Starting phenix.real_space_refine on Sat Jun 14 16:15:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8irn_35680/06_2025/8irn_35680_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8irn_35680/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8irn_35680/06_2025/8irn_35680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8irn_35680/06_2025/8irn_35680.map" model { file = "/net/cci-nas-00/data/ceres_data/8irn_35680/06_2025/8irn_35680_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8irn_35680/06_2025/8irn_35680_trim.cif" } resolution = 2.7 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= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.48, per 1000 atoms: 0.58 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: 5.08 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.60 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: 6.00 Time building geometry restraints manager: 6.07 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: 0.05 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: 1.190 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: 0.330 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 41.240 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.910 ------------------------------------------------------------------------------- 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 (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: 1.56 (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 TRP 0.007 0.001 TRP A 380 HIS 0.002 0.001 HIS A 541 PHE 0.022 0.001 PHE A 203 TYR 0.017 0.001 TYR B 309 ARG 0.006 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 2) link_NAG-ASN : angle 1.79481 ( 6) link_BETA1-4 : bond 0.00303 ( 2) link_BETA1-4 : angle 2.23680 ( 6) hydrogen bonds : bond 0.10899 ( 511) hydrogen bonds : angle 4.98289 ( 1461) SS BOND : bond 0.00178 ( 8) SS BOND : angle 2.61047 ( 16) covalent geometry : bond 0.00375 ( 8332) covalent geometry : angle 0.59347 (11340) *********************** 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 : 1.137 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: 2.5508 time to fit residues: 272.1854 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 : 1.206 ------------------------------------------------------------------------------- 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 91 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.109572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.086684 restraints weight = 30788.531| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.81 r_work: 0.2869 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0950 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= 0.163 Angle : 0.548 6.581 11368 Z= 0.290 Chirality : 0.040 0.166 1356 Planarity : 0.005 0.063 1400 Dihedral : 8.569 110.754 1242 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.82 % Allowed : 6.64 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1076 helix: 2.05 (0.21), residues: 658 sheet: -4.59 (0.57), residues: 20 loop : -0.55 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 380 HIS 0.004 0.001 HIS B 360 PHE 0.017 0.001 PHE A 203 TYR 0.011 0.001 TYR B 309 ARG 0.004 0.000 ARG B 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 2) link_NAG-ASN : angle 1.96264 ( 6) link_BETA1-4 : bond 0.00396 ( 2) link_BETA1-4 : angle 2.79719 ( 6) hydrogen bonds : bond 0.04453 ( 511) hydrogen bonds : angle 4.40192 ( 1461) SS BOND : bond 0.00078 ( 8) SS BOND : angle 1.36292 ( 16) covalent geometry : bond 0.00371 ( 8332) covalent geometry : angle 0.54086 (11340) *********************** 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 : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.7548 (m-30) cc_final: 0.7070 (m-30) REVERT: A 548 GLU cc_start: 0.6552 (mt-10) cc_final: 0.5778 (pt0) REVERT: B 19 LYS cc_start: 0.5877 (OUTLIER) cc_final: 0.5245 (tttt) REVERT: B 35 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8112 (mmpt) REVERT: B 403 ARG cc_start: 0.7326 (mtm-85) cc_final: 0.7057 (mtt180) REVERT: B 494 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8106 (mtt) REVERT: B 548 GLU cc_start: 0.6551 (mt-10) cc_final: 0.5863 (pt0) outliers start: 7 outliers final: 3 residues processed: 92 average time/residue: 2.2063 time to fit residues: 219.1341 Evaluate