Starting phenix.real_space_refine on Fri Aug 9 06:59:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3d_42946/08_2024/8v3d_42946_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3d_42946/08_2024/8v3d_42946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3d_42946/08_2024/8v3d_42946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3d_42946/08_2024/8v3d_42946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3d_42946/08_2024/8v3d_42946_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3d_42946/08_2024/8v3d_42946_trim.cif" } resolution = 2.95 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= 0.078 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 100 5.16 5 C 8344 2.51 5 N 2018 2.21 5 O 2174 1.98 5 H 13001 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 65": "OD1" <-> "OD2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B ASP 421": "OD1" <-> "OD2" Residue "C ASP 11": "OD1" <-> "OD2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C GLU 425": "OE1" <-> "OE2" Residue "C TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 300": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25637 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6366 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 383} Chain breaks: 2 Chain: "B" Number of atoms: 6366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6366 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 383} Chain breaks: 2 Chain: "C" Number of atoms: 6366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6366 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 383} Chain breaks: 2 Chain: "D" Number of atoms: 6531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 6531 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 9, 'TRANS': 386} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'A1AFC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.30, per 1000 atoms: 0.48 Number of scatterers: 25637 At special positions: 0 Unit cell: (115.649, 122.015, 128.381, 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 100 16.00 O 2174 8.00 N 2018 7.00 C 8344 6.00 H 13001 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.46 Conformation dependent library (CDL) restraints added in 2.6 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3018 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 63 removed outlier: 3.606A pdb=" N MET A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 93 removed outlier: 3.563A pdb=" N LEU A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Proline residue: A 83 - end of helix Proline residue: A 91 - end of helix Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 103 through 106 removed outlier: 4.538A pdb=" N ASN A 106 " --> pdb=" O ILE A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 113 through 153 removed outlier: 4.165A pdb=" N PHE A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 242 removed outlier: 3.720A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 4.278A pdb=" N GLU A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 370 removed outlier: 5.312A pdb=" N VAL A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 416 removed outlier: 4.541A pdb=" N MET A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 452 through 474 Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 34 through 63 Processing helix chain 'B' and resid 67 through 93 Proline residue: B 83 - end of helix Proline residue: B 91 - end of helix Processing helix chain 'B' and resid 93 through 102 Processing helix chain 'B' and resid 103 through 106 removed outlier: 4.557A pdb=" N ASN B 106 " --> pdb=" O ILE B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 113 through 153 removed outlier: 3.704A pdb=" N PHE B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 242 removed outlier: 3.749A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Proline residue: B 236 - end of helix removed outlier: 4.289A pdb=" N GLU B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 370 removed outlier: 5.301A pdb=" N VAL B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 416 removed outlier: 4.387A pdb=" N MET B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'B' and resid 423 through 438 Processing helix chain 'B' and resid 452 through 474 Processing helix chain 'C' and resid 12 through 22 Processing helix chain 'C' and resid 31 through 63 removed outlier: 3.530A pdb=" N LYS C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Proline residue: C 37 - end of helix removed outlier: 3.704A pdb=" N ILE C 40 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 93 Proline residue: C 83 - end of helix Proline residue: C 91 - end of helix Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 103 through 106 removed outlier: 4.559A pdb=" N ASN C 106 " --> pdb=" O ILE C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 113 through 153 Processing helix chain 'C' and resid 187 through 242 Proline residue: C 236 - end of helix removed outlier: 4.156A pdb=" N GLU C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 370 removed outlier: 4.004A pdb=" N ILE C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 416 Processing helix chain 'C' and resid 418 through 422 Processing helix chain 'C' and resid 423 through 438 Processing helix chain 'C' and resid 452 through 474 Processing helix chain 'D' and resid 6 through 16 Processing helix chain 'D' and resid 30 through 