90) cc_final: 0.6384 (m-70) REVERT: C 292 ASP cc_start: 0.8314 (m-30) cc_final: 0.8071 (m-30) REVERT: C 313 MET cc_start: 0.8973 (mmm) cc_final: 0.8627 (mmm) REVERT: C 353 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8021 (mm110) outliers start: 37 outliers final: 11 residues processed: 159 average time/residue: 1.8035 time to fit residues: 302.1843 Evaluate side-chains 148 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 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 35 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3664 r_free = 0.3664 target = 0.145691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.127623 restraints weight = 8324.201| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.21 r_work: 0.3354 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8937 Z= 0.196 Angle : 0.726 7.373 12132 Z= 0.365 Chirality : 0.051 0.204 1349 Planarity : 0.006 0.074 1550 Dihedral : 7.943 88.187 1249 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.53 % Allowed : 18.50 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1094 helix: 1.07 (0.25), residues: 455 sheet: 0.64 (0.36), residues: 206 loop : 0.87 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 340 HIS 0.008 0.002 HIS B 101 PHE 0.011 0.002 PHE B 200 TYR 0.010 0.002 TYR B 53 ARG 0.004 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.05725 ( 455) hydrogen bonds : angle 4.79085 ( 1161) covalent geometry : bond 0.00457 ( 8937) covalent geometry : angle 0.72627 (12132) *********************** 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 166 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 1.106 Fit side-chains REVERT: A 44 MET cc_start: -0.0019 (ptt) cc_final: -0.0309 (ttp) REVERT: A 64 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8231 (pt) REVERT: A 68 LYS cc_start: 0.8569 (tppt) cc_final: 0.8122 (mppt) REVERT: A 95 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7609 (mtt-85) REVERT: A 176 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7652 (mtp) REVERT: A 210 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7779 (ttm110) REVERT: A 215 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7851 (mtpt) REVERT: A 359 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6684 (mmtm) REVERT: B 95 ARG cc_start: 0.7820 (ptp-110) cc_final: 0.7206 (mtt90) REVERT: B 210 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8007 (ttm110) REVERT: B 314 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: B 334 GLU cc_start: 0.7576 (pm20) cc_final: 0.7112 (pm20) REVERT: B 354 GLN cc_start: 0.7607 (mp-120) cc_final: 0.7246 (pm20) REVERT: C 47 MET cc_start: 0.4208 (ptt) cc_final: 0.3818 (ptp) REVERT: C 95 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7501 (mtp85) REVERT: C 173 HIS cc_start: 0.7018 (p90) cc_final: 0.6457 (m-70) REVERT: C 292 ASP cc_start: 0.8265 (m-30) cc_final: 0.8026 (m-30) REVERT: C 313 MET cc_start: 0.9012 (mmm) cc_final: 0.8660 (mmm) REVERT: C 353 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7941 (mm110) REVERT: C 359 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7779 (mmmm) outliers start: 33 outliers final: 13 residues processed: 156 average time/residue: 1.7566 time to fit residues: 288.3458 Evaluate side-chains 153 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 176 MET 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 118 LYS 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 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 323 SER Chi-restraints excluded: chain C residue 359 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 0.0020 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.146348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128269 restraints weight = 8297.179| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.22 r_work: 0.3355 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2887 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= 0.175 Angle : 0.697 7.123 12132 Z= 0.348 Chirality : 0.050 0.202 1349 Planarity : 0.005 0.064 1550 Dihedral : 7.374 88.295 1246 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.85 % Allowed : 18.29 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1094 helix: 1.16 (0.25), residues: 455 sheet: 0.65 (0.36), residues: 208 loop : 0.86 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 340 HIS 0.007 0.002 HIS B 101 PHE 0.010 0.002 PHE A 262 TYR 0.009 0.001 TYR B 53 ARG 0.003 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.05368 ( 455) hydrogen bonds : angle 4.73062 ( 1161) covalent geometry : bond 0.00404 ( 8937) covalent geometry : angle 0.69658 (12132) *********************** 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 169 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.987 Fit side-chains REVERT: A 64 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8227 (pt) REVERT: A 68 LYS cc_start: 0.8560 (tppt) cc_final: 0.8020 (mppt) REVERT: A 95 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7639 (mtt-85) REVERT: A 118 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8266 (mtpm) REVERT: A 125 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.6407 (mp0) REVERT: A 176 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7766 (mtp) REVERT: A 210 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7786 (ttm110) REVERT: A 215 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7805 (mtpt) REVERT: A 359 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6730 (mmtm) REVERT: A 370 VAL cc_start: 0.8023 (m) cc_final: 0.7712 (p) REVERT: B 64 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8507 (pt) REVERT: B 95 ARG cc_start: 0.7815 (ptp-110) cc_final: 0.7157 (mtt90) REVERT: B 210 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8028 (ttm110) REVERT: B 314 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: B 334 GLU cc_start: 0.7551 (pm20) cc_final: 0.7065 (pm20) REVERT: B 354 GLN cc_start: 0.7613 (mp-120) cc_final: 0.7244 (pm20) REVERT: C 47 MET cc_start: 0.3969 (ptt) cc_final: 0.3433 (ptm) REVERT: C 95 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7465 (mtp85) REVERT: C 173 HIS cc_start: 0.7031 (p90) cc_final: 0.6345 (m-70) REVERT: C 210 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7708 (ttm110) REVERT: C 284 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7780 (mtpt) REVERT: C 292 ASP cc_start: 0.8256 (m-30) cc_final: 0.8016 (m-30) REVERT: C 313 MET cc_start: 0.9022 (mmm) cc_final: 0.8697 (mmm) REVERT: C 353 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7962 (mm110) REVERT: C 359 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7768 (mmmm) outliers start: 36 outliers final: 16 residues processed: 157 average time/residue: 1.4943 time to fit residues: 246.8502 Evaluate side-chains 160 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 96 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 MET 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 A residue 359 LYS Chi-restraints excluded: chain B residue 64 ILE 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 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 284 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 359 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 74 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128054 restraints weight = 8409.437| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.22 r_work: 0.3355 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 0.037 8937 Z= 0.179 Angle : 0.706 7.747 12132 Z= 0.352 Chirality : 0.050 0.202 1349 Planarity : 0.005 0.066 1550 Dihedral : 7.350 88.678 1245 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.96 % Allowed : 18.40 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1094 helix: 1.17 (0.25), residues: 455 sheet: 0.61 (0.36), residues: 208 loop : 0.87 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 340 HIS 0.007 0.002 HIS B 101 PHE 0.010 0.002 PHE A 262 TYR 0.009 0.001 TYR B 279 ARG 0.003 0.000 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.05456 ( 455) hydrogen bonds : angle 4.73820 ( 1161) covalent geometry : bond 0.00413 ( 8937) covalent geometry : angle 0.70630 (12132) *********************** 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 163 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 1.077 Fit side-chains REVERT: A 44 MET cc_start: 0.0130 (ptt) cc_final: -0.0142 (ttp) REVERT: A 64 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8235 (pt) REVERT: A 68 LYS cc_start: 0.8581 (tppt) cc_final: 0.8030 (mppt) REVERT: A 95 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7637 (mtt-85) REVERT: A 118 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8297 (mtpm) REVERT: A 125 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: A 176 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7718 (mtp) REVERT: A 210 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7793 (ttm110) REVERT: A 215 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7823 (mtpt) REVERT: A 359 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.6731 (mmtm) REVERT: A 370 VAL cc_start: 0.8031 (m) cc_final: 0.7717 (p) REVERT: B 64 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8519 (pt) REVERT: B 95 ARG cc_start: 0.7793 (ptp-110) cc_final: 0.7107 (mtm-85) REVERT: B 118 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8381 (tmtt) REVERT: B 210 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8023 (ttm110) REVERT: B 314 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: B 334 GLU cc_start: 0.7571 (pm20) cc_final: 0.7134 (pm20) REVERT: B 354 GLN cc_start: 0.7507 (mp-120) cc_final: 0.7151 (pm20) REVERT: C 68 LYS cc_start: 0.8672 (tppt) cc_final: 0.8096 (mppt) REVERT: C 95 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7419 (mtp85) REVERT: C 173 HIS cc_start: 0.6999 (p90) cc_final: 0.6328 (m-70) REVERT: C 210 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7717 (ttm110) REVERT: C 215 LYS cc_start: 0.8823 (mttt) cc_final: 0.8413 (mmtm) REVERT: C 284 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7837 (mtpt) REVERT: C 292 ASP cc_start: 0.8243 (m-30) cc_final: 