side-chains 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.110779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.087969 restraints weight = 30867.921| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.85 r_work: 0.2886 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8344 Z= 0.115 Angle : 0.519 7.573 11368 Z= 0.269 Chirality : 0.038 0.161 1356 Planarity : 0.005 0.062 1400 Dihedral : 8.175 104.673 1242 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.47 % Allowed : 7.23 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.61 (0.26), residues: 1076 helix: 2.16 (0.21), residues: 658 sheet: -4.59 (0.58), residues: 20 loop : -0.49 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 298 HIS 0.002 0.000 HIS B 360 PHE 0.009 0.001 PHE A 189 TYR 0.008 0.001 TYR B 388 ARG 0.005 0.000 ARG A 508 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 2) link_NAG-ASN : angle 1.94649 ( 6) link_BETA1-4 : bond 0.00483 ( 2) link_BETA1-4 : angle 2.76236 ( 6) hydrogen bonds : bond 0.04019 ( 511) hydrogen bonds : angle 4.21314 ( 1461) SS BOND : bond 0.00141 ( 8) SS BOND : angle 0.74159 ( 16) covalent geometry : bond 0.00251 ( 8332) covalent geometry : angle 0.51301 (11340) *********************** 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 : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.7920 (t80) cc_final: 0.7681 (t80) REVERT: A 390 ASP cc_start: 0.7448 (m-30) cc_final: 0.7102 (m-30) REVERT: A 548 GLU cc_start: 0.6541 (mt-10) cc_final: 0.5722 (pt0) REVERT: B 19 LYS cc_start: 0.5863 (OUTLIER) cc_final: 0.5208 (tttt) REVERT: B 35 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8157 (mmpt) REVERT: B 403 ARG cc_start: 0.7296 (mtm-85) cc_final: 0.6989 (mtt180) REVERT: B 548 GLU cc_start: 0.6500 (mt-10) cc_final: 0.5785 (pt0) outliers start: 4 outliers final: 2 residues processed: 88 average time/residue: 2.1858 time to fit residues: 207.7180 Evaluate side-chains 88 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 0.7980 chunk 62 optimal weight: 0.0170 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.088698 restraints weight = 30820.292| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.81 r_work: 0.2904 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8344 Z= 0.105 Angle : 0.508 8.775 11368 Z= 0.260 Chirality : 0.038 0.160 1356 Planarity : 0.004 0.061 1400 Dihedral : 8.024 95.831 1242 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.35 % Allowed : 7.93 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.74 (0.26), residues: 1076 helix: 2.27 (0.21), residues: 660 sheet: -4.27 (0.71), residues: 20 loop : -0.48 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 298 HIS 0.002 0.001 HIS B 360 PHE 0.009 0.001 PHE A 166 TYR 0.007 0.001 TYR B 388 ARG 0.006 0.000 ARG A 508 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 2) link_NAG-ASN : angle 1.82144 ( 6) link_BETA1-4 : bond 0.00454 ( 2) link_BETA1-4 : angle 2.71746 ( 6) hydrogen bonds : bond 0.03725 ( 511) hydrogen bonds : angle 4.05493 ( 1461) SS BOND : bond 0.00311 ( 8) SS BOND : angle 0.82613 ( 16) covalent geometry : bond 0.00229 ( 8332) covalent geometry : angle 0.50201 (11340) *********************** 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 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.7927 (t80) cc_final: 0.7619 (t80) REVERT: A 390 ASP cc_start: 0.7468 (m-30) cc_final: 0.7212 (m-30) REVERT: A 548 GLU cc_start: 0.6584 (mt-10) cc_final: 0.5746 (pt0) REVERT: B 19 LYS cc_start: 0.5936 (OUTLIER) cc_final: 0.5296 (tttt) REVERT: B 35 LYS cc_start: 0.8547 (mtmt) cc_final: 0.8207 (mmpt) REVERT: B 41 GLU cc_start: 0.8229 (mp0) cc_final: 0.7926 (mp0) REVERT: B 403 ARG cc_start: 0.7292 (mtm-85) cc_final: 0.6957 (mtt180) REVERT: B 548 GLU cc_start: 0.6483 (mt-10) cc_final: 0.5783 (pt0) outliers start: 3 outliers final: 0 residues processed: 88 average time/residue: 2.2268 time to fit residues: 211.7407 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 : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.109975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.087303 restraints weight = 31362.300| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.83 r_work: 0.2898 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1429 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= 