Starting phenix.real_space_refine on Mon Nov 18 11:42:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irn_35680/11_2024/8irn_35680_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irn_35680/11_2024/8irn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irn_35680/11_2024/8irn_35680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irn_35680/11_2024/8irn_35680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irn_35680/11_2024/8irn_35680_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irn_35680/11_2024/8irn_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-5513/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: 8.61, per 1000 atoms: 0.53 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: 4.79 Conformation dependent library (CDL) restraints added in 1.6 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: 1.39 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: 6.80 Time building geometry restraints manager: 5.43 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: 0.00 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.310 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 38.790 Find NCS groups from input model: 0.410 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:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.930 ------------------------------------------------------------------------------- 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 8332 Z= 0.226 Angle : 0.593 10.309 11340 Z= 0.315 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 *********************** 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 : 1.344 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: 2.6130 time to fit residues: 278.9695 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 : 1.292 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 8332 Z= 0.240 Angle : 0.541 6.581 11340 Z= 0.288 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 *********************** 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 : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.7436 (m-30) cc_final: 0.7070 (m-30) REVERT: A 548 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6028 (pt0) REVERT: B 19 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.5714 (tttt) REVERT: B 494 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7830 (mtt) REVERT: B 548 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6097 (pt0) outliers start: 7 outliers final: 3 residues processed: 92 average time/residue: 2.2823 time to fit residues: 226.4648 Evaluate side-chains 88 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 54 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8332 Z= 0.235 Angle : 0.538 7.611 11340 Z= 0.282 Chirality : 0.039 0.164 1356 Planarity : 0.005 0.062 1400 Dihedral : 8.201 104.113 1242 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.35 % Allowed : 7.81 % Favored : 91.84 % 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: 1.50 (0.26), residues: 1076 helix: 2.07 (0.21), residues: 658 sheet: -4.56 (0.60), residues: 20 loop : -0.52 (0.30), residues: 398 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 0.014 0.001 PHE B 442 TYR 0.009 0.001 TYR B 388 ARG 0.005 0.000 ARG A 508 *********************** 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 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6005 (pt0) REVERT: B 19 LYS cc_start: 0.6323 (OUTLIER) cc_final: 0.5776 (tttt) REVERT: B 548 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6054 (pt0) outliers start: 3 outliers final: 2 residues processed: 85 average time/residue: 2.1280 time to fit residues: 196.3681 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 : 1.395 ------------------------------------------------------------------------------- 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 97 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.003 0.035 8332 Z= 0.216 Angle : 0.529 8.661 11340 Z= 0.275 Chirality : 0.039 0.165 1356 Planarity : 0.005 0.062 1400 Dihedral : 7.800 97.349 1242 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 0.70 % Allowed : 8.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1076 helix: 2.20 (0.21), residues: 646 sheet: -4.43 (0.66), residues: 20 loop : -0.57 (0.30), residues: 410 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 0.010 0.001 PHE A 189 TYR 0.009 0.001 TYR B 388 ARG 0.003 0.000 ARG A 508 *********************** 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: 6 poor density : 84 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6028 (pt0) REVERT: B 19 LYS cc_start: 0.6456 (OUTLIER) cc_final: 0.5893 (tttt) REVERT: B 41 GLU cc_start: 0.7975 (mp0) cc_final: 0.7755 (mp0) REVERT: B 548 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6103 (pt0) outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 2.0368 time to fit residues: 187.9198 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 : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8332 Z= 0.291 Angle : 0.558 9.375 11340 Z= 0.290 Chirality : 0.040 0.168 1356 Planarity : 0.005 0.061 1400 Dihedral : 7.527 91.229 1242 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 0.93 % Allowed : 8.39 % 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: 1.53 (0.26), residues: 1076 helix: 2.14 (0.21), residues: 646 sheet: -4.36 (0.69), residues: 20 loop : -0.53 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 380 HIS 0.002 0.001 HIS B 541 PHE 0.011 0.001 PHE A 189 TYR 0.010 0.001 TYR B 388 ARG 0.004 0.000 ARG A 508 *********************** 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 93 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 1.160 Fit side-chains REVERT: A 520 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8556 (mtt) REVERT: A 548 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6044 (pt0) REVERT: B 19 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.5918 (tttt) REVERT: B 32 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.4861 (mtm110) REVERT: B 41 GLU cc_start: 0.7979 (mp0) cc_final: 0.7748 (mp0) REVERT: B 548 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6176 (pt0) outliers start: 8 outliers final: 2 residues processed: 88 average time/residue: 2.1436 time to fit residues: 205.3943 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 : 1.391 ------------------------------------------------------------------------------- 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 520 MET Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8332 Z= 0.291 Angle : 0.569 9.989 11340 Z= 0.295 Chirality : 0.040 0.168 1356 Planarity : 0.005 0.060 1400 Dihedral : 7.227 87.457 1238 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.97 % Favored : 96.84 % Rotamer: Outliers : 1.40 % Allowed : 8.86 % Favored : 89.74 % 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: 1.54 (0.26), residues: 1076 helix: 2.09 (0.21), residues: 646 sheet: -4.29 (0.71), residues: 20 loop : -0.42 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 380 HIS 0.003 0.001 HIS B 541 PHE 0.011 0.001 PHE A 189 TYR 0.011 0.001 TYR A 388 ARG 0.005 0.000 ARG A 508 *********************** 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 94 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 1.480 Fit side-chains REVERT: A 32 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.4710 (mtm110) REVERT: A 548 GLU cc_start: 0.6621 (mt-10) cc_final: 0.5949 (pt0) REVERT: B 19 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.5950 (tttt) REVERT: B 32 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.4939 (mtm110) REVERT: B 41 GLU cc_start: 0.7968 (mp0) cc_final: 0.7733 (mp0) REVERT: B 548 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6084 (pt0) outliers start: 12 outliers final: 3 residues processed: 85 average time/residue: 2.0969 time to fit residues: 194.9856 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 210 LEU 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 393 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8332 Z= 0.176 Angle : 0.535 10.473 11340 Z= 0.274 Chirality : 0.039 0.163 1356 Planarity : 0.004 0.061 1400 Dihedral : 6.878 83.506 1238 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 0.47 % Allowed : 10.02 % 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 (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: 1.68 (0.26), residues: 1076 helix: 2.23 (0.21), residues: 648 sheet: -4.24 (0.74), residues: 20 loop : -0.42 (0.31), residues: 408 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 0.009 0.001 PHE B 166 TYR 0.009 0.001 TYR B 388 ARG 0.005 0.000 ARG A 508 *********************** 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 84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.253 Fit side-chains REVERT: A 548 GLU cc_start: 0.6597 (mt-10) cc_final: 0.5938 (pt0) REVERT: B 19 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.5935 (tttt) REVERT: B 32 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.4948 (mtm110) REVERT: B 41 GLU cc_start: 0.7985 (mp0) cc_final: 0.7758 (mp0) REVERT: B 548 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6090 (pt0) outliers start: 4 outliers final: 1 residues processed: 82 average time/residue: 2.0659 time to fit residues: 183.9560 Evaluate side-chains 83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8332 Z= 0.292 Angle : 0.571 10.873 11340 Z= 0.294 Chirality : 0.040 0.170 1356 Planarity : 0.005 0.060 1400 Dihedral : 6.666 78.362 1238 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.97 % Favored : 96.84 % Rotamer: Outliers : 0.82 % Allowed : 10.14 % 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 (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: 1.62 (0.26), residues: 1076 helix: 2.15 (0.21), residues: 646 sheet: -4.09 (0.77), residues: 20 loop : -0.40 