0.8005 (m-30) REVERT: C 313 MET cc_start: 0.9030 (mmm) cc_final: 0.8717 (mmm) REVERT: C 353 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7981 (mm110) outliers start: 37 outliers final: 18 residues processed: 152 average time/residue: 1.5854 time to fit residues: 253.7726 Evaluate side-chains 158 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 96 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 MET 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 A residue 359 LYS Chi-restraints excluded: chain B residue 64 ILE 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 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 66 THR 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 284 LYS 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 99 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.145862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.127758 restraints weight = 8383.548| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.22 r_work: 0.3350 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8937 Z= 0.186 Angle : 0.715 8.194 12132 Z= 0.357 Chirality : 0.051 0.204 1349 Planarity : 0.006 0.069 1550 Dihedral : 7.363 88.931 1245 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.96 % Allowed : 18.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1094 helix: 1.16 (0.25), residues: 455 sheet: 0.57 (0.36), residues: 208 loop : 0.86 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 340 HIS 0.007 0.002 HIS B 101 PHE 0.010 0.002 PHE A 262 TYR 0.009 0.001 TYR B 279 ARG 0.003 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.05557 ( 455) hydrogen bonds : angle 4.75037 ( 1161) covalent geometry : bond 0.00432 ( 8937) covalent geometry : angle 0.71530 (12132) *********************** 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 163 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.957 Fit side-chains REVERT: A 64 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8221 (pt) REVERT: A 68 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8103 (mppt) REVERT: A 95 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7648 (mtt-85) REVERT: A 125 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: A 176 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7755 (mtp) REVERT: A 210 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7795 (ttm110) REVERT: A 215 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7834 (mtpt) REVERT: A 359 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6735 (mmtm) REVERT: A 370 VAL cc_start: 0.8038 (m) cc_final: 0.7759 (p) REVERT: B 47 MET cc_start: 0.5371 (ptt) cc_final: 0.4910 (mtt) REVERT: B 64 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8527 (pt) REVERT: B 95 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7169 (mtt90) REVERT: B 210 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8045 (ttm110) REVERT: B 314 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: B 334 GLU cc_start: 0.7595 (pm20) cc_final: 0.7156 (pm20) REVERT: B 354 GLN cc_start: 0.7503 (mp-120) cc_final: 0.7144 (pm20) REVERT: C 68 LYS cc_start: 0.8662 (tppt) cc_final: 0.8076 (mppt) REVERT: C 95 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7468 (mtp85) REVERT: C 173 HIS cc_start: 0.6996 (p90) cc_final: 0.6428 (m-70) REVERT: C 210 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7714 (ttm110) REVERT: C 292 ASP cc_start: 0.8235 (m-30) cc_final: 0.7992 (m-30) REVERT: C 313 MET cc_start: 0.9043 (mmm) cc_final: 0.8697 (mmm) REVERT: C 353 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8031 (mm110) outliers start: 37 outliers final: 21 residues processed: 149 average time/residue: 1.6602 time to fit residues: 260.0793 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 : 1.071 ------------------------------------------------------------------------------- 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 125 GLU Chi-restraints excluded: chain A residue 176 MET 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 A residue 359 LYS 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 314 GLN Chi-restraints excluded: chain B residue 328 LYS 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 66 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 97 optimal weight: 0.0870 chunk 22 optimal weight: 0.7980 chunk 56 optimal weight: 0.0870 chunk 89 optimal weight: 0.9980 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.146624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.128910 restraints weight = 8514.959| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.19 r_work: 0.3360 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8937 Z= 0.136 Angle : 0.646 8.488 12132 Z= 0.319 Chirality : 0.047 0.183 1349 Planarity : 0.005 0.043 1550 Dihedral : 7.126 87.154 1245 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.74 % Allowed : 18.