Starting phenix.real_space_refine on Sun Aug 24 02:22:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8irn_35680/08_2025/8irn_35680_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8irn_35680/08_2025/8irn_35680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8irn_35680/08_2025/8irn_35680_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8irn_35680/08_2025/8irn_35680_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8irn_35680/08_2025/8irn_35680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8irn_35680/08_2025/8irn_35680.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 5304 2.51 5 N 1316 2.21 5 O 1472 1.98 5 H 8208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16352 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'EMU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'EMU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.62, per 1000 atoms: 0.22 Number of scatterers: 16352 At special positions: 0 Unit cell: (94.461, 106.375, 101.269, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1472 8.00 N 1316 7.00 C 5304 6.00 H 8208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 464.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 68.4% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 62 through 74 removed outlier: 4.245A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 117 through 149 Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.857A pdb=" N ALA A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.857A pdb=" N LEU A 207 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.344A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.917A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 405 removed outlier: 3.660A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 444 through 451 removed outlier: 4.005A pdb=" N GLY A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 480 through 496 Proline residue: A 486 - end of helix Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.771A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 523 Proline residue: A 512 - end of helix removed outlier: 3.758A pdb=" N MET A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 554 removed outlier: 4.541A pdb=" N TRP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ASP A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 62 through 74 removed outlier: 4.246A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 117 through 149 Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.871A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.740A pdb=" N VAL B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.416A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 294 through 313 Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.898A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.891A pdb=" N ILE B 374 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN B 375 " --> pdb=" O SER B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 371 through 375' Processing helix chain 'B' and resid 376 through 406 removed outlier: 3.581A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 444 through 451 removed outlier: 3.982A pdb=" N GLY B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 480 through 496 Proline residue: B 486 - end of helix Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.813A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 523 Proline residue: B 512 - end of helix removed outlier: 3.763A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 541 through 554 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 242 Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 275 removed outlier: 3.740A pdb=" N SER A 274 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 274 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 287 removed outlier: 3.877A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA7, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA8, first strand: chain 'B' and resid 241 through 242 515 hydrogen bonds defined for protein. 