Starting phenix.real_space_refine on Sat Dec 28 16:26:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdm_38281/12_2024/8xdm_38281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdm_38281/12_2024/8xdm_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_38281/12_2024/8xdm_38281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdm_38281/12_2024/8xdm_38281.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdm_38281/12_2024/8xdm_38281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdm_38281/12_2024/8xdm_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.91, per 1000 atoms: 0.90 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: 2.63 Conformation dependent library (CDL) restraints added in 999.3 milliseconds 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: 1.51 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: 2.90 Time building geometry restraints manager: 2.95 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: 9.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.320 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.350 ------------------------------------------------------------------------------- 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= 0.195 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 *********************** 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 : 1.002 Fit side-chains REVERT: A 84 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7260 (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: 0.3078 (tmm) REVERT: B 68 LYS cc_start: 0.6163 (OUTLIER) cc_final: 0.5911 (tptp) REVERT: B 72 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7073 (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: 1.5384 time to fit residues: 324.5106 Evaluate side-chains 132 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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: 0.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2023 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= 0.207 Angle : 0.663 6.460 12132 Z= 0.331 Chirality : 0.049 0.172 1349 Planarity : 0.005 0.038 1550 Dihedral : 7.967 86.066 1259 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.10 % Allowed : 18.61 % 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: 1.20 (0.25), residues: 453 sheet: 1.16 (0.36), residues: 205 loop : 1.04 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.007 0.002 HIS A 40 PHE 0.009 0.002 PHE A 255 TYR 0.011 0.001 TYR A 69 ARG 0.003 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.980 Fit side-chains REVERT: A 64 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8089 (pt) REVERT: A 95 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7231 (mtt-85) REVERT: A 359 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6497 (mmtm) REVERT: B 47 MET cc_start: 0.4975 (ptt) cc_final: 0.3459 (tmm) REVERT: B 95 ARG cc_start: 0.7165 (ptp-110) cc_final: 0.6734 (mtt90) REVERT: B 354 GLN cc_start: 0.7471 (mp-120) cc_final: 0.7253 (pm20) REVERT: C 47 MET cc_start: 0.3536 (ptt) cc_final: 0.3247 (ptm) REVERT: C 68 LYS cc_start: 0.8056 (tppt) cc_final: 0.7338 (mppt) REVERT: C 173 HIS cc_start: 0.6767 (p-80) cc_final: 0.6436 (m-70) REVERT: C 313 MET cc_start: 0.8781 (mmm) cc_final: 0.8522 (mmm) outliers start: 29 outliers final: 10 residues processed: 169 average time/residue: 1.5814 time to fit residues: 280.8932 Evaluate side-chains 145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 145 SER Chi-restraints excluded: chain B residue 157 ASP 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 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 C 353 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8937 Z= 0.302 Angle : 0.737 7.646 12132 Z= 0.370 Chirality : 0.052 0.218 1349 Planarity : 0.006 0.069 1550 Dihedral : 7.698 88.319 1246 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.74 % Allowed : 17.65 % 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: 1.29 (0.25), residues: 1094 helix: 0.99 (0.25), residues: 455 sheet: 0.93 (0.35), residues: 208 loop : 0.91 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 340 HIS 0.007 0.002 HIS A 40 PHE 0.012 0.002 PHE A 262 TYR 0.010 0.002 TYR B 53 ARG 0.004 0.001 ARG A 256 *********************** 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 168 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 1.090 Fit side-chains REVERT: A 64 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8240 (pt) REVERT: A 68 LYS cc_start: 0.8189 (tppt) cc_final: 0.7869 (mppt) REVERT: A 95 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7408 (mtt-85) REVERT: A 215 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7683 (mtpt) REVERT: A 359 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6754 (mmtm) REVERT: B 95 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6901 (mtm-85) REVERT: B 210 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7907 (ttm110) REVERT: B 314 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: B 334 GLU cc_start: 0.7188 (pm20) cc_final: 0.6920 (pm20) REVERT: B 354 GLN cc_start: 0.7518 (mp-120) cc_final: 0.7289 (pm20) REVERT: C 95 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6958 (ptp-110) REVERT: C 173 HIS cc_start: 0.6911 (p90) cc_final: 0.6495 (m-70) REVERT: C 313 MET cc_start: 0.8864 (mmm) cc_final: 0.8511 (mmm) REVERT: C 353 GLN cc_start: 0.8244 (mm-40) cc_final: 0.8041 (mm110) outliers start: 35 outliers final: 12 residues processed: 157 average time/residue: 1.5601 