Starting phenix.real_space_refine on Tue Mar 19 16:27:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x83_38134/03_2024/8x83_38134_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x83_38134/03_2024/8x83_38134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x83_38134/03_2024/8x83_38134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x83_38134/03_2024/8x83_38134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x83_38134/03_2024/8x83_38134_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x83_38134/03_2024/8x83_38134_neut_trim_updated.pdb" } resolution = 2.8 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 72 5.16 5 Na 2 4.78 5 C 7820 2.51 5 N 2048 2.21 5 O 2116 1.98 5 H 12424 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 83": "OD1" <-> "OD2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 391": "OD1" <-> "OD2" Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ASP 391": "OD1" <-> "OD2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C GLU 354": "OE1" <-> "OE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C ASP 391": "OD1" <-> "OD2" Residue "C PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D GLU 354": "OE1" <-> "OE2" Residue "D ASP 389": "OD1" <-> "OD2" Residue "D ASP 391": "OD1" <-> "OD2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24482 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 6107 Classifications: {'peptide': 380} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Chain: "B" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 6107 Classifications: {'peptide': 380} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Chain: "C" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 6107 Classifications: {'peptide': 380} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Chain: "D" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 6107 Classifications: {'peptide': 380} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' NA': 2, 'FRU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 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} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.60, per 1000 atoms: 0.43 Number of scatterers: 24482 At special positions: 0 Unit cell: (110.67, 110.67, 106.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 Na 2 11.00 O 2116 8.00 N 2048 7.00 C 7820 6.00 H 12424 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: 21.33 Conformation dependent library (CDL) restraints added in 2.3 seconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 79.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 38 through 63 Processing helix chain 'A' and resid 74 through 99 Processing helix chain 'A' and resid 102 through 118 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 125 through 160 Processing helix chain 'A' and resid 169 through 214 removed outlier: 3.783A pdb=" N TYR A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 263 through 320 removed outlier: 6.329A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 356 Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 372 through 387 removed outlier: 3.963A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 424 removed outlier: 3.822A pdb=" N LEU A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 38 through 63 Processing helix chain 'B' and resid 74 through 99 Processing helix chain 'B' and resid 102 through 118 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 125 through 160 Processing helix chain 'B' and resid 169 through 214 removed outlier: 3.783A pdb=" N TYR B 175 " --> pdb=" O ASN B 171 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 263 through 320 removed outlier: 6.329A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 356 Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 372 through 387 removed outlier: 3.963A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 424 removed outlier: 3.822A pdb=" N LEU B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 16 Processing helix chain 'C' and resid 38 through 63 Processing helix chain 'C' and