0.126 Angle : 0.520 9.571 11368 Z= 0.266 Chirality : 0.038 0.162 1356 Planarity : 0.004 0.061 1400 Dihedral : 7.207 89.966 1238 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 0.58 % Allowed : 8.04 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.78 (0.26), residues: 1076 helix: 2.29 (0.21), residues: 660 sheet: -4.25 (0.71), residues: 20 loop : -0.43 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.002 0.001 HIS B 541 PHE 0.009 0.001 PHE A 189 TYR 0.007 0.001 TYR B 388 ARG 0.003 0.000 ARG A 508 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 2) link_NAG-ASN : angle 1.83113 ( 6) link_BETA1-4 : bond 0.00480 ( 2) link_BETA1-4 : angle 2.84900 ( 6) hydrogen bonds : bond 0.03869 ( 511) hydrogen bonds : angle 4.02598 ( 1461) SS BOND : bond 0.00271 ( 8) SS BOND : angle 1.21320 ( 16) covalent geometry : bond 0.00287 ( 8332) covalent geometry : angle 0.51318 (11340) *********************** 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 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.7899 (t80) cc_final: 0.7612 (t80) REVERT: A 548 GLU cc_start: 0.6588 (mt-10) cc_final: 0.5755 (pt0) REVERT: B 19 LYS cc_start: 0.5981 (OUTLIER) cc_final: 0.5335 (tttt) REVERT: B 35 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8187 (mmpt) REVERT: B 41 GLU cc_start: 0.8262 (mp0) cc_final: 0.7920 (mp0) REVERT: B 403 ARG cc_start: 0.7311 (mtm-85) cc_final: 0.7025 (mtt180) REVERT: B 548 GLU cc_start: 0.6492 (mt-10) cc_final: 0.5775 (pt0) outliers start: 5 outliers final: 1 residues processed: 89 average time/residue: 2.1765 time to fit residues: 209.3922 Evaluate side-chains 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 19 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3288 r_free = 0.3288 target = 0.108791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.086596 restraints weight = 31297.491| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.79 r_work: 0.2847 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8344 Z= 0.153 Angle : 0.545 10.203 11368 Z= 0.278 Chirality : 0.039 0.167 1356 Planarity : 0.004 0.061 1400 Dihedral : 6.910 85.362 1238 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 0.82 % Allowed : 8.28 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.75 (0.26), residues: 1076 helix: 2.32 (0.21), residues: 648 sheet: -4.19 (0.74), residues: 20 loop : -0.45 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 298 HIS 0.002 0.001 HIS B 541 PHE 0.011 0.001 PHE A 442 TYR 0.009 0.001 TYR B 388 ARG 0.002 0.000 ARG A 508 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 2) link_NAG-ASN : angle 1.85414 ( 6) link_BETA1-4 : bond 0.00372 ( 2) link_BETA1-4 : angle 3.07927 ( 6) hydrogen bonds : bond 0.04064 ( 511) hydrogen bonds : angle 4.05943 ( 1461) SS BOND : bond 0.00322 ( 8) SS BOND : angle 1.45378 ( 16) covalent geometry : bond 0.00350 ( 8332) covalent geometry : angle 0.53658 (11340) *********************** 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 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.7833 (t80) cc_final: 0.7534 (t80) REVERT: A 548 GLU cc_start: 0.6565 (mt-10) cc_final: 0.5697 (pt0) REVERT: B 19 LYS cc_start: 0.6037 (OUTLIER) cc_final: 0.5380 (tttt) REVERT: B 35 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8119 (mmpt) REVERT: B 41 GLU cc_start: 0.8281 (mp0) cc_final: 0.7922 (mp0) REVERT: B 548 GLU cc_start: 0.6648 (mt-10) cc_final: 0.5789 (pt0) outliers start: 7 outliers final: 2 residues processed: 86 average time/residue: 2.0307 time to fit residues: 189.7195 Evaluate side-chains 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 393 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3300 r_free = 0.3300 target = 0.109902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.087326 restraints weight = 30942.141| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.81 r_work: 0.2887 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8344 Z= 0.110 Angle : 0.525 10.768 11368 Z= 0.265 Chirality : 0.038 0.161 1356 Planarity : 0.004 0.061 1400 Dihedral : 6.558 79.930 1238 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 0.23 % Allowed : 9.09 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.82 (0.26), residues: 1076 helix: 2.29 (0.21), residues: 660 sheet: -4.22 (0.74), residues: 20 loop : -0.35 