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.003 0.001 HIS B 541 PHE 0.012 0.001 PHE A 189 TYR 0.011 0.001 TYR A 388 ARG 0.003 0.000 ARG A 508 *********************** 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 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 1.295 Fit side-chains REVERT: A 32 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.4890 (mtm110) REVERT: A 548 GLU cc_start: 0.6591 (mt-10) cc_final: 0.5922 (pt0) REVERT: B 19 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.5962 (tttt) REVERT: B 32 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.4961 (mtm110) REVERT: B 41 GLU cc_start: 0.7998 (mp0) cc_final: 0.7770 (mp0) REVERT: B 548 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6018 (pt0) outliers start: 7 outliers final: 0 residues processed: 83 average time/residue: 2.0906 time to fit residues: 188.4947 Evaluate side-chains 83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8332 Z= 0.203 Angle : 0.546 11.142 11340 Z= 0.279 Chirality : 0.039 0.165 1356 Planarity : 0.004 0.060 1400 Dihedral : 6.301 71.115 1238 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.26), residues: 1076 helix: 2.20 (0.21), residues: 648 sheet: -4.19 (0.75), residues: 20 loop : -0.42 (0.31), residues: 408 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 0.010 0.001 PHE A 189 TYR 0.010 0.001 TYR B 388 ARG 0.003 0.000 ARG A 508 *********************** 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 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 1.345 Fit side-chains REVERT: A 32 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.4900 (mtm110) REVERT: A 494 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7536 (mmt) REVERT: A 548 GLU cc_start: 0.6539 (mt-10) cc_final: 0.5895 (pt0) REVERT: B 19 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.5945 (tttt) REVERT: B 32 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.4966 (mtm110) REVERT: B 41 GLU cc_start: 0.7962 (mp0) cc_final: 0.7741 (mp0) REVERT: B 548 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6027 (pt0) outliers start: 6 outliers final: 0 residues processed: 83 average time/residue: 2.0867 time to fit residues: 188.2107 Evaluate side-chains 84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 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 62 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8332 Z= 0.149 Angle : 0.522 10.096 11340 Z= 0.265 Chirality : 0.038 0.158 1356 Planarity : 0.004 0.060 1400 Dihedral : 5.476 54.877 1238 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.53 % Favored : 96.38 % Rotamer: Outliers : 0.35 % Allowed : 10.49 % 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 (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: 1.79 (0.27), residues: 1076 helix: 2.21 (0.21), residues: 662 sheet: -4.08 (0.78), residues: 20 loop : -0.28 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 298 HIS 0.001 0.000 HIS A 360 PHE 0.009 0.001 PHE B 189 TYR 0.008 0.001 TYR B 388 ARG 0.004 0.000 ARG A 508 ********************** 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 85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 1.332 Fit side-chains REVERT: A 32 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.4900 (mtm110) REVERT: A 41 GLU cc_start: 0.8004 (mp0) cc_final: 0.7790 (mp0) REVERT: A 548 GLU cc_start: 0.6557 (mt-10) cc_final: 0.5870 (pt0) REVERT: B 19 LYS cc_start: 0.6572 (OUTLIER) cc_final: 0.5903 (tttt) REVERT: B 41 GLU cc_start: 0.7933 (mp0) cc_final: 0.7728 (mp0) REVERT: B 548 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6047 (pt0) outliers start: 3 outliers final: 0 residues processed: 83 average time/residue: 2.1711 time to fit residues: 195.2839 Evaluate side-chains 82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 91 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 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 = 0.3273 r_free = 0.3273 target = 0.107923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.085920 restraints weight = 31141.478| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.76 r_work: 0.2856 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8332 Z= 0.229 Angle : 0.540 6.862 11340 Z= 0.278 Chirality : 0.039 0.174 1356 Planarity : 0.004 0.060 1400 Dihedral : 5.056 54.033 1238 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.16 % Favored : 96.75 % Rotamer: Outliers : 0.35 % Allowed : 10.84 % 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 (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: 1.76 (0.27), residues: 1076 helix: 2.26 (0.21), residues: 650 sheet: -4.06 (0.78), residues: 20 loop : -0.36 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.003 0.001 HIS B 541 PHE 0.011 0.001 PHE A 189 TYR 0.010 0.001 TYR B 388 ARG 0.002 0.000 ARG A 508 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5091.38 seconds wall clock time: 91 minutes 8.68 seconds (5468.68 seconds total)