Starting phenix.real_space_refine on Sat Apr 13 02:42:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmi_36422/04_2024/8jmi_36422_neut_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmi_36422/04_2024/8jmi_36422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmi_36422/04_2024/8jmi_36422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmi_36422/04_2024/8jmi_36422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmi_36422/04_2024/8jmi_36422_neut_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmi_36422/04_2024/8jmi_36422_neut_trim.pdb" } resolution = 2.6 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= 0.007 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 96 5.16 5 C 8872 2.51 5 N 2212 2.21 5 O 2264 1.98 5 H 13812 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 264": "OD1" <-> "OD2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 27256 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "B" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "C" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "D" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.99, per 1000 atoms: 0.48 Number of scatterers: 27256 At special positions: 0 Unit cell: (116.25, 116.25, 103.23, 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 96 16.00 O 2264 8.00 N 2212 7.00 C 8872 6.00 H 13812 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 Links applied ALPHA1-4 " BGC E 1 " - " GLC E 2 " " BGC F 1 " - " GLC F 2 " " BGC G 1 " - " GLC G 2 " " BGC H 1 " - " GLC H 2 " Time building additional restraints: 23.01 Conformation dependent library (CDL) restraints added in 2.3 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 58 through 73 Proline residue: A 65 - end of helix removed outlier: 3.703A pdb=" N VAL A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 95 through 123 Processing helix chain 'A' and resid 125 through 164 removed outlier: 4.015A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 177 through 214 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 242 through 287 removed outlier: 4.479A pdb=" N ASP A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 339 removed outlier: 3.570A pdb=" N PHE A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 387 removed outlier: 3.901A pdb=" N ILE A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 443 through 450 removed outlier: 3.822A pdb=" N GLY A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 73 Proline residue: B 65 - end of helix removed outlier: 3.704A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 95 through 123 Processing helix chain 'B' and resid 125 through 164 removed outlier: 4.030A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLY B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 177 through 214 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 242 through 287 removed outlier: 4.479A pdb=" N ASP B 264 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 339 removed outlier: 3.570A pdb=" N PHE B 298 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N SER B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 387 removed outlier: 3.900A pdb=" N ILE B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 443 through 450 removed outlier: 3.821A pdb=" N GLY B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 73 Proline residue: C 65 - end of helix removed outlier: 3.703A pdb=" N VAL C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 95 through 123 Processing helix chain 'C' and resid 125 through 164 removed outlier: 4.016A pdb=" N VAL C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY C 131 " --> pdb=" O LYS C 127 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 165 through 168 Processing helix chain 'C' and resid 177 through 214 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 242 through 287 removed outlier: 4.478A pdb=" N ASP C 264 " --> pdb=" O TRP C 260 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 339 removed outlier: 3.573A pdb=" N PHE C 298 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N SER C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 387 removed outlier: 3.893A pdb=" N ILE C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 421 through 440 Processing helix chain 'C' and resid 443 through 450 removed outlier: 3.822A pdb=" N GLY C 450 " --> pdb=" O ASN C 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 73 Proline residue: D 65 - end of helix removed outlier: 3.704A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 95 through 123 Processing helix chain 'D' and resid 125 through 164 removed outlier: 4.030A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLY D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 177 through 214 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 242 through 287 removed outlier: 4.478A pdb=" N ASP D 264 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 339 removed outlier: 3.568A pdb=" N PHE D 298 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 387 removed outlier: 3.895A pdb=" N ILE D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 421 through 440 Processing helix chain 'D' and resid 443 through 450 removed outlier: 3.822A pdb=" N GLY D 450 " --> pdb=" O ASN D 446 " (cutoff:3.500A) 988 hydrogen bonds defined for protein. 