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.26), residues: 1094 helix: 1.32 (0.25), residues: 455 sheet: 0.66 (0.36), residues: 208 loop : 0.95 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 79 HIS 0.005 0.002 HIS B 101 PHE 0.009 0.001 PHE A 255 TYR 0.008 0.001 TYR B 279 ARG 0.002 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 455) hydrogen bonds : angle 4.58300 ( 1161) covalent geometry : bond 0.00302 ( 8937) covalent geometry : angle 0.64634 (12132) *********************** 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 164 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.0007 (ptt) cc_final: -0.0316 (ttp) REVERT: A 64 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8204 (pt) REVERT: A 68 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8156 (mppt) REVERT: A 95 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7614 (mtt-85) REVERT: A 118 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8327 (mtpm) REVERT: A 125 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.6230 (mp0) REVERT: A 176 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7675 (mtp) REVERT: A 359 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6724 (mmtm) REVERT: A 370 VAL cc_start: 0.8001 (m) cc_final: 0.7742 (p) REVERT: B 47 MET cc_start: 0.5465 (OUTLIER) cc_final: 0.5000 (mtt) REVERT: B 64 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8542 (pt) REVERT: B 95 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7135 (mtt90) REVERT: B 118 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8369 (tmtt) REVERT: B 210 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8029 (ttm110) REVERT: B 314 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: B 334 GLU cc_start: 0.7596 (pm20) cc_final: 0.7083 (pm20) REVERT: B 354 GLN cc_start: 0.7510 (mp-120) cc_final: 0.7156 (pm20) REVERT: C 68 LYS cc_start: 0.8637 (tppt) cc_final: 0.8102 (mppt) REVERT: C 95 ARG cc_start: 0.7849 (ptp-110) cc_final: 0.7476 (mtp85) REVERT: C 173 HIS cc_start: 0.6983 (p90) cc_final: 0.6456 (m-70) REVERT: C 292 ASP cc_start: 0.8184 (m-30) cc_final: 0.7952 (m-30) REVERT: C 313 MET cc_start: 0.9042 (mmm) cc_final: 0.8708 (mmm) REVERT: C 353 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7958 (mm110) outliers start: 35 outliers final: 19 residues processed: 152 average time/residue: 1.6524 time to fit residues: 264.9433 Evaluate side-chains 158 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 176 MET 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 324 THR Chi-restraints excluded: chain A residue 359 LYS 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 314 GLN Chi-restraints excluded: chain B residue 328 LYS 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 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 9 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.144085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125954 restraints weight = 8429.877| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.22 r_work: 0.3326 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8937 Z= 0.251 Angle : 0.806 8.725 12132 Z= 0.406 Chirality : 0.055 0.217 1349 Planarity : 0.006 0.081 1550 Dihedral : 7.565 91.413 1245 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.96 % Allowed : 18.18 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1094 helix: 1.04 (0.25), residues: 455 sheet: 0.52 (0.36), residues: 208 loop : 0.81 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP A 340 HIS 0.008 0.003 HIS B 101 PHE 0.013 0.002 PHE A 262 TYR 0.011 0.002 TYR B 279 ARG 0.004 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.06573 ( 455) hydrogen bonds : angle 4.89238 ( 1161) covalent geometry : bond 0.00601 ( 8937) covalent geometry : angle 0.80565 (12132) *********************** 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 158 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.0326 (ptt) cc_final: -0.0054 (ttp) REVERT: A 64 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8160 (pt) REVERT: A 68 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8090 (mppt) REVERT: A 95 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7695 (mtt-85) REVERT: A 125 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: A 176 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7789 (mtp) REVERT: A 215 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7888 (mtpt) REVERT: A 370 VAL cc_start: 0.8129 (m) cc_final: 0.7814 (p) REVERT: B 47 MET cc_start: 0.5515 (OUTLIER) cc_final: 0.5131 (mtt) REVERT: B 64 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8557 (pt) REVERT: B 95 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7101 (mtm-85) REVERT: B 210 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8053 (ttm110) REVERT: B 314 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: B 334 GLU cc_start: 0.7640 (pm20) cc_final: 0.7197 (pm20) REVERT: B 354 GLN cc_start: 0.7507 (mp-120) cc_final: 0.7230 (pm20) REVERT: C 68 LYS cc_start: 0.8683 (tppt) cc_final: 0.8044 (mppt) REVERT: C 95 ARG cc_start: 0.7763 (ptp-110) cc_final: 0.7438 (mtp85) REVERT: C 173 HIS cc_start: 0.7023 (p90) cc_final: 0.6430 (m-70) REVERT: C 215 LYS cc_start: 0.8818 (mttt) cc_final: 0.8425 (mmtm) REVERT: C 292 