resid 74 through 99 Processing helix chain 'C' and resid 102 through 118 Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 125 through 160 Processing helix chain 'C' and resid 169 through 214 removed outlier: 3.783A pdb=" N TYR C 175 " --> pdb=" O ASN C 171 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Proline residue: C 177 - end of helix Processing helix chain 'C' and resid 263 through 320 removed outlier: 6.329A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 356 Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 372 through 387 removed outlier: 3.963A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 424 removed outlier: 3.822A pdb=" N LEU C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 38 through 63 Processing helix chain 'D' and resid 74 through 99 Processing helix chain 'D' and resid 102 through 118 Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 125 through 160 Processing helix chain 'D' and resid 169 through 214 removed outlier: 3.783A pdb=" N TYR D 175 " --> pdb=" O ASN D 171 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Proline residue: D 177 - end of helix Processing helix chain 'D' and resid 263 through 320 removed outlier: 6.329A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 356 Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 372 through 387 removed outlier: 3.963A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 424 removed outlier: 3.822A pdb=" N LEU D 416 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 22 through 26 Processing sheet with id= B, first strand: chain 'B' and resid 22 through 26 Processing sheet with id= C, first strand: chain 'C' and resid 22 through 26 Processing sheet with id= D, first strand: chain 'D' and resid 22 through 26 984 hydrogen bonds defined for protein. 2952 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: 9.24 Time building geometry restraints manager: 21.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 12392 1.02 - 1.22: 36 1.22 - 1.42: 4996 1.42 - 1.61: 7172 1.61 - 1.81: 112 Bond restraints: 24708 Sorted by residual: bond pdb=" C VAL D 417 " pdb=" N ALA D 418 " ideal model delta sigma weight residual 1.335 1.516 -0.181 1.31e-02 5.83e+03 1.91e+02 bond pdb=" C VAL A 417 " pdb=" N ALA A 418 " ideal model delta sigma weight residual 1.335 1.516 -0.181 1.31e-02 5.83e+03 1.91e+02 bond pdb=" C VAL B 417 " pdb=" N ALA B 418 " ideal model delta sigma weight residual 1.335 1.516 -0.181 1.31e-02 5.83e+03 1.91e+02 bond pdb=" C VAL C 417 " pdb=" N ALA C 418 " ideal model delta sigma weight residual 1.335 1.516 -0.181 1.31e-02 5.83e+03 1.91e+02 bond pdb=" NE ARG A 424 " pdb=" HE ARG A 424 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 24703 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.10: 428 107.10 - 113.83: 29348 113.83 - 120.56: 8748 120.56 - 127.29: 5984 127.29 - 134.03: 116 Bond angle restraints: 44624 Sorted by residual: angle pdb=" CA ALA A 418 " pdb=" C ALA A 418 " pdb=" N LEU A 419 " ideal model delta sigma weight residual 117.30 109.95 7.35 1.16e+00 7.43e-01 4.01e+01 angle pdb=" CA ALA B 418 " pdb=" C ALA B 418 " pdb=" N LEU B 419 " ideal model delta sigma weight residual 117.30 109.95 7.35 1.16e+00 7.43e-01 4.01e+01 angle pdb=" CA ALA D 418 " pdb=" C ALA D 418 " pdb=" N LEU D 419 " ideal model delta sigma weight residual 117.30 109.95 7.35 1.16e+00 7.43e-01 4.01e+01 angle pdb=" CA ALA C 418 " pdb=" C ALA C 418 " pdb=" N LEU C 419 " ideal model delta sigma weight residual 117.30 109.95 7.35 1.16e+00 7.43e-01 4.01e+01 angle pdb=" O VAL A 417 " pdb=" C VAL A 417 " pdb=" N ALA A 418 " ideal model delta sigma weight residual 121.87 116.25 5.62 9.70e-01 1.06e+00 3.36e+01 ... (remaining 44619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 10295 16.56 - 33.11: 917 33.11 - 49.67: 204 49.67 - 66.23: 132 66.23 - 82.79: 16 Dihedral angle restraints: 11564 sinusoidal: 6244 harmonic: 5320 Sorted by residual: dihedral pdb=" N ASN B 120 " pdb=" CA ASN B 120 " pdb=" CB ASN B 120 " pdb=" CG ASN B 120 " ideal model