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 298 HIS 0.002 0.001 HIS B 541 PHE 0.008 0.001 PHE A 166 TYR 0.007 0.001 TYR B 388 ARG 0.003 0.000 ARG A 508 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 2) link_NAG-ASN : angle 1.82469 ( 6) link_BETA1-4 : bond 0.00419 ( 2) link_BETA1-4 : angle 3.25336 ( 6) hydrogen bonds : bond 0.03777 ( 511) hydrogen bonds : angle 3.99423 ( 1461) SS BOND : bond 0.00227 ( 8) SS BOND : angle 1.26575 ( 16) covalent geometry : bond 0.00240 ( 8332) covalent geometry : angle 0.51675 (11340) *********************** 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 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.6519 (mt-10) cc_final: 0.5665 (pt0) REVERT: B 19 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.5315 (tttt) REVERT: B 35 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8114 (mmpt) REVERT: B 41 GLU cc_start: 0.8292 (mp0) cc_final: 0.7943 (mp0) REVERT: B 494 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7925 (mtt) REVERT: B 548 GLU cc_start: 0.6630 (mt-10) cc_final: 0.5778 (pt0) outliers start: 2 outliers final: 0 residues processed: 85 average time/residue: 2.0489 time to fit residues: 189.2789 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 494 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.110272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.087738 restraints weight = 31057.511| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.82 r_work: 0.2881 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8344 Z= 0.111 Angle : 0.527 11.128 11368 Z= 0.264 Chirality : 0.038 0.161 1356 Planarity : 0.004 0.061 1400 Dihedral : 5.934 66.196 1238 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.53 % Favored : 96.38 % Rotamer: Outliers : 0.70 % Allowed : 8.62 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.91 (0.27), residues: 1076 helix: 2.36 (0.21), residues: 660 sheet: -4.07 (0.77), residues: 20 loop : -0.30 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 298 HIS 0.001 0.000 HIS B 541 PHE 0.009 0.001 PHE A 189 TYR 0.007 0.001 TYR B 388 ARG 0.003 0.000 ARG A 508 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 2) link_NAG-ASN : angle 1.80802 ( 6) link_BETA1-4 : bond 0.00191 ( 2) link_BETA1-4 : angle 3.77728 ( 6) hydrogen bonds : bond 0.03712 ( 511) hydrogen bonds : angle 3.96080 ( 1461) SS BOND : bond 0.00201 ( 8) SS BOND : angle 1.18646 ( 16) covalent geometry : bond 0.00247 ( 8332) covalent geometry : angle 0.51698 (11340) *********************** 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 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.6487 (mt-10) cc_final: 0.5628 (pt0) REVERT: B 19 LYS cc_start: 0.6005 (OUTLIER) cc_final: 0.5295 (tttt) REVERT: B 35 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8116 (mmpt) REVERT: B 41 GLU cc_start: 0.8291 (mp0) cc_final: 0.7942 (mp0) REVERT: B 494 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7911 (mtt) REVERT: B 548 GLU cc_start: 0.6598 (mt-10) cc_final: 0.5697 (pt0) outliers start: 6 outliers final: 0 residues processed: 88 average time/residue: 2.0093 time to fit residues: 191.8808 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 494 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.110280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.087754 restraints weight = 30897.106| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.81 r_work: 0.2879 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1696 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= 0.112 Angle : 0.529 9.975 11368 Z= 0.265 Chirality : 0.038 0.162 1356 Planarity : 0.004 0.061 1400 Dihedral : 5.317 55.542 1238 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.35 % Allowed : 9.21 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.93 (0.27), residues: 1076 helix: 2.35 (0.21), residues: 660 sheet: -4.15 (0.75), residues: 20 loop : -0.26 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 298 HIS 0.002 0.000 HIS B 541 PHE 0.009 0.001 PHE A 189 TYR 0.007 0.001 TYR B 388 ARG 0.003 0.000 ARG A 508 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 2) link_NAG-ASN : angle 1.99002 ( 6) link_BETA1-4 : bond 0.00193 ( 2) link_BETA1-4 : angle 4.38239 ( 6) hydrogen bonds : bond 0.03711 ( 511) hydrogen bonds : angle 3.94314 ( 1461) SS