1461 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: 4.14 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8204 1.03 - 1.23: 13 1.23 - 1.42: 3416 1.42 - 1.62: 4823 1.62 - 1.81: 84 Bond restraints: 16540 Sorted by residual: bond pdb=" C6 EMU B 701 " pdb=" N10 EMU B 701 " ideal model delta sigma weight residual 1.338 1.450 -0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" C6 EMU A 701 " pdb=" N10 EMU A 701 " ideal model delta sigma weight residual 1.338 1.449 -0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" NZ LYS A 19 " pdb=" HZ2 LYS A 19 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" NZ LYS B 19 " pdb=" HZ3 LYS B 19 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" NZ LYS B 19 " pdb=" HZ1 LYS B 19 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 16535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 29736 2.06 - 4.12: 167 4.12 - 6.19: 19 6.19 - 8.25: 4 8.25 - 10.31: 2 Bond angle restraints: 29928 Sorted by residual: angle pdb=" N LEU A 248 " pdb=" CA LEU A 248 " pdb=" CB LEU A 248 " ideal model delta sigma weight residual 114.17 110.07 4.10 1.14e+00 7.69e-01 1.29e+01 angle pdb=" N LEU B 248 " pdb=" CA LEU B 248 " pdb=" CB LEU B 248 " ideal model delta sigma weight residual 114.17 110.17 4.00 1.14e+00 7.69e-01 1.23e+01 angle pdb=" C2 EMU A 701 " pdb=" N3 EMU A 701 " pdb=" C4 EMU A 701 " ideal model delta sigma weight residual 111.69 122.00 -10.31 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C2 EMU B 701 " pdb=" N3 EMU B 701 " pdb=" C4 EMU B 701 " ideal model delta sigma weight residual 111.69 121.91 -10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C5 EMU A 701 " pdb=" C4 EMU A 701 " pdb=" N3 EMU A 701 " ideal model delta sigma weight residual 126.32 118.13 8.19 3.00e+00 1.11e-01 7.45e+00 ... (remaining 29923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 7452 24.81 - 49.63: 290 49.63 - 74.44: 133 74.44 - 99.25: 2 99.25 - 124.07: 3 Dihedral angle restraints: 7880 sinusoidal: 4246 harmonic: 3634 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sinusoidal sigma weight residual 93.00 164.43 -71.43 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CB CYS B 78 " pdb=" SG CYS B 78 " pdb=" SG CYS B 123 " pdb=" CB CYS B 123 " ideal model delta sinusoidal sigma weight residual 93.00 163.76 -70.76 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 144.66 35.34 0 5.00e+00 4.00e-02 5.00e+01 ... (remaining 7877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1011 0.041 - 0.082: 266 0.082 - 0.123: 77 0.123 - 0.163: 1 0.163 - 0.204: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 270 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE B 502 " pdb=" N ILE B 502 " pdb=" C ILE B 502 " pdb=" CB ILE B 502 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE A 105 " pdb=" N ILE A 105 " pdb=" C ILE A 105 " pdb=" CB ILE A 105 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1353 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO B 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO A 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 203 " -0.012 2.00e-02 2.50e+03 7.54e-03 1.70e+00 pdb=" CG PHE A 203 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 203 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 203 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 203 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 203 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 203 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 203 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 203 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 203 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 203 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 203 " -0.000 2.00e-02 2.50e+03 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 788 2.17 - 2.78: 32959 2.78 - 3.39: 49453 3.39 - 3.99: 63350 3.99 - 4.60: 100037 Nonbonded interactions: 246587 Sorted by model distance: nonbonded pdb="HD22 ASN A 67 " pdb=" OG1 THR A 135 " model vdw 1.565 2.450 nonbonded pdb="HD22 ASN B 67 " pdb=" OG1 THR B 135 " model vdw 1.571 2.450 nonbonded pdb="HG23 THR A 162 " pdb=" HE1 PHE A 386 " model vdw 1.618 2.270 nonbonded pdb="HH22 ARG B 333 " pdb=" OD1 ASP B 347 " model vdw 1.626 2.450 nonbonded pdb=" OD1 ASN A 163 " pdb=" HG SER A 437 " model vdw 1.627 2.450 ... (remaining 246582 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.870 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: 0.100 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.330 Find NCS groups from input model: 0.210 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:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 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 : 0.004 0.112 8344 Z= 0.181 Angle : 0.604 10.309 11368 Z= 0.318 Chirality : 0.039 0.204 1356 Planarity : 0.004 0.062 1400 Dihedral : 13.273 124.066 2936 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.26), residues: 1076 helix: 2.11 (0.21), residues: 654 sheet: -5.08 (0.50), residues: 20 loop : -0.42 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 403 TYR 0.017 0.001 TYR B 309 PHE 0.022 0.001 PHE A 203 TRP 0.007 0.001 TRP A 380 HIS 0.002 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8332) covalent geometry : angle 0.59347 (11340) SS BOND : bond 0.00178 ( 8) SS BOND : angle 2.61047 ( 16) hydrogen bonds : bond 0.10899 ( 511) hydrogen bonds : angle 4.98289 ( 1461) link_BETA1-4 : bond 0.00303 ( 2) link_BETA1-4 : angle 2.23680 ( 6) link_NAG-ASN : bond 0.00297 ( 2) link_NAG-ASN : angle 1.79481 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.7453 (m-30) cc_final: 0.7017 (m-30) REVERT: A 548 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6018 (pt0) REVERT: B 19 LYS cc_start: 0.6145 (OUTLIER) cc_final: 0.5596 (tttt) REVERT: B 548 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6141 (pt0) outliers start: 2 outliers final: 2 residues processed: 100 average time/residue: 1.3993 time to fit residues: 148.5232 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.109984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.087093 restraints weight = 30927.274| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.81 r_work: 0.2863 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8344 Z= 0.155 Angle : 0.545 6.314 11368 Z= 0.288 Chirality : 0.039 0.159 1356 Planarity : 0.005 0.063 1400 Dihedral : 8.584 111.323 1242 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.82 % Allowed : 6.53 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.26), residues: 1076 helix: 2.07 (0.21), residues: 658 sheet: -4.60 (0.57), residues: 20 loop : -0.54 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.009 0.001 TYR B 388 PHE 0.016 0.001 PHE A 203 TRP 0.006 0.001 TRP A 380 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8332) covalent geometry : angle 0.53717 (11340) SS BOND : bond 0.00090 ( 8) SS BOND : angle 1.35075 ( 16) hydrogen bonds : bond 0.04412 ( 511) hydrogen bonds : angle 4.39376 ( 1461) link_BETA1-4 : bond 0.00297 ( 2) link_BETA1-4 : angle 2.83733 ( 6) link_NAG-ASN : bond 0.00348 ( 2) link_NAG-ASN : angle 1.95668 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.7514 (m-30) cc_final: 0.7023 (m-30) REVERT: A 548 GLU cc_start: 0.6508 (mt-10) cc_final: 0.5733 (pt0) REVERT: B 19 LYS cc_start: 0.5809 (OUTLIER) cc_final: 0.5168 (tttt) REVERT: B 35 LYS cc_start: 0.8495 (mtmt) cc_final: 0.8123 (mmpt) REVERT: B 403 ARG cc_start: 0.7314 (mtm-85) cc_final: 0.7045 (mtt180) REVERT: B 494 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8095 (mtt) REVERT: B 548 GLU cc_start: 0.6501 (mt-10) cc_final: 0.5831 (pt0) outliers start: 7 outliers final: 3 residues processed: 92 average time/residue: 1.2184 time to fit residues: 120.5565 Evaluate side-chains 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 494 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.087882 restraints weight = 31527.750| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.81 r_work: 0.2880 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8344 Z= 0.131 Angle : 0.526 7.527 11368 Z= 0.274 