delta sinusoidal sigma weight residual -180.00 -121.21 -58.79 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ASN A 120 " pdb=" CA ASN A 120 " pdb=" CB ASN A 120 " pdb=" CG ASN A 120 " ideal model delta sinusoidal sigma weight residual -180.00 -121.21 -58.79 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ASN C 120 " pdb=" CA ASN C 120 " pdb=" CB ASN C 120 " pdb=" CG ASN C 120 " ideal model delta sinusoidal sigma weight residual -180.00 -121.21 -58.79 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 11561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1492 0.035 - 0.069: 388 0.069 - 0.104: 100 0.104 - 0.139: 16 0.139 - 0.173: 8 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CA VAL D 417 " pdb=" N VAL D 417 " pdb=" C VAL D 417 " pdb=" CB VAL D 417 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA VAL B 417 " pdb=" N VAL B 417 " pdb=" C VAL B 417 " pdb=" CB VAL B 417 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA VAL C 417 " pdb=" N VAL C 417 " pdb=" C VAL C 417 " pdb=" CB VAL C 417 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 2001 not shown) Planarity restraints: 3520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 423 " 0.135 2.00e-02 2.50e+03 1.50e-01 3.35e+02 pdb=" CD GLN C 423 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN C 423 " -0.129 2.00e-02 2.50e+03 pdb=" NE2 GLN C 423 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN C 423 " 0.225 2.00e-02 2.50e+03 pdb="HE22 GLN C 423 " -0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 423 " 0.135 2.00e-02 2.50e+03 1.50e-01 3.35e+02 pdb=" CD GLN B 423 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN B 423 " -0.129 2.00e-02 2.50e+03 pdb=" NE2 GLN B 423 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 423 " 0.225 2.00e-02 2.50e+03 pdb="HE22 GLN B 423 " -0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 423 " 0.135 2.00e-02 2.50e+03 1.50e-01 3.35e+02 pdb=" CD GLN A 423 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 423 " -0.129 2.00e-02 2.50e+03 pdb=" NE2 GLN A 423 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 423 " 0.225 2.00e-02 2.50e+03 pdb="HE22 GLN A 423 " -0.219 2.00e-02 2.50e+03 ... (remaining 3517 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1460 2.20 - 2.80: 51720 2.80 - 3.40: 71768 3.40 - 4.00: 92760 4.00 - 4.60: 146235 Nonbonded interactions: 363943 Sorted by model distance: nonbonded pdb=" OD1 ASN D 401 " pdb=" HG1 THR D 403 " model vdw 1.599 1.850 nonbonded pdb=" OD1 ASN C 401 " pdb=" HG1 THR C 403 " model vdw 1.599 1.850 nonbonded pdb=" OD1 ASN A 401 " pdb=" HG1 THR A 403 " model vdw 1.599 1.850 nonbonded pdb=" OD1 ASN B 401 " pdb=" HG1 THR B 403 " model vdw 1.599 1.850 nonbonded pdb=" O SER D 73 " pdb=" H LYS D 77 " model vdw 1.637 1.850 ... (remaining 363938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 425) selection = (chain 'B' and resid 1 through 425) selection = (chain 'C' and resid 1 through 425) selection = (chain 'D' and resid 1 through 425) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.360 Extract box with map and model: 4.540 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 81.180 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.100 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:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.005 0.181 12284 Z= 0.299 Angle : 0.597 7.346 16668 Z= 0.375 Chirality : 0.034 0.173 2004 Planarity : 0.003 0.041 2032 Dihedral : 14.831 82.787 4452 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.22 % Allowed : 12.23 % Favored : 86.54 % 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: 2.34 (0.21), residues: 1504 helix: 2.08 (0.14), residues: 1244 sheet: 0.86 (0.73), residues: 48 loop : -1.52 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 154 HIS 0.002 0.000 HIS A 278 PHE 0.010 0.001 PHE A 315 TYR 0.007 0.001 TYR C 312 ARG 0.002 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 ARG cc_start: 0.7525 (mmt180) cc_final: 0.7274 (mpp-170) REVERT: B 399 ARG cc_start: 0.7523 (mmt180) cc_final: 