48 Proline residue: D 44 - end of helix Processing helix chain 'D' and resid 48 through 59 Processing helix chain 'D' and resid 62 through 89 Proline residue: D 72 - end of helix removed outlier: 4.336A pdb=" N GLU D 75 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 109 removed outlier: 3.564A pdb=" N LYS D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 146 Processing helix chain 'D' and resid 146 through 160 Processing helix chain 'D' and resid 181 through 238 Processing helix chain 'D' and resid 240 through 294 removed outlier: 5.580A pdb=" N PHE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE D 272 " --> pdb=" O GLY D 268 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 338 Proline residue: D 309 - end of helix removed outlier: 3.728A pdb=" N PHE D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 374 through 397 removed outlier: 4.161A pdb=" N PHE D 378 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN D 379 " --> pdb=" O LEU D 375 " (cutoff:3.500A) 1033 hydrogen bonds defined for protein. 3081 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: 8.86 Time building geometry restraints manager: 23.51 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: 12971 1.03 - 1.23: 32 1.23 - 1.42: 5391 1.42 - 1.62: 7372 1.62 - 1.81: 169 Bond restraints: 25935 Sorted by residual: bond pdb=" C03 A1AFC D 501 " pdb=" S04 A1AFC D 501 " ideal model delta sigma weight residual 1.730 1.597 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" C05 A1AFC D 501 " pdb=" S04 A1AFC D 501 " ideal model delta sigma weight residual 1.730 1.620 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C05 A1AFC D 501 " pdb=" N06 A1AFC D 501 " ideal model delta sigma weight residual 1.290 1.391 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C02 A1AFC D 501 " pdb=" N06 A1AFC D 501 " ideal model delta sigma weight residual 1.375 1.472 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C02 A1AFC D 501 " pdb=" C03 A1AFC D 501 " ideal model delta sigma weight residual 1.362 1.420 -0.058 2.00e-02 2.50e+03 8.30e+00 ... (remaining 25930 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.22: 255 106.22 - 113.17: 30640 113.17 - 120.12: 8140 120.12 - 127.07: 7741 127.07 - 134.01: 129 Bond angle restraints: 46905 Sorted by residual: angle pdb=" C ALA C 346 " pdb=" N TYR C 347 " pdb=" CA TYR C 347 " ideal model delta sigma weight residual 122.31 115.72 6.59 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C03 A1AFC D 501 " pdb=" S04 A1AFC D 501 " pdb=" C05 A1AFC D 501 " ideal model delta sigma weight residual 90.02 99.28 -9.26 3.00e+00 1.11e-01 9.52e+00 angle pdb=" C GLY B 7 " pdb=" N LEU B 8 " pdb=" CA LEU B 8 " ideal model delta sigma weight residual 121.54 127.43 -5.89 1.91e+00 2.74e-01 9.51e+00 angle pdb=" CA ILE C 40 " pdb=" CB ILE C 40 " pdb=" CG1 ILE C 40 " ideal model delta sigma weight residual 110.40 115.37 -4.97 1.70e+00 3.46e-01 8.56e+00 angle pdb=" C GLY C 348 " pdb=" N VAL C 349 " pdb=" CA VAL C 349 " ideal model delta sigma weight residual 120.46 117.30 3.16 1.37e+00 5.33e-01 5.32e+00 ... (remaining 46900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 10729 17.70 - 35.41: 996 35.41 - 53.11: 352 53.11 - 70.82: 104 70.82 - 88.52: 11 Dihedral angle restraints: 12192 sinusoidal: 6431 harmonic: 5761 Sorted by residual: dihedral pdb=" CA ASP A 421 " pdb=" CB ASP A 421 " pdb=" CG ASP A 421 " pdb=" OD1 ASP A 421 " ideal model delta sinusoidal sigma weight residual -30.00 -88.27 58.27 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CB GLU B 115 " pdb=" CG GLU B 115 " pdb=" CD GLU B 115 " pdb=" OE1 GLU B 115 " ideal model delta sinusoidal sigma weight residual 0.00 -88.52 88.52 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU B 63 " pdb=" CG GLU B 63 " pdb=" CD GLU B 63 " pdb=" OE1 GLU B 63 " ideal model delta sinusoidal sigma weight residual 0.00 88.37 -88.37 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 12189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1524 0.032 - 0.063: 341 0.063 - 0.095: 167 0.095 - 0.127: 38 0.127 - 0.159: 6 Chirality restraints: 2076 Sorted by residual: chirality pdb=" CA TYR C 347 " pdb=" N TYR C 347 " pdb=" C TYR C 347 " pdb=" CB TYR C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE A 170 " pdb=" N ILE A 170 " pdb=" C ILE A 170 " pdb=" CB ILE A 170 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CB ILE B 398 " pdb=" CA ILE B 398 " pdb=" CG1 ILE B 398 " pdb=" CG2 ILE B 398 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 2073 not shown) Planarity restraints: 3642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 347 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C TYR C 347 " 0.034 2.00e-02 2.50e+03 pdb=" O TYR C 347 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY C 348 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 235 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO A 236 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 170 " 0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO B 171 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 171 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 171 " 0.026 5.00e-02 4.00e+02 ... (remaining 3639 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 230 2.06 - 2.69: 40428 2.69 - 3.33: 77941 3.33 - 3.96: 96598 3.96 - 4.60: 153655 Nonbonded interactions: 368852 Sorted by model distance: nonbonded pdb=" OE1 GLU C 424 " pdb=" H GLU C 424 " model vdw 1.424 2.450 nonbonded pdb=" O ASN B 28 " pdb="HD21 ASN B 28 " model vdw 1.528 2.450 nonbonded pdb="HE21 GLN C 435 " pdb=" OE1 GLN D 360 " model vdw 1.579 2.450 nonbonded pdb=" HZ2 LYS C 86 " pdb=" OD1 ASP C 213 " model vdw 1.599 2.450 nonbonded pdb=" O TYR D 18 " pdb="HH22 ARG D 90 " model vdw 1.606 2.450 ... (remaining 368847 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' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.360 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 83.170 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 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:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 12934 Z= 0.201 Angle : 0.506 9.257 17544 Z= 0.272 Chirality : 0.035 0.159 2076 Planarity : 0.004 0.048 2113 Dihedral : 17.455 88.525 4581 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.59 % Allowed : 26.91 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.21), residues: 1558 helix: 2.19 (0.14), residues: 1259 sheet: -0.27 (1.06), residues: 24 loop : -1.81 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 419 HIS 0.003 0.001 HIS B 24 PHE 0.013 0.001 PHE A 399 TYR 0.017 0.001 TYR C 347 ARG 0.001 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 2.101 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6974 (m-30) REVERT: B 51 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7904 (tt) REVERT: D 171 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.5622 (p90) outliers start: 36 outliers final: 29 residues processed: 229 average time/residue: 1.9829 time to fit residues: 509.2858 Evaluate side-chains 226 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 194 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.0464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12934 Z= 0.202 Angle : 0.504 6.994 17544 Z= 0.276 Chirality : 0.036 0.173 2076 Planarity : 0.004 0.048 2113 Dihedral : 6.558 58.485 1750 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.31 % Allowed : 25.11 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.21), residues: 1558 helix: 2.63 (0.14), residues: 1264 sheet: -0.14 (1.10), residues: 24 loop : -1.79 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 104 HIS 0.003 0.001 HIS A 229 PHE 0.015 0.001 PHE A 399 TYR 0.018 0.001 TYR C 347 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 204 time to evaluate : 2.168 Fit side-chains revert: symmetry clash REVERT: B 51 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7812 (tt) REVERT: B 86 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7829 (mttm) REVERT: B 234 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7199 (ttt) REVERT: D 171 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.5662 (p90) outliers start: 46 outliers final: 20 residues processed: 243 average time/residue: 2.2080 time to fit residues: 600.0685 Evaluate side-chains 218 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 194 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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: 0.8110 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12934 Z= 0.231 Angle : 0.508 7.253 17544 Z= 0.278 Chirality : 0.036 0.182 2076 Planarity : 0.004 0.049 2113 Dihedral : 5.607 59.342 1726 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.60 % Allowed : 24.46 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.21), residues: 1558 helix: 2.65 (0.14), residues: 1264 sheet: -0.08 (1.12), residues: 24 loop : -1.82 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 419 HIS 0.003 0.001 HIS B 24 PHE 0.020 0.002 PHE B 36 TYR 0.021 0.001 TYR C 347 ARG 0.002 0.000 ARG C 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 205 time to evaluate : 2.176 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.6929 (m-30) REVERT: A 438 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7117 (mp10) REVERT: B 51 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7841 (tt) REVERT: B 86 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7894 (mttm) REVERT: B 178 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7606 (mmt90) REVERT: D 80 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8054 (m-40) REVERT: D 171 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.5394 (p90) outliers start: 50 outliers final: 27 residues processed: 242 average time/residue: 1.6520 time to fit residues: 447.3413 Evaluate side-chains 232 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 198 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.8137 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12934 Z= 0.291 Angle : 0.534 7.676 17544 Z= 0.293 Chirality : 0.037 0.189 2076 Planarity : 0.004 0.052 2113 Dihedral : 5.749 59.638 1726 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.39 % Allowed : 24.03 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.21), residues: 1558 helix: 2.55 (0.14), residues: 1263 sheet: -0.01 (1.13), residues: 24 loop : -1.83 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 104 HIS 0.004 0.001 HIS C 229 PHE 0.018 0.002 PHE C 399 TYR 0.022 0.001 TYR C 347 ARG 0.002 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 203 time to evaluate : 2.061 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.6945 (m-30) REVERT: A 438 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.7106 (mp10) REVERT: B 51 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7851 (tt) REVERT: B 86 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7856 (mttm) REVERT: B 178 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7608 (mmt90) REVERT: D 80 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8095 (m-40) REVERT: D 171 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.5111 (p90) outliers start: 61 outliers final: 33 residues processed: 249 average time/residue: 1.9823 time to fit residues: 557.3005 Evaluate side-chains 234 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 194 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8157 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12934 Z= 0.339 Angle : 0.562 7.901 17544 Z= 0.308 Chirality : 0.038 0.194 2076 Planarity : 0.004 0.053 2113 Dihedral : 5.878 61.176 1726 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.53 % Allowed : 23.88 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.21), residues: 1558 helix: 2.36 (0.14), residues: 1263 sheet: -0.00 (1.15), residues: 24 loop : -1.82 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 104 HIS 0.005 0.001 HIS C 229 PHE 0.017 0.002 PHE C 399 TYR 0.022 0.002 TYR C 347 ARG 0.003 0.000 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 199 time to evaluate : 2.286 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6940 (m-30) REVERT: A 178 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6288 (mpt-90) REVERT: A 438 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.7133 (mp10) REVERT: A 439 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7843 (mttp) REVERT: B 51 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7888 (tt) REVERT: B 86 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7911 (mttm) REVERT: B 158 ARG cc_start: 0.7873 (mmt90) cc_final: 0.7568 (mmt90) REVERT: B 178 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7633 (mmt90) REVERT: C 19 MET cc_start: 0.8466 (mtp) cc_final: 0.8254 (mtp) REVERT: D 80 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8120 (m-40) outliers start: 63 outliers final: 39 residues processed: 248 average time/residue: 2.0628 time to fit residues: 576.9929 Evaluate side-chains 242 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 195 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.8103 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12934 Z= 0.176 Angle : 0.492 6.891 17544 Z= 0.269 Chirality : 0.036 0.169 2076 Planarity : 0.004 0.049 2113 Dihedral : 5.746 60.461 1726 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.17 % Allowed : 24.82 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.21), residues: 1558 helix: 2.65 (0.14), residues: 1257 sheet: -0.02 (1.14), residues: 24 loop : -1.83 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 419 HIS 0.003 0.000 HIS B 24 PHE 0.017 0.001 PHE B 36 TYR 0.017 0.001 TYR C 347 ARG 0.001 0.000 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 205 time to evaluate : 2.156 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7367 (m-30) cc_final: 0.6899 (m-30) REVERT: A 438 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: A 439 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7829 (mttp) REVERT: B 51 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7858 (tt) REVERT: B 158 ARG cc_start: 0.7872 (mmt90) cc_final: 0.7581 (mmt90) REVERT: B 178 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7611 (mmt90) REVERT: B 234 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7247 (ttt) REVERT: C 19 MET cc_start: 0.8412 (mtp) cc_final: 0.8208 (mtp) REVERT: D 80 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8085 (m-40) REVERT: D 171 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.4792 (p90) outliers start: 44 outliers final: 29 residues processed: 241 average time/residue: 2.0537 time to fit residues: 553.8204 Evaluate side-chains 235 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 199 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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: 0.8141 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12934 Z= 0.293 Angle : 0.544 7.585 17544 Z= 0.296 Chirality : 0.037 0.192 2076 Planarity : 0.004 0.052 2113 Dihedral : 5.825 61.424 1726 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.81 % Allowed : 24.53 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.21), residues: 1558 helix: 2.50 (0.14), residues: 1263 sheet: -0.01 (1.16), residues: 24 loop : -1.82 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 104 HIS 0.004 0.001 HIS A 229 PHE 0.018 0.002 PHE C 399 TYR 0.023 0.001 TYR C 347 ARG 0.002 0.000 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 200 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7700 (ttp-170) REVERT: A 438 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: A 439 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7759 (mttp) REVERT: B 51 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7876 (tt) REVERT: B 158 ARG cc_start: 0.7840 (mmt90) cc_final: 0.7547 (mmt90) REVERT: B 178 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7621 (mmt90) REVERT: D 80 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8147 (m-40) REVERT: D 171 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.4874 (p90) outliers start: 53 outliers final: 34 residues processed: 243 average time/residue: 2.1137 time to fit residues: 574.0004 Evaluate side-chains 235 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8153 