Chirality : 0.039 0.163 1356 Planarity : 0.005 0.062 1400 Dihedral : 8.622 104.745 1242 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.47 % Allowed : 7.46 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.26), residues: 1076 helix: 2.14 (0.21), residues: 658 sheet: -4.50 (0.61), residues: 20 loop : -0.51 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 508 TYR 0.008 0.001 TYR B 388 PHE 0.009 0.001 PHE A 189 TRP 0.007 0.001 TRP B 298 HIS 0.002 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8332) covalent geometry : angle 0.51999 (11340) SS BOND : bond 0.00589 ( 8) SS BOND : angle 0.82291 ( 16) hydrogen bonds : bond 0.04116 ( 511) hydrogen bonds : angle 4.22759 ( 1461) link_BETA1-4 : bond 0.00440 ( 2) link_BETA1-4 : angle 2.76596 ( 6) link_NAG-ASN : bond 0.00404 ( 2) link_NAG-ASN : angle 1.92031 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.6530 (mt-10) cc_final: 0.5733 (pt0) REVERT: B 19 LYS cc_start: 0.5898 (OUTLIER) cc_final: 0.5241 (tttt) REVERT: B 35 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8170 (mmpt) REVERT: B 403 ARG cc_start: 0.7305 (mtm-85) cc_final: 0.6997 (mtt180) REVERT: B 548 GLU cc_start: 0.6514 (mt-10) cc_final: 0.5800 (pt0) outliers start: 4 outliers final: 0 residues processed: 88 average time/residue: 1.1796 time to fit residues: 111.4394 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.082901 restraints weight = 31372.064| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.81 r_work: 0.2826 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8344 Z= 0.219 Angle : 0.583 8.776 11368 Z= 0.304 Chirality : 0.041 0.170 1356 Planarity : 0.005 0.061 1400 Dihedral : 7.843 96.838 1238 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.16 % Favored : 96.56 % Rotamer: Outliers : 1.28 % Allowed : 7.58 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.26), residues: 1076 helix: 2.08 (0.21), residues: 644 sheet: -4.23 (0.72), residues: 20 loop : -0.51 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 508 TYR 0.012 0.001 TYR B 388 PHE 0.017 0.002 PHE B 442 TRP 0.007 0.001 TRP A 380 HIS 0.003 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 8332) covalent geometry : angle 0.57520 (11340) SS BOND : bond 0.00509 ( 8) SS BOND : angle 1.64964 ( 16) hydrogen bonds : bond 0.04617 ( 511) hydrogen bonds : angle 4.26555 ( 1461) link_BETA1-4 : bond 0.00538 ( 2) link_BETA1-4 : angle 2.90616 ( 6) link_NAG-ASN : bond 0.00449 ( 2) link_NAG-ASN : angle 1.97162 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.449 Fit side-chains REVERT: A 203 PHE cc_start: 0.7972 (t80) cc_final: 0.7678 (t80) REVERT: A 548 GLU cc_start: 0.6633 (mt-10) cc_final: 0.5800 (pt0) REVERT: B 19 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5456 (tttt) REVERT: B 35 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8168 (mmpt) REVERT: B 548 GLU cc_start: 0.6612 (mt-10) cc_final: 0.5917 (pt0) outliers start: 11 outliers final: 5 residues processed: 90 average time/residue: 1.1955 time to fit residues: 115.8500 Evaluate side-chains 89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.081779 restraints weight = 31378.031| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.80 r_work: 0.2781 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8344 Z= 0.238 Angle : 0.607 9.482 11368 Z= 0.315 Chirality : 0.042 0.173 1356 Planarity : 0.005 0.060 1400 Dihedral : 7.616 91.108 1238 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.79 % Favored : 96.84 % Rotamer: Outliers : 1.75 % Allowed : 8.16 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.26), residues: 1076 helix: 1.94 (0.20), residues: 644 sheet: -4.39 (0.68), residues: 20 loop : -0.53 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 508 TYR 0.013 0.002 TYR A 388 PHE 0.014 0.002 PHE B 442 TRP 0.007 0.001 TRP A 380 HIS 0.003 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 8332) covalent geometry : angle 0.59447 (11340) SS BOND : bond 0.00568 ( 8) SS BOND : angle 2.41396 ( 16) hydrogen bonds : bond 0.04709 ( 511) hydrogen bonds : angle 4.30249 ( 1461) link_BETA1-4 : bond 0.00566 ( 2) link_BETA1-4 : angle 3.05392 ( 6) link_NAG-ASN : bond 0.00470 ( 2) link_NAG-ASN : angle 2.06298 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.410 Fit side-chains REVERT: A 548 GLU cc_start: 0.6532 (mt-10) cc_final: 0.5691 (pt0) REVERT: B 19 LYS cc_start: 0.6141 (OUTLIER) cc_final: 0.5498 (tttt) REVERT: B 32 ARG cc_start: 0.6329 (OUTLIER) cc_final: 0.4836 (mtm110) REVERT: B 35 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8137 (mmpt) REVERT: B 401 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7649 (mpm) REVERT: B 494 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8329 (mtp) REVERT: B 548 GLU cc_start: 0.6652 (mt-10) cc_final: 0.5887 (pt0) outliers start: 15 outliers final: 6 residues processed: 88 average time/residue: 1.0290 time to fit residues: 98.2580 Evaluate side-chains 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 494 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.106516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.083830 restraints weight = 31041.918| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.79 r_work: 0.2818 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8344 Z= 0.143 Angle : 0.559 9.911 11368 Z= 0.286 Chirality : 0.039 0.165 1356 Planarity : 0.004 0.059 1400 Dihedral : 7.279 88.201 1238 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.62 % Favored : 96.19 % Rotamer: Outliers : 0.82 % Allowed : 9.67 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.26), residues: 1076 helix: 2.11 (0.21), residues: 646 sheet: -4.21 (0.74), residues: 20 loop : -0.53 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 508 TYR 0.010 0.001 TYR B 388 PHE 0.010 0.001 PHE A 189 TRP 0.007 0.001 TRP B 298 HIS 0.002 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8332) covalent geometry : angle 0.54741 (11340) SS BOND : bond 0.00435 ( 8) SS BOND : angle 2.08612 ( 16) hydrogen bonds : bond 0.04172 ( 511) hydrogen bonds : angle 4.19304 ( 1461) link_BETA1-4 : bond 0.00507 ( 2) link_BETA1-4 : angle 3.04485 ( 6) link_NAG-ASN : bond 0.00365 ( 2) link_NAG-ASN : angle 1.99840 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.449 Fit side-chains REVERT: A 548 GLU cc_start: 0.6531 (mt-10) cc_final: 0.5691 (pt0) REVERT: B 19 LYS cc_start: 0.6121 (OUTLIER) cc_final: 0.5423 (tttt) REVERT: B 32 ARG cc_start: 0.6319 (OUTLIER) cc_final: 0.4837 (mtm110) REVERT: B 35 LYS cc_start: 0.8491 (mtmt) cc_final: 0.8124 (mmpt) REVERT: B 41 GLU cc_start: 0.8253 (mp0) cc_final: 0.7896 (mp0) REVERT: B 401 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8056 (mpm) REVERT: B 548 GLU cc_start: 0.6653 (mt-10) cc_final: 0.5817 (pt0) outliers start: 7 outliers final: 1 residues processed: 83 average time/residue: 1.0134 time to fit residues: 91.1083 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 401 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.106527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.083681 restraints weight = 31056.987| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.80 r_work: 0.2824 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8344 Z= 0.159 Angle : 0.564 10.369 11368 Z= 0.288 Chirality : 0.039 0.166 1356 Planarity : 0.004 0.060 1400 Dihedral : 7.019 84.515 1238 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.16 % Favored : 96.65 % Rotamer: Outliers : 0.70 % Allowed : 10.26 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.26), residues: 1076 helix: 2.14 (0.21), residues: 646 sheet: -4.22 (0.74), residues: 20 loop : -0.52 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 508 TYR 0.010 0.001 TYR A 388 PHE 0.010 0.001 PHE A 189 TRP 0.007 0.001 TRP B 298 HIS 0.002 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8332) covalent geometry : angle 0.55288 (11340) SS BOND : bond 0.00413 ( 8) SS BOND : angle 2.01623 ( 16) hydrogen bonds : bond 0.04229 ( 511) hydrogen bonds : angle 4.17801 ( 1461) link_BETA1-4 : bond 0.00476 ( 2) link_BETA1-4 : angle 3.17278 ( 6) link_NAG-ASN : bond 0.00355 ( 2) link_NAG-ASN : angle 