0.7273 (mpp-170) REVERT: C 399 ARG cc_start: 0.7524 (mmt180) cc_final: 0.7273 (mpp-170) REVERT: D 399 ARG cc_start: 0.7524 (mmt180) cc_final: 0.7274 (mpp-170) outliers start: 16 outliers final: 4 residues processed: 136 average time/residue: 2.9718 time to fit residues: 436.9783 Evaluate side-chains 124 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 113 ASN D 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12284 Z= 0.227 Angle : 0.447 4.444 16668 Z= 0.244 Chirality : 0.033 0.148 2004 Planarity : 0.003 0.033 2032 Dihedral : 4.334 55.270 1760 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.53 % Allowed : 10.09 % Favored : 88.38 % 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: 2.80 (0.21), residues: 1504 helix: 2.43 (0.14), residues: 1244 sheet: 0.76 (0.75), residues: 48 loop : -1.62 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 154 HIS 0.001 0.000 HIS B 349 PHE 0.011 0.002 PHE B 11 TYR 0.009 0.001 TYR D 56 ARG 0.004 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7733 (tp-100) cc_final: 0.6917 (tm-30) REVERT: A 272 LYS cc_start: 0.7406 (tppt) cc_final: 0.6741 (tmmt) REVERT: A 354 GLU cc_start: 0.8222 (mm-30) cc_final: 0.8001 (mm-30) REVERT: B 5 GLN cc_start: 0.7736 (tp-100) cc_final: 0.6920 (tm-30) REVERT: B 272 LYS cc_start: 0.7406 (tppt) cc_final: 0.6740 (tmmt) REVERT: B 354 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7999 (mm-30) REVERT: C 5 GLN cc_start: 0.7738 (tp-100) cc_final: 0.6921 (tm-30) REVERT: C 272 LYS cc_start: 0.7407 (tppt) cc_final: 0.6741 (tmmt) REVERT: C 354 GLU cc_start: 0.8223 (mm-30) cc_final: 0.8000 (mm-30) REVERT: D 5 GLN cc_start: 0.7734 (tp-100) cc_final: 0.6916 (tm-30) REVERT: D 272 LYS cc_start: 0.7407 (tppt) cc_final: 0.6742 (tmmt) REVERT: D 354 GLU cc_start: 0.8223 (mm-30) cc_final: 0.8001 (mm-30) outliers start: 20 outliers final: 8 residues processed: 169 average time/residue: 2.4503 time to fit residues: 454.6056 Evaluate side-chains 152 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 113 ASN D 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12284 Z= 0.288 Angle : 0.466 4.390 16668 Z= 0.254 Chirality : 0.035 0.142 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.568 56.754 1760 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.53 % Allowed : 10.09 % Favored : 88.38 % 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: 2.67 (0.21), residues: 1504 helix: 2.36 (0.14), residues: 1240 sheet: 0.59 (0.81), residues: 48 loop : -1.66 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 154 HIS 0.003 0.001 HIS B 349 PHE 0.011 0.002 PHE D 11 TYR 0.010 0.001 TYR C 56 ARG 0.001 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8106 (tp-100) cc_final: 0.7155 (tm-30) REVERT: A 272 LYS cc_start: 0.7610 (tppt) cc_final: 0.6891 (tmmt) REVERT: A 424 ARG cc_start: 0.6383 (mpt90) cc_final: 0.6133 (ttt90) REVERT: B 5 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7153 (tm-30) REVERT: B 272 LYS cc_start: 0.7609 (tppt) cc_final: 0.6891 (tmmt) REVERT: B 424 ARG cc_start: 0.6382 (mpt90) cc_final: 0.6133 (ttt90) REVERT: C 5 GLN cc_start: 0.8105 (tp-100) cc_final: 0.7154 (tm-30) REVERT: C 272 LYS cc_start: 0.7610 (tppt) cc_final: 0.6891 (tmmt) REVERT: C 424 ARG cc_start: 0.6380 (mpt90) cc_final: 0.6131 (ttt90) REVERT: D 5 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7155 (tm-30) REVERT: D 272 LYS cc_start: 0.7610 (tppt) cc_final: 0.6891 (tmmt) REVERT: D 424 ARG cc_start: 0.6380 (mpt90) cc_final: 0.6130 (ttt90) outliers start: 20 outliers final: 9 residues processed: 172 average time/residue: 2.4503 time to fit residues: 463.0133 Evaluate side-chains 157 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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: 0.7776 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12284 Z= 0.187 Angle : 0.407 4.088 16668 Z= 0.223 Chirality : 0.033 0.133 2004 Planarity : 0.003 0.034 2032 Dihedral : 4.331 57.994 1760 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.22 % Allowed : 11.31 % Favored : 87.46 % 