time to fit residues: 258.1654 Evaluate side-chains 148 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 18 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 157 ASP 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 323 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8937 Z= 0.212 Angle : 0.655 6.887 12132 Z= 0.324 Chirality : 0.048 0.204 1349 Planarity : 0.005 0.049 1550 Dihedral : 7.291 84.991 1246 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.53 % Allowed : 17.97 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.25), residues: 1094 helix: 1.19 (0.25), residues: 455 sheet: 0.80 (0.35), residues: 206 loop : 0.96 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 79 HIS 0.006 0.002 HIS A 161 PHE 0.010 0.001 PHE A 255 TYR 0.008 0.001 TYR B 53 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8204 (pt) REVERT: A 68 LYS cc_start: 0.8271 (tppt) cc_final: 0.7993 (mppt) REVERT: A 95 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7365 (mtt-85) REVERT: A 359 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6736 (mmtm) REVERT: B 47 MET cc_start: 0.5565 (ptt) cc_final: 0.4010 (tmm) REVERT: B 64 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8478 (pt) REVERT: B 95 ARG cc_start: 0.7301 (ptp-110) cc_final: 0.6835 (mtm-85) REVERT: B 210 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7896 (ttm110) REVERT: B 314 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: B 334 GLU cc_start: 0.7240 (pm20) cc_final: 0.6958 (pm20) REVERT: B 354 GLN cc_start: 0.7504 (mp-120) cc_final: 0.7272 (pm20) REVERT: C 95 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7093 (mtp85) REVERT: C 173 HIS cc_start: 0.7006 (p90) cc_final: 0.6566 (m-70) REVERT: C 313 MET cc_start: 0.8880 (mmm) cc_final: 0.8574 (mmm) outliers start: 33 outliers final: 14 residues processed: 157 average time/residue: 1.6272 time to fit residues: 268.5293 Evaluate side-chains 152 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 210 ARG Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 64 ILE 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 234 SER Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 353 GLN B 297 ASN C 246 GLN C 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8937 Z= 0.414 Angle : 0.817 8.689 12132 Z= 0.414 Chirality : 0.055 0.227 1349 Planarity : 0.007 0.089 1550 Dihedral : 7.738 90.763 1245 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.17 % Allowed : 17.75 % 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: 1.08 (0.25), residues: 1094 helix: 0.94 (0.25), residues: 455 sheet: 0.60 (0.36), residues: 208 loop : 0.77 (0.30), 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 0.014 0.003 PHE A 262 TYR 0.012 0.002 TYR B 53 ARG 0.005 0.001 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8198 (pt) REVERT: A 68 LYS cc_start: 0.8332 (tppt) cc_final: 0.7966 (mppt) REVERT: A 95 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7522 (mtt-85) REVERT: A 125 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: A 215 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7704 (mtpt) REVERT: A 284 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7991 (mttt) REVERT: B 64 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8494 (pt) REVERT: B 95 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6960 (mtm-85) REVERT: B 210 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7928 (ttm110) REVERT: B 314 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: B 334 GLU cc_start: 0.7317 (pm20) cc_final: 0.6998 (pm20) REVERT: B 354 GLN cc_start: 0.7465 (mp-120) cc_final: 0.7178 (pm20) REVERT: C 95 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7092 (mtp85) REVERT: C 173 HIS cc_start: 0.7091 (p90) cc_final: 0.6583 (m-70) REVERT: C 313 MET cc_start: 0.8938 (mmm) cc_final: 0.8557 (mmm) REVERT: C 353 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7954 (mm110) outliers start: 39 outliers final: 18 residues processed: 159 average time/residue: 1.6367 time to fit residues: 273.3313 Evaluate side-chains 155 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU 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 284 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 18 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 157 ASP 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 234 SER Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8937 Z= 0.214 Angle : 0.664 7.097 12132 Z= 0.328 Chirality : 0.048 0.210 1349 Planarity : 0.005 0.048 1550 Dihedral : 7.315 85.586 1245 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.64 % Allowed : 18.18 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.26), residues: 1094 helix: 1.16 (0.25), residues: 455 sheet: 0.60 (0.36), residues: 206 loop : 0.81 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 79 HIS 0.006 0.002 HIS B 101 PHE 0.009 0.002 PHE A 255 TYR 0.008 0.001 TYR B 279 ARG 0.002 0.000 ARG A 177 *********************** 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 167 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8226 (pt) REVERT: A 68 LYS cc_start: 0.8322 (tppt) cc_final: 0.7914 (mppt) REVERT: A 95 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7445 (mtt-85) REVERT: A 125 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.5951 (mp0) REVERT: A 370 VAL cc_start: 0.8021 (m) cc_final: 0.7803 (p) REVERT: B 64 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8489 (pt) REVERT: B 95 ARG cc_start: 0.7401 (ptp-110) cc_final: 