ASP cc_start: 0.8297 (m-30) cc_final: 0.8056 (m-30) REVERT: C 313 MET cc_start: 0.9036 (mmm) cc_final: 0.8714 (mmm) REVERT: C 353 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8023 (mm110) outliers start: 37 outliers final: 20 residues processed: 147 average time/residue: 1.5046 time to fit residues: 233.1576 Evaluate side-chains 150 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 125 GLU Chi-restraints excluded: chain A residue 176 MET 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 33 SER 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 145 SER Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 324 THR 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 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 94 optimal weight: 1.9990 chunk 65 optimal weight: 0.0270 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 4 optimal weight: 0.0000 overall best weight: 0.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 297 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 = 0.3678 r_free = 0.3678 target = 0.147713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130176 restraints weight = 8417.828| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.17 r_work: 0.3375 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2998 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= 0.118 Angle : 0.621 8.103 12132 Z= 0.303 Chirality : 0.046 0.177 1349 Planarity : 0.004 0.043 1550 Dihedral : 7.011 85.963 1245 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.10 % Allowed : 19.04 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.26), residues: 1094 helix: 1.35 (0.25), residues: 455 sheet: 0.59 (0.36), residues: 206 loop : 0.93 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 79 HIS 0.004 0.001 HIS B 101 PHE 0.009 0.001 PHE C 31 TYR 0.007 0.001 TYR B 294 ARG 0.002 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 455) hydrogen bonds : angle 4.49524 ( 1161) covalent geometry : bond 0.00257 ( 8937) covalent geometry : angle 0.62057 (12132) ********************** 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: 29 poor density : 130 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.0361 (ptt) cc_final: 0.0020 (ttp) REVERT: A 64 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8183 (pt) REVERT: A 68 LYS cc_start: 0.8527 (tppt) cc_final: 0.8124 (mppt) REVERT: A 95 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7476 (mtt-85) REVERT: A 370 VAL cc_start: 0.7992 (m) cc_final: 0.7747 (p) REVERT: B 47 MET cc_start: 0.5615 (OUTLIER) cc_final: 0.5304 (mtt) REVERT: B 64 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8539 (pt) REVERT: B 95 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7091 (mtt90) REVERT: B 210 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7972 (ttm110) REVERT: B 314 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: B 334 GLU cc_start: 0.7633 (pm20) cc_final: 0.7121 (pm20) REVERT: B 354 GLN cc_start: 0.7531 (mp-120) cc_final: 0.7233 (pm20) REVERT: C 68 LYS cc_start: 0.8640 (tppt) cc_final: 0.8123 (mppt) REVERT: C 95 ARG cc_start: 0.7846 (ptp-110) cc_final: 0.7459 (mtp85) REVERT: C 173 HIS cc_start: 0.6936 (p90) cc_final: 0.6427 (m-70) REVERT: C 292 ASP cc_start: 0.8148 (m-30) cc_final: 0.7928 (m-30) REVERT: C 313 MET cc_start: 0.9041 (mmm) cc_final: 0.8706 (mmm) REVERT: C 353 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7986 (mm110) outliers start: 29 outliers final: 15 residues processed: 148 average time/residue: 1.4389 time to fit residues: 224.8614 Evaluate side-chains 146 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 33 SER 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 210 ARG Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 324 THR 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 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 20 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.6240 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.146558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128619 restraints weight = 8389.152| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.21 r_work: 0.3363 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3059 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= 0.160 Angle : 0.689 9.014 12132 Z= 0.340 Chirality : 0.049 0.191 1349 Planarity : 0.005 0.052 1550 Dihedral : 7.207 88.342 1245 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.21 % Allowed : 18.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1094 helix: 1.30 (0.25), residues: 455 sheet: 0.65 (0.37), residues: 208 loop : 0.90 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 79 HIS 0.006 0.002 HIS B 101 PHE 0.009 0.002 PHE A 262 TYR 0.009 0.001 TYR B 279 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.05034 ( 455) hydrogen bonds : angle 4.62371 ( 1161) covalent geometry : bond 0.00368 ( 8937) covalent geometry : angle 0.68856 (12132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9161.62 seconds wall clock time: 161 minutes 8.13 seconds (9668.13 seconds total)