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: 3.08 (0.21), residues: 1504 helix: 2.65 (0.14), residues: 1240 sheet: 0.49 (0.78), residues: 48 loop : -1.50 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 154 HIS 0.001 0.000 HIS B 337 PHE 0.011 0.001 PHE C 11 TYR 0.005 0.001 TYR D 56 ARG 0.001 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 160 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8107 (tp-100) cc_final: 0.7107 (tm-30) REVERT: A 272 LYS cc_start: 0.7690 (tppt) cc_final: 0.6989 (tmmt) REVERT: A 391 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.6343 (t0) REVERT: B 5 GLN cc_start: 0.8137 (tp-100) cc_final: 0.7150 (tm-30) REVERT: B 272 LYS cc_start: 0.7691 (tppt) cc_final: 0.6988 (tmmt) REVERT: C 5 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7151 (tm-30) REVERT: C 272 LYS cc_start: 0.7690 (tppt) cc_final: 0.6989 (tmmt) REVERT: C 391 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.6343 (t0) REVERT: D 5 GLN cc_start: 0.8137 (tp-100) cc_final: 0.7149 (tm-30) REVERT: D 272 LYS cc_start: 0.7691 (tppt) cc_final: 0.6989 (tmmt) REVERT: D 391 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.6344 (t0) outliers start: 16 outliers final: 4 residues processed: 168 average time/residue: 2.7801 time to fit residues: 507.9262 Evaluate side-chains 159 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 113 ASN D 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12284 Z= 0.240 Angle : 0.432 4.226 16668 Z= 0.237 Chirality : 0.034 0.138 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.492 58.659 1760 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.45 % Allowed : 12.46 % Favored : 86.09 % 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: 2.99 (0.21), residues: 1504 helix: 2.59 (0.14), residues: 1240 sheet: 0.67 (0.79), residues: 48 loop : -1.55 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 174 HIS 0.002 0.001 HIS D 306 PHE 0.010 0.001 PHE C 11 TYR 0.007 0.001 TYR A 56 ARG 0.002 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8276 (tp-100) cc_final: 0.7283 (tm-30) REVERT: A 272 LYS cc_start: 0.7727 (tppt) cc_final: 0.7024 (tmmt) REVERT: A 391 ASP cc_start: 0.6408 (OUTLIER) cc_final: 0.6142 (t0) REVERT: B 5 GLN cc_start: 0.8279 (tp-100) cc_final: 0.7285 (tm-30) REVERT: B 272 LYS cc_start: 0.7727 (tppt) cc_final: 0.7022 (tmmt) REVERT: C 5 GLN cc_start: 0.8281 (tp-100) cc_final: 0.7288 (tm-30) REVERT: C 272 LYS cc_start: 0.7728 (tppt) cc_final: 0.7025 (tmmt) REVERT: C 391 ASP cc_start: 0.6408 (OUTLIER) cc_final: 0.6141 (t0) REVERT: D 5 GLN cc_start: 0.8279 (tp-100) cc_final: 0.7286 (tm-30) REVERT: D 272 LYS cc_start: 0.7729 (tppt) cc_final: 0.7025 (tmmt) REVERT: D 391 ASP cc_start: 0.6356 (OUTLIER) cc_final: 0.6102 (t0) outliers start: 19 outliers final: 4 residues processed: 168 average time/residue: 2.4124 time to fit residues: 446.4019 Evaluate side-chains 159 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 391 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.7784 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12284 Z= 0.210 Angle : 0.416 4.169 16668 Z= 0.228 Chirality : 0.033 0.135 2004 Planarity : 0.003 0.034 2032 Dihedral : 3.411 15.241 1752 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.84 % Allowed : 13.00 % Favored : 86.16 % 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: 3.11 (0.21), residues: 1504 helix: 2.66 (0.14), residues: 1240 sheet: 0.67 (0.78), residues: 48 loop : -1.40 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 174 HIS 0.002 0.000 HIS A 337 PHE 0.010 0.001 PHE B 11 TYR 0.005 0.001 TYR D 122 ARG 0.001 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8296 (tp-100) cc_final: 0.7288 (tm-30) REVERT: A 272 LYS cc_start: 0.7736 (tppt) cc_final: 0.7027 (tmmt) REVERT: A 391 ASP cc_start: 0.6372 (OUTLIER) cc_final: 0.6122 (t0) REVERT: B 5 GLN cc_start: 0.8299 (tp-100) cc_final: 0.7291 (tm-30) REVERT: B 272 LYS cc_start: 0.7710 (tppt) cc_final: 0.7035 (tmmt) REVERT: C 5 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7291 (tm-30) REVERT: C 272 LYS cc_start: 0.7736 (tppt) cc_final: 0.7026 (tmmt) REVERT: C 391 ASP cc_start: 0.6373 (OUTLIER) cc_final: 0.6117 (t0) REVERT: D 5 GLN cc_start: 0.8296 (tp-100) cc_final: 0.7288 (tm-30) REVERT: D 272 LYS cc_start: 0.7736 (tppt) cc_final: 0.7026 (tmmt) REVERT: D 391 ASP cc_start: 0.6378 (OUTLIER) cc_final: 0.6124 (t0) outliers start: 11 outliers final: 0 residues processed: 160 average time/residue: 2.5077 time to fit residues: 441.1119 Evaluate side-chains 149 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 146 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain D residue 391 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12284 Z= 0.203 Angle : 0.413 4.115 16668 Z= 0.226 Chirality : 0.033 0.136 2004 Planarity : 0.003 0.033 2032 Dihedral : 3.372 14.881 1752 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.22 % Allowed : 13.15 % Favored : 85.63 % 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: 3.19 (0.21), residues: 1504 helix: 2.71 (0.14), residues: 1240 sheet: 0.56 (0.78), residues: 48 loop : -1.34 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 174 HIS 0.002 0.000 HIS D 337 PHE 0.010 0.001 PHE B 11 TYR 0.005 0.001 TYR B 326 ARG 0.001 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8318 (tp-100) cc_final: 0.7327 (tm-30) REVERT: A 272 LYS cc_start: 0.7738 (tppt) cc_final: 0.7035 (tmmt) REVERT: A 391 ASP cc_start: 0.6505 (OUTLIER) cc_final: 0.6199 (t0) REVERT: B 5 GLN cc_start: 0.8319 (tp-100) cc_final: 0.7330 (tm-30) REVERT: B 272 LYS cc_start: 0.7714 (tppt) cc_final: 0.7049 (tmmt) REVERT: C 5 GLN cc_start: 0.8319 (tp-100) cc_final: 0.7330 (tm-30) REVERT: C 272 LYS cc_start: 0.7721 (tppt) cc_final: 0.7051 (tmmt) REVERT: C 391 ASP cc_start: 0.6506 (OUTLIER) cc_final: 0.6193 (t0) REVERT: D 5 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7326 (tm-30) REVERT: D 272 LYS cc_start: 0.7720 (tppt) cc_final: 0.7050 (tmmt) REVERT: D 391 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.6194 (t0) outliers start: 16 outliers final: 4 residues processed: 159 average time/residue: 2.7118 time to fit residues: 471.0617 Evaluate side-chains 162 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 391 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN B 421 GLN C 113 ASN D 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12284 Z= 0.244 Angle : 0.435 4.235 16668 Z= 0.238 Chirality : 0.034 0.136 2004 Planarity : 0.003 0.034 2032 Dihedral : 3.528 17.947 1752 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.22 % Allowed : 13.38 % Favored : 85.40 % 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: 3.01 (0.21), residues: 1504 helix: 2.56 (0.14), residues: 1244 sheet: 0.52 (0.79), residues: 48 loop : -1.30 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.002 0.001 HIS D 306 PHE 0.010 0.002 PHE A 11 TYR 0.006 0.001 TYR D 56 ARG 0.003 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7332 (tm-30) REVERT: A 272 LYS cc_start: 0.7784 (tppt) cc_final: 0.7067 (tmmt) REVERT: A 391 ASP cc_start: 0.6457 (OUTLIER) cc_final: 0.6160 (t0) REVERT: B 5 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7333 (tm-30) REVERT: B 272 LYS cc_start: 0.7763 (tppt) cc_final: 0.7077 (tmmt) REVERT: C 5 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7332 (tm-30) REVERT: C 272 LYS cc_start: 0.7788 (tppt) cc_final: 0.7066 (tmmt) REVERT: D 5 GLN cc_start: 0.8320 (tp-100) cc_final: 0.7332 (tm-30) REVERT: D 272 LYS cc_start: 0.7786 (tppt) cc_final: 0.7065 (tmmt) REVERT: D 391 ASP cc_start: 0.6451 (OUTLIER) cc_final: 0.6157 (t0) outliers start: 16 outliers final: 7 residues processed: 163 average time/residue: 2.6868 time to fit residues: 476.5462 Evaluate side-chains 163 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 391 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 123 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12284 Z= 0.155 Angle : 0.406 4.020 16668 Z= 0.221 Chirality : 0.033 0.138 2004 Planarity : 0.003 0.032 2032 Dihedral : 3.258 12.376 1752 