0.7086 (mtt90) REVERT: B 210 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7883 (ttm110) REVERT: B 314 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: B 334 GLU cc_start: 0.7232 (pm20) cc_final: 0.6933 (pm20) REVERT: B 354 GLN cc_start: 0.7495 (mp-120) cc_final: 0.7288 (pm20) REVERT: C 95 ARG cc_start: 0.7414 (ptp-110) cc_final: 0.7115 (mtp85) REVERT: C 173 HIS cc_start: 0.6991 (p90) cc_final: 0.6560 (m-70) REVERT: C 313 MET cc_start: 0.8925 (mmm) cc_final: 0.8584 (mmm) outliers start: 34 outliers final: 18 residues processed: 157 average time/residue: 1.5811 time to fit residues: 261.9038 Evaluate side-chains 154 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 324 THR 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 171 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0870 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 C 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8937 Z= 0.284 Angle : 0.722 7.961 12132 Z= 0.360 Chirality : 0.051 0.216 1349 Planarity : 0.006 0.069 1550 Dihedral : 7.471 87.675 1245 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.17 % Allowed : 17.75 % 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: 1.22 (0.26), residues: 1094 helix: 1.13 (0.25), residues: 455 sheet: 0.56 (0.36), residues: 208 loop : 0.81 (0.31), 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 0.010 0.001 TYR B 279 ARG 0.003 0.001 ARG A 256 *********************** 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: 39 poor density : 124 time to evaluate : 1.010 Fit side-chains REVERT: A 64 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8239 (pt) REVERT: A 68 LYS cc_start: 0.8323 (tppt) cc_final: 0.7898 (mppt) REVERT: A 95 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7486 (mtt-85) REVERT: A 125 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6090 (mp0) REVERT: A 210 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7655 (ttm110) REVERT: A 215 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7661 (mtpt) REVERT: A 370 VAL cc_start: 0.8084 (m) cc_final: 0.7839 (p) REVERT: B 47 MET cc_start: 0.5484 (ptt) cc_final: 0.4824 (mtt) REVERT: B 64 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8482 (pt) REVERT: B 95 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7035 (mtm-85) REVERT: B 210 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7882 (ttm110) REVERT: B 314 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: B 334 GLU cc_start: 0.7270 (pm20) cc_final: 0.6979 (pm20) REVERT: C 47 MET cc_start: 0.3619 (ptp) cc_final: 0.1022 (ppp) REVERT: C 95 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.7080 (mtp85) REVERT: C 173 HIS cc_start: 0.7001 (p90) cc_final: 0.6557 (m-70) REVERT: C 210 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7512 (ttm110) REVERT: C 313 MET cc_start: 0.8943 (mmm) cc_final: 0.8606 (mmm) outliers start: 39 outliers final: 19 residues processed: 151 average time/residue: 1.6424 time to fit residues: 260.7520 Evaluate side-chains 155 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 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 323 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 C 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 : 0.003 0.033 8937 Z= 0.209 Angle : 0.657 7.402 12132 Z= 0.323 Chirality : 0.048 0.206 1349 Planarity : 0.005 0.046 1550 Dihedral : 7.234 85.214 1245 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.53 % Allowed : 18.40 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.26), residues: 1094 helix: 1.28 (0.25), residues: 455 sheet: 0.56 (0.36), residues: 206 loop : 0.84 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 79 HIS 0.006 0.002 HIS B 101 PHE 0.008 0.001 PHE A 255 TYR 0.008 0.001 TYR B 279 ARG 0.002 0.000 ARG A 177 *********************** 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 163 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8216 (pt) REVERT: A 68 LYS cc_start: 0.8317 (tppt) cc_final: 0.8017 (mppt) REVERT: A 95 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7437 (mtt-85) REVERT: A 125 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.5928 (mp0) REVERT: B 47 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.5044 (mtt) REVERT: B 64 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8496 (pt) REVERT: B 95 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7127 (mtt90) REVERT: B 118 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8311 (tmtt) REVERT: B 210 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7883 (ttm110) REVERT: B 314 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: B 334 GLU cc_start: 0.7286 (pm20) cc_final: 0.6972 (pm20) REVERT: C 47 MET cc_start: 0.3455 (ptp) cc_final: 0.0960 (ppp) REVERT: C 68 LYS cc_start: 0.8380 (tppt) cc_final: 0.7941 (mppt) REVERT: C 95 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7133 (mtp85) REVERT: C 173 HIS cc_start: 0.6926 (p90) cc_final: 0.6510 (m-70) REVERT: C 313 MET cc_start: 0.8943 (mmm) cc_final: 0.8588 (mmm) outliers start: 33 outliers final: 21 residues processed: 152 average time/residue: 1.5669 time to fit residues: 250.8375 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 : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 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 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 98 optimal weight: 0.0980 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.0970 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 