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12934 Z= 0.318 Angle : 0.559 7.837 17544 Z= 0.305 Chirality : 0.038 0.192 2076 Planarity : 0.004 0.053 2113 Dihedral : 5.924 62.589 1726 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.17 % Allowed : 24.32 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.21), residues: 1558 helix: 2.36 (0.14), residues: 1263 sheet: 0.05 (1.18), residues: 24 loop : -1.82 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 104 HIS 0.005 0.001 HIS A 229 PHE 0.017 0.002 PHE C 399 TYR 0.022 0.002 TYR C 347 ARG 0.003 0.000 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 200 time to evaluate : 2.080 Fit side-chains REVERT: A 178 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6301 (mpt-90) REVERT: A 402 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7783 (ttt180) REVERT: A 438 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: A 439 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7716 (mttp) REVERT: B 51 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7887 (tt) REVERT: B 158 ARG cc_start: 0.7873 (mmt90) cc_final: 0.7571 (mmt90) REVERT: B 178 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7650 (mmt90) REVERT: D 80 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8128 (m-40) outliers start: 58 outliers final: 39 residues processed: 247 average time/residue: 2.1642 time to fit residues: 610.9162 Evaluate side-chains 241 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 195 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.8112 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12934 Z= 0.190 Angle : 0.509 7.075 17544 Z= 0.276 Chirality : 0.036 0.169 2076 Planarity : 0.004 0.050 2113 Dihedral : 5.809 62.147 1726 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.17 % Allowed : 25.47 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.21), residues: 1558 helix: 2.60 (0.14), residues: 1257 sheet: 0.04 (1.17), residues: 24 loop : -1.84 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 419 HIS 0.004 0.001 HIS B 24 PHE 0.020 0.001 PHE D 185 TYR 0.018 0.001 TYR C 347 ARG 0.001 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 200 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7633 (ttp-170) REVERT: A 438 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.7060 (mp10) REVERT: A 439 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7771 (mttp) REVERT: B 51 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7804 (tt) REVERT: B 158 ARG cc_start: 0.7873 (mmt90) cc_final: 0.7576 (mmt90) REVERT: B 178 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7637 (mmt90) REVERT: D 80 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8115 (m-40) REVERT: D 171 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.4891 (p90) outliers start: 44 outliers final: 30 residues processed: 236 average time/residue: 2.0264 time to fit residues: 535.6302 Evaluate side-chains 232 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 195 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8152 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12934 Z= 0.322 Angle : 0.562 7.814 17544 Z= 0.306 Chirality : 0.038 0.189 2076 Planarity : 0.004 0.053 2113 Dihedral : 5.899 63.030 1725 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.38 % Allowed : 25.04 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.21), residues: 1558 helix: 2.39 (0.14), residues: 1266 sheet: 0.04 (1.18), residues: 24 loop : -1.89 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 104 HIS 0.005 0.001 HIS A 229 PHE 0.018 0.002 PHE C 399 TYR 0.025 0.002 TYR C 347 ARG 0.004 0.000 ARG D 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 193 time to evaluate : 2.022 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: A 402 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7796 (ttt180) REVERT: A 438 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7107 (mp10) REVERT: A 439 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7741 (mttp) REVERT: B 51 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7871 (tt) REVERT: B 158 ARG cc_start: 0.7881 (mmt90) cc_final: 0.7585 (mmt90) REVERT: B 178 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7652 (mmt90) REVERT: D 80 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8187 (m-40) outliers start: 47 outliers final: 33 residues processed: 230 average time/residue: 2.1771 time to fit residues: 559.3812 Evaluate side-chains 232 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.148335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.126127 restraints weight = 41363.253| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.22 r_work: 0.3382 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12934 Z= 0.288 Angle : 0.554 7.788 17544 Z= 0.301 Chirality : 0.038 0.183 2076 Planarity : 0.004 0.052 2113 Dihedral : 5.936 63.870 1725 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.09 % Allowed : 25.47 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.21), residues: 1558 helix: 2.37 (0.14), residues: 1266 sheet: 0.01 (1.18), residues: 24 loop : -1.90 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 104 HIS 0.004 0.001 HIS C 24 PHE 0.020 0.002 PHE D 185 TYR 0.021 0.002 TYR C 347 ARG 0.002 0.000 ARG D 90 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 8944.51 seconds wall clock time: 159 minutes 23.08 seconds (9563.08 seconds total)