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.23 % Allowed : 13.76 % Favored : 86.01 % 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: 3.39 (0.21), residues: 1504 helix: 2.85 (0.14), residues: 1240 sheet: 0.57 (0.77), residues: 48 loop : -1.27 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 174 HIS 0.001 0.000 HIS D 337 PHE 0.010 0.001 PHE B 11 TYR 0.004 0.001 TYR B 326 ARG 0.005 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7315 (tm-30) REVERT: A 25 VAL cc_start: 0.7853 (p) cc_final: 0.7619 (p) REVERT: A 272 LYS cc_start: 0.7775 (tppt) cc_final: 0.7091 (tmmt) REVERT: A 391 ASP cc_start: 0.6685 (OUTLIER) cc_final: 0.6358 (t0) REVERT: B 5 GLN cc_start: 0.8296 (tp-100) cc_final: 0.7320 (tm-30) REVERT: B 272 LYS cc_start: 0.7747 (tppt) cc_final: 0.7071 (tmmt) REVERT: C 5 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7320 (tm-30) REVERT: C 272 LYS cc_start: 0.7778 (tppt) cc_final: 0.7061 (tmmt) REVERT: C 391 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.6359 (t0) REVERT: D 5 GLN cc_start: 0.8292 (tp-100) cc_final: 0.7315 (tm-30) REVERT: D 272 LYS cc_start: 0.7774 (tppt) cc_final: 0.7090 (tmmt) REVERT: D 391 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.6357 (t0) outliers start: 3 outliers final: 0 residues processed: 163 average time/residue: 2.7229 time to fit residues: 482.3789 Evaluate side-chains 158 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain D residue 391 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.7767 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12284 Z= 0.173 Angle : 0.405 4.083 16668 Z= 0.222 Chirality : 0.033 0.133 2004 Planarity : 0.003 0.033 2032 Dihedral : 3.221 12.475 1752 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.54 % Allowed : 13.46 % Favored : 86.01 % 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: 3.39 (0.21), residues: 1504 helix: 2.83 (0.14), residues: 1244 sheet: 0.57 (0.77), residues: 48 loop : -1.20 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.002 0.000 HIS A 337 PHE 0.010 0.001 PHE C 11 TYR 0.005 0.001 TYR B 326 ARG 0.004 0.000 ARG A 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8300 (tp-100) cc_final: 0.7325 (tm-30) REVERT: A 272 LYS cc_start: 0.7761 (tppt) cc_final: 0.7085 (tmmt) REVERT: A 391 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6384 (t0) REVERT: B 5 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7327 (tm-30) REVERT: B 272 LYS cc_start: 0.7751 (tppt) cc_final: 0.7075 (tmmt) REVERT: C 5 GLN cc_start: 0.8294 (tp-100) cc_final: 0.7324 (tm-30) REVERT: C 272 LYS cc_start: 0.7762 (tppt) cc_final: 0.7086 (tmmt) REVERT: C 391 ASP cc_start: 0.6710 (OUTLIER) cc_final: 0.6361 (t0) REVERT: D 5 GLN cc_start: 0.8300 (tp-100) cc_final: 0.7326 (tm-30) REVERT: D 272 LYS cc_start: 0.7759 (tppt) cc_final: 0.7084 (tmmt) REVERT: D 391 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6382 (t0) outliers start: 7 outliers final: 4 residues processed: 159 average time/residue: 2.7951 time to fit residues: 483.8524 Evaluate side-chains 161 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 391 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.138603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109305 restraints weight = 37766.754| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.64 r_work: 0.3054 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12284 Z= 0.172 Angle : 0.401 4.119 16668 Z= 0.220 Chirality : 0.033 0.135 2004 Planarity : 0.003 0.033 2032 Dihedral : 3.220 12.505 1752 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.92 % Allowed : 13.15 % Favored : 85.93 % 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: 3.42 (0.21), residues: 1504 helix: 2.85 (0.14), residues: 1244 sheet: 0.56 (0.76), residues: 48 loop : -1.18 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 174 HIS 0.001 0.000 HIS D 337 PHE 0.010 0.001 PHE D 11 TYR 0.005 0.001 TYR B 56 ARG 0.004 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8350.92 seconds wall clock time: 146 minutes 35.83 seconds (8795.83 seconds total)