2928 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: 10.02 Time building geometry restraints manager: 23.74 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: 13772 1.03 - 1.23: 41 1.23 - 1.42: 5787 1.42 - 1.61: 7840 1.61 - 1.81: 152 Bond restraints: 27592 Sorted by residual: bond pdb=" C3 BGC H 1 " pdb=" O3 BGC H 1 " ideal model delta sigma weight residual 1.408 1.492 -0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C3 BGC E 1 " pdb=" O3 BGC E 1 " ideal model delta sigma weight residual 1.408 1.491 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C3 BGC F 1 " pdb=" O3 BGC F 1 " ideal model delta sigma weight residual 1.408 1.491 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C3 BGC G 1 " pdb=" O3 BGC G 1 " ideal model delta sigma weight residual 1.408 1.490 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 GLC G 2 " pdb=" O5 GLC G 2 " ideal model delta sigma weight residual 1.402 1.474 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 27587 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.22: 778 107.22 - 113.91: 32068 113.91 - 120.59: 10511 120.59 - 127.28: 6334 127.28 - 133.97: 133 Bond angle restraints: 49824 Sorted by residual: angle pdb=" C TYR D 262 " pdb=" N MET D 263 " pdb=" CA MET D 263 " ideal model delta sigma weight residual 120.44 118.00 2.44 1.30e+00 5.92e-01 3.51e+00 angle pdb=" C TRP C 152 " pdb=" CA TRP C 152 " pdb=" CB TRP C 152 " ideal model delta sigma weight residual 112.76 109.33 3.43 1.86e+00 2.89e-01 3.40e+00 angle pdb=" C TYR B 262 " pdb=" N MET B 263 " pdb=" CA MET B 263 " ideal model delta sigma weight residual 120.44 118.05 2.39 1.30e+00 5.92e-01 3.39e+00 angle pdb=" C TRP B 152 " pdb=" CA TRP B 152 " pdb=" CB TRP B 152 " ideal model delta sigma weight residual 112.76 109.34 3.42 1.86e+00 2.89e-01 3.39e+00 angle pdb=" C TRP A 152 " pdb=" CA TRP A 152 " pdb=" CB TRP A 152 " ideal model delta sigma weight residual 112.76 109.34 3.42 1.86e+00 2.89e-01 3.38e+00 ... (remaining 49819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 11648 17.55 - 35.11: 1021 35.11 - 52.66: 322 52.66 - 70.21: 80 70.21 - 87.76: 9 Dihedral angle restraints: 13080 sinusoidal: 7076 harmonic: 6004 Sorted by residual: dihedral pdb=" CB MET D 98 " pdb=" CG MET D 98 " pdb=" SD MET D 98 " pdb=" CE MET D 98 " ideal model delta sinusoidal sigma weight residual -180.00 -120.50 -59.50 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET B 98 " pdb=" CG MET B 98 " pdb=" SD MET B 98 " pdb=" CE MET B 98 " ideal model delta sinusoidal sigma weight residual -180.00 -120.54 -59.46 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB ARG A 286 " pdb=" CG ARG A 286 " pdb=" CD ARG A 286 " pdb=" NE ARG A 286 " ideal model delta sinusoidal sigma weight residual -60.00 -119.46 59.46 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 13077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1508 0.027 - 0.055: 381 0.055 - 0.082: 214 0.082 - 0.109: 62 0.109 - 0.137: 15 Chirality restraints: 2180 Sorted by residual: chirality pdb=" C1 GLC E 2 " pdb=" O4 BGC E 1 " pdb=" C2 GLC E 2 " pdb=" O5 GLC E 2 " both_signs ideal model delta sigma weight residual False 2.40 2.38 0.02 2.00e-02 2.50e+03 1.21e+00 chirality pdb=" C1 GLC G 2 " pdb=" O4 BGC G 1 " pdb=" C2 GLC G 2 " pdb=" O5 GLC G 2 " both_signs ideal model delta sigma weight residual False 2.40 2.38 0.02 2.00e-02 2.50e+03 1.11e+00 chirality pdb=" CA ILE B 218 " pdb=" N ILE B 218 " pdb=" C ILE B 218 " pdb=" CB ILE B 218 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 2177 not shown) Planarity restraints: 3836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 142 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.08e+00 pdb=" C TYR B 142 " 0.030 2.00e-02 2.50e+03 pdb=" O TYR B 142 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL B 143 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 142 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C TYR C 142 " -0.030 2.00e-02 2.50e+03 pdb=" O TYR C 142 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 143 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 142 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C TYR D 142 " 0.030 2.00e-02 2.50e+03 pdb=" O TYR D 142 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL D 143 " -0.010 2.00e-02 2.50e+03 ... (remaining 3833 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 2173 2.21 - 2.81: 58534 2.81 - 3.41: 80688 3.41 - 4.00: 104783 4.00 - 4.60: 161104 Nonbonded interactions: 407282 Sorted by model distance: nonbonded pdb="HH22 ARG B 346 " pdb=" O GLN B 452 " model vdw 1.616 1.850 nonbonded pdb="HH22 ARG D 346 " pdb=" O GLN D 452 " model vdw 1.617 1.850 nonbonded pdb="HH22 ARG A 346 " pdb=" O GLN A 452 " model vdw 1.617 1.850 nonbonded pdb="HH22 ARG C 346 " pdb=" O GLN C 452 " model vdw 1.617 1.850 nonbonded pdb=" HH TYR A 208 " pdb=" OD1 ASN A 226 " model vdw 1.648 1.850 ... (remaining 407277 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.400 Extract box with map and model: 4.790 Check model and map are aligned: 0.440 Set scattering table: 0.220 Process input model: 88.140 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.150 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:14.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 13780 Z= 0.242 Angle : 0.538 5.497 18700 Z= 0.285 Chirality : 0.035 0.137 2180 Planarity : 0.004 0.033 2276 Dihedral : 15.877 87.765 5160 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.88 % Allowed : 16.64 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.54 (0.21), residues: 1620 helix: 2.29 (0.15), residues: 1192 sheet: None (None), residues: 0 loop : -0.03 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 152 HIS 0.001 0.000 HIS D 118 PHE 0.010 0.001 PHE B 66 TYR 0.011 0.001 TYR D 241 ARG 0.002 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 2.068 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 224 average time/residue: 3.2918 time to fit residues: 797.3011 Evaluate side-chains 215 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 398 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 ASN B 441 GLN C 441 GLN D 253 ASN D 441 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.0529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13780 Z= 0.266 Angle : 0.517 5.137 18700 Z= 0.282 Chirality : 0.037 0.130 2180 Planarity : 0.004 0.030 2276 Dihedral : 5.174 47.119 2017 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.54 % Allowed : 16.44 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.20), residues: 1620 helix: 2.75 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.15 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 355 HIS 0.002 0.001 HIS A 197 PHE 0.014 0.002 PHE D 419 TYR 0.013 0.002 TYR D 241 ARG 0.002 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 205 time to evaluate : 2.224 Fit side-chains REVERT: A 214 MET cc_start: 0.6319 (ptp) cc_final: 0.6114 (ptp) REVERT: B 214 MET cc_start: 0.6251 (ptp) cc_final: 0.6045 (ptp) REVERT: C 214 MET cc_start: 0.6314 (ptp) cc_final: 0.6111 (ptp) outliers start: 8 outliers final: 3 residues processed: 212 average time/residue: 3.4703 time to fit residues: 792.4897 Evaluate side-chains 200 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN B 441 GLN C 441 GLN D 229 GLN D 441 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13780 Z= 0.283 Angle : 0.533 5.322 18700 Z= 0.291 Chirality : 0.038 0.130 2180 Planarity : 0.004 0.033 2276 Dihedral : 3.876 18.542 1988 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.70 % Allowed : 15.49 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.88 (0.20), residues: 1620 helix: 2.70 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.31 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 355 HIS 0.003 0.001 HIS B 197 PHE 0.015 0.002 PHE D 66 TYR 0.015 0.002 TYR B 276 ARG 0.003 0.000 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 211 time to evaluate : 2.201 Fit side-chains REVERT: A 253 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8108 (m-40) REVERT: A 310 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8584 (mt-10) REVERT: B 253 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8086 (m-40) REVERT: C 253 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8085 (m-40) REVERT: D 253 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8078 (m-40) outliers start: 25 outliers final: 16 residues processed: 227 average time/residue: 3.2924 time to fit residues: 808.9119 Evaluate side-chains 215 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 195 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 398 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 229 GLN B 441 GLN C 229 GLN C 441 GLN D 229 GLN D 441 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13780 Z= 0.225 Angle : 0.506 5.178 18700 Z= 0.274 Chirality : 0.036 0.132 2180 Planarity : 0.004 0.033 2276 Dihedral : 3.810 18.099 1988 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.15 % Allowed : 16.03 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.96 (0.20), residues: 1620 helix: 2.77 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.33 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 355 HIS 0.002