1.99022 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.417 Fit side-chains REVERT: A 32 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.4611 (mtm110) REVERT: A 548 GLU cc_start: 0.6497 (mt-10) cc_final: 0.5656 (pt0) REVERT: B 19 LYS cc_start: 0.6125 (OUTLIER) cc_final: 0.5428 (tttt) REVERT: B 32 ARG cc_start: 0.6293 (OUTLIER) cc_final: 0.4802 (mtm110) REVERT: B 35 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8140 (mmpt) REVERT: B 41 GLU cc_start: 0.8265 (mp0) cc_final: 0.7900 (mp0) REVERT: B 401 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8081 (mpm) REVERT: B 548 GLU cc_start: 0.6636 (mt-10) cc_final: 0.5763 (pt0) outliers start: 6 outliers final: 0 residues processed: 85 average time/residue: 1.0412 time to fit residues: 95.3740 Evaluate side-chains 85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 401 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.108092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.086019 restraints weight = 31304.510| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.76 r_work: 0.2843 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8344 Z= 0.131 Angle : 0.549 10.887 11368 Z= 0.278 Chirality : 0.039 0.164 1356 Planarity : 0.004 0.060 1400 Dihedral : 6.614 78.266 1238 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.72 % Favored : 96.10 % Rotamer: Outliers : 1.05 % Allowed : 9.91 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.26), residues: 1076 helix: 2.19 (0.21), residues: 648 sheet: -4.19 (0.75), residues: 20 loop : -0.43 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 508 TYR 0.009 0.001 TYR B 388 PHE 0.009 0.001 PHE A 189 TRP 0.007 0.001 TRP B 298 HIS 0.002 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8332) covalent geometry : angle 0.53805 (11340) SS BOND : bond 0.00334 ( 8) SS BOND : angle 1.79970 ( 16) hydrogen bonds : bond 0.04017 ( 511) hydrogen bonds : angle 4.12164 ( 1461) link_BETA1-4 : bond 0.00409 ( 2) link_BETA1-4 : angle 3.38582 ( 6) link_NAG-ASN : bond 0.00321 ( 2) link_NAG-ASN : angle 1.91657 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.453 Fit side-chains REVERT: A 32 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.4677 (mtm110) REVERT: A 494 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7658 (mmt) REVERT: A 548 GLU cc_start: 0.6481 (mt-10) cc_final: 0.5660 (pt0) REVERT: B 19 LYS cc_start: 0.6181 (OUTLIER) cc_final: 0.5411 (tttt) REVERT: B 32 ARG cc_start: 0.6335 (OUTLIER) cc_final: 0.4836 (mtm110) REVERT: B 35 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8134 (mmpt) REVERT: B 41 GLU cc_start: 0.8288 (mp0) cc_final: 0.7922 (mp0) REVERT: B 401 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8102 (mpm) REVERT: B 548 GLU cc_start: 0.6648 (mt-10) cc_final: 0.5777 (pt0) outliers start: 9 outliers final: 0 residues processed: 83 average time/residue: 0.9531 time to fit residues: 85.7954 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 401 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.086373 restraints weight = 31192.462| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.76 r_work: 0.2852 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8344 Z= 0.128 Angle : 0.549 11.165 11368 Z= 0.277 Chirality : 0.038 0.163 1356 Planarity : 0.004 0.060 1400 Dihedral : 6.090 66.334 1238 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.16 % Favored : 96.65 % Rotamer: Outliers : 0.82 % Allowed : 10.02 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.26), residues: 1076 helix: 2.23 (0.21), residues: 650 sheet: -4.12 (0.77), residues: 20 loop : -0.42 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 508 TYR 0.009 0.001 TYR B 388 PHE 0.010 0.001 PHE A 189 TRP 0.008 0.001 TRP B 298 HIS 0.001 0.000 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8332) covalent geometry : angle 0.53727 (11340) SS BOND : bond 0.00320 ( 8) SS BOND : angle 1.71391 ( 16) hydrogen bonds : bond 0.03967 ( 511) hydrogen bonds : angle 4.08922 ( 1461) link_BETA1-4 : bond 0.00243 ( 2) link_BETA1-4 : angle 3.84137 ( 6) link_NAG-ASN : bond 0.00303 ( 2) link_NAG-ASN : angle 1.95590 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.334 Fit side-chains REVERT: A 32 ARG cc_start: 0.6338 (OUTLIER) cc_final: 0.4746 (mtm110) REVERT: A 494 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7655 (mmt) REVERT: A 548 GLU cc_start: 0.6499 (mt-10) cc_final: 0.5683 (pt0) REVERT: B 19 LYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5407 (tttt) REVERT: B 32 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.4853 (mtm110) REVERT: B 35 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8137 (mmpt) REVERT: B 41 GLU cc_start: 0.8309 (mp0) cc_final: 0.7958 (mp0) REVERT: B 548 GLU cc_start: 0.6612 (mt-10) cc_final: 0.5741 (pt0) outliers start: 7 outliers final: 1 residues processed: 85 average time/residue: 0.8933 time to fit residues: 82.1287 Evaluate side-chains 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.108982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.086423 restraints weight = 31030.823| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.80 r_work: 0.2871 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8344 Z= 0.109 Angle : 0.536 9.226 11368 Z= 0.269 Chirality : 0.038 0.161 1356 Planarity : 0.004 0.060 1400 Dihedral : 5.316 54.685 1238 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.00 % Rotamer: Outliers : 0.47 % Allowed : 10.49 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.27), residues: 1076 helix: 2.21 (0.21), residues: 662 sheet: -4.11 (0.77), residues: 20 loop : -0.32 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 508 TYR 0.008 0.001 TYR B 388 PHE 0.009 0.001 PHE B 189 TRP 0.008 0.001 TRP B 298 HIS 0.001 0.000 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8332) covalent geometry : angle 0.52117 (11340) SS BOND : bond 0.00301 ( 8) SS BOND : angle 1.47196 ( 16) hydrogen bonds : bond 0.03758 ( 511) hydrogen bonds : angle 4.01353 ( 1461) link_BETA1-4 : bond 0.00272 ( 2) link_BETA1-4 : angle 4.51053 ( 6) link_NAG-ASN : bond 0.00258 ( 2) link_NAG-ASN : angle 2.11129 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.427 Fit side-chains REVERT: A 32 ARG cc_start: 0.6308 (OUTLIER) cc_final: 0.4729 (mtm110) REVERT: A 41 GLU cc_start: 0.8325 (mp0) cc_final: 0.7972 (mp0) REVERT: A 548 GLU cc_start: 0.6482 (mt-10) cc_final: 0.5662 (pt0) REVERT: B 19 LYS cc_start: 0.6157 (OUTLIER) cc_final: 0.5371 (tttt) REVERT: B 35 LYS cc_start: 0.8454 (mtmt) cc_final: 0.8121 (mmpt) REVERT: B 41 GLU cc_start: 0.8285 (mp0) cc_final: 0.7933 (mp0) REVERT: B 548 GLU cc_start: 0.6630 (mt-10) cc_final: 0.5758 (pt0) outliers start: 4 outliers final: 0 residues processed: 84 average time/residue: 0.8545 time to fit residues: 77.6382 Evaluate side-chains 81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain B residue 19 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.085521 restraints weight = 31376.770| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.75 r_work: 0.2839 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8344 Z= 0.174 Angle : 0.563 7.572 11368 Z= 0.285 Chirality : 0.040 0.175 1356 Planarity : 0.004 0.060 1400 Dihedral : 5.057 54.014 1238 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 0.58 % Allowed : 10.61 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.27), residues: 1076 helix: 2.25 (0.21), residues: 648 sheet: -3.96 (0.81), residues: 20 loop : -0.34 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 508 TYR 0.010 0.001 TYR B 388 PHE 0.011 0.001 PHE A 189 TRP 0.007 0.001 TRP A 482 HIS 0.002 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8332) covalent geometry : angle 0.54596 (11340) SS BOND : bond 0.00322 ( 8) SS BOND : angle 1.92030 ( 16) hydrogen bonds : bond 0.04136 ( 511) hydrogen bonds : angle 4.06925 ( 1461) link_BETA1-4 : bond 0.00420 ( 2) link_BETA1-4 : angle 4.49670 ( 6) link_NAG-ASN : bond 0.00342 ( 2) link_NAG-ASN : angle 2.47768 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4563.91 seconds wall clock time: 78 minutes 10.26 seconds (4690.26 seconds total)