C 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8937 Z= 0.173 Angle : 0.629 8.202 12132 Z= 0.307 Chirality : 0.046 0.193 1349 Planarity : 0.004 0.043 1550 Dihedral : 7.051 84.270 1245 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.32 % Allowed : 18.18 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.47 (0.26), residues: 1094 helix: 1.38 (0.25), residues: 455 sheet: 0.72 (0.37), residues: 204 loop : 0.88 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.005 0.001 HIS B 101 PHE 0.008 0.001 PHE A 255 TYR 0.007 0.001 TYR B 294 ARG 0.002 0.000 ARG A 177 *********************** 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 165 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8200 (pt) REVERT: A 68 LYS cc_start: 0.8277 (tppt) cc_final: 0.7988 (mppt) REVERT: A 95 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7407 (mtt-85) REVERT: B 47 MET cc_start: 0.5533 (OUTLIER) cc_final: 0.5191 (mtt) REVERT: B 64 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8506 (pt) REVERT: B 95 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7104 (mtt90) REVERT: B 118 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8318 (tmtt) REVERT: B 210 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7869 (ttm110) REVERT: B 314 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: B 334 GLU cc_start: 0.7266 (pm20) cc_final: 0.6907 (pm20) REVERT: C 47 MET cc_start: 0.3325 (ptp) cc_final: 0.0883 (ppp) REVERT: C 68 LYS cc_start: 0.8353 (tppt) cc_final: 0.7950 (mppt) REVERT: C 95 ARG cc_start: 0.7412 (ptp-110) cc_final: 0.7130 (mtp85) REVERT: C 173 HIS cc_start: 0.6946 (p90) cc_final: 0.6521 (m-70) REVERT: C 313 MET cc_start: 0.8935 (mmm) cc_final: 0.8596 (mmm) outliers start: 31 outliers final: 17 residues processed: 153 average time/residue: 1.6198 time to fit residues: 260.7850 Evaluate side-chains 156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 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 A residue 324 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain C residue 14 SER 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 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 0.0060 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.0040 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 overall best weight: 0.3608 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8937 Z= 0.172 Angle : 0.631 8.092 12132 Z= 0.308 Chirality : 0.046 0.188 1349 Planarity : 0.004 0.042 1550 Dihedral : 6.971 83.239 1245 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.67 % Allowed : 19.04 % 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: 1.52 (0.26), residues: 1094 helix: 1.44 (0.25), residues: 455 sheet: 0.74 (0.37), residues: 204 loop : 0.89 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.005 0.001 HIS B 101 PHE 0.008 0.001 PHE A 255 TYR 0.007 0.001 TYR B 279 ARG 0.002 0.000 ARG A 335 ********************** 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 155 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8193 (pt) REVERT: A 68 LYS cc_start: 0.8269 (tppt) cc_final: 0.8000 (mppt) REVERT: A 95 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7387 (mtt-85) REVERT: B 47 MET cc_start: 0.5615 (OUTLIER) cc_final: 0.5344 (mtt) REVERT: B 64 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8482 (pt) REVERT: B 95 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7109 (mtt90) REVERT: B 118 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8313 (tmtt) REVERT: B 210 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7846 (ttm110) REVERT: B 314 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: B 334 GLU cc_start: 0.7193 (pm20) cc_final: 0.6848 (pm20) REVERT: C 47 MET cc_start: 0.3135 (ptp) cc_final: 0.0827 (ppp) REVERT: C 95 ARG cc_start: 0.7426 (ptp-110) cc_final: 0.7134 (mtp85) REVERT: C 173 HIS cc_start: 0.6982 (p90) cc_final: 0.6528 (m-70) REVERT: C 313 MET cc_start: 0.8936 (mmm) cc_final: 0.8598 (mmm) outliers start: 25 outliers final: 16 residues processed: 145 average time/residue: 1.6427 time to fit residues: 253.3897 Evaluate side-chains 152 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 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 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 336 LYS Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 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 80 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.0060 chunk 76 optimal weight: 0.0370 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.149575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131984 restraints weight = 8339.048| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.20 r_work: 0.3409 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2965 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= 0.162 Angle : 0.620 9.585 12132 Z= 0.302 Chirality : 0.046 0.180 1349 Planarity : 0.004 0.042 1550 Dihedral : 6.846 81.535 1245 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.89 % Allowed : 19.25 % 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: 1.58 (0.26), residues: 1094 helix: 1.50 (0.25), residues: 455 sheet: 0.75 (0.37), residues: 204 loop : 0.93 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.004 0.001 HIS B 101 PHE 0.008 0.001 PHE A 255 TYR 0.007 0.001 TYR B 294 ARG 0.002 0.000 ARG A 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4724.89 seconds wall clock time: 85 minutes 11.07 seconds (5111.07 seconds total)