BOND : bond 0.00214 ( 8) SS BOND : angle 1.21967 ( 16) covalent geometry : bond 0.00249 ( 8332) covalent geometry : angle 0.51634 (11340) *********************** 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 89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.6516 (mt-10) cc_final: 0.5640 (pt0) REVERT: B 19 LYS cc_start: 0.6026 (OUTLIER) cc_final: 0.5326 (tttt) REVERT: B 32 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.4637 (mtm110) REVERT: B 35 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8112 (mmpt) REVERT: B 41 GLU cc_start: 0.8270 (mp0) cc_final: 0.7919 (mp0) REVERT: B 548 GLU cc_start: 0.6611 (mt-10) cc_final: 0.5710 (pt0) outliers start: 3 outliers final: 0 residues processed: 87 average time/residue: 2.0363 time to fit residues: 191.9702 Evaluate side-chains 85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 102 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.108366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.085843 restraints weight = 30893.638| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.80 r_work: 0.2848 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1710 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= 0.143 Angle : 0.542 7.897 11368 Z= 0.275 Chirality : 0.039 0.173 1356 Planarity : 0.004 0.061 1400 Dihedral : 4.872 54.570 1238 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.16 % Favored : 96.75 % Rotamer: Outliers : 0.23 % Allowed : 9.56 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.90 (0.27), residues: 1076 helix: 2.40 (0.21), residues: 648 sheet: -4.06 (0.78), residues: 20 loop : -0.33 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 298 HIS 0.003 0.001 HIS B 541 PHE 0.009 0.001 PHE B 189 TYR 0.009 0.001 TYR B 388 ARG 0.002 0.000 ARG A 508 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 2) link_NAG-ASN : angle 2.53307 ( 6) link_BETA1-4 : bond 0.00328 ( 2) link_BETA1-4 : angle 4.42860 ( 6) hydrogen bonds : bond 0.03971 ( 511) hydrogen bonds : angle 4.00045 ( 1461) SS BOND : bond 0.00263 ( 8) SS BOND : angle 1.56568 ( 16) covalent geometry : bond 0.00329 ( 8332) covalent geometry : angle 0.52612 (11340) ********************** 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: 2 poor density : 85 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.6536 (mt-10) cc_final: 0.5646 (pt0) REVERT: B 19 LYS cc_start: 0.6125 (OUTLIER) cc_final: 0.5394 (tttt) REVERT: B 32 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.4722 (mtm110) REVERT: B 35 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8103 (mmpt) REVERT: B 41 GLU cc_start: 0.8280 (mp0) cc_final: 0.7931 (mp0) REVERT: B 548 GLU cc_start: 0.6657 (mt-10) cc_final: 0.5762 (pt0) outliers start: 2 outliers final: 0 residues processed: 86 average time/residue: 2.1144 time to fit residues: 197.0143 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 59 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3287 r_free = 0.3287 target = 0.108958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.087029 restraints weight = 31067.134| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.76 r_work: 0.2865 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1764 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= 0.140 Angle : 0.534 6.702 11368 Z= 0.272 Chirality : 0.039 0.168 1356 Planarity : 0.004 0.060 1400 Dihedral : 4.746 53.610 1238 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 0.35 % Allowed : 9.67 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.83 (0.26), residues: 1076 helix: 2.33 (0.21), residues: 650 sheet: -4.12 (0.76), residues: 20 loop : -0.33 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 298 HIS 0.002 0.001 HIS B 541 PHE 0.009 0.001 PHE A 189 TYR 0.008 0.001 TYR B 388 ARG 0.003 0.000 ARG A 508 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 2) link_NAG-ASN : angle 2.67390 ( 6) link_BETA1-4 : bond 0.00252 ( 2) link_BETA1-4 : angle 3.88842 ( 6) hydrogen bonds : bond 0.03936 ( 511) hydrogen bonds : angle 4.00285 ( 1461) SS BOND : bond 0.00256 ( 8) SS BOND : angle 1.54769 ( 16) covalent geometry : bond 0.00316 ( 8332) covalent geometry : angle 0.52006 (11340) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9627.31 seconds wall clock time: 163 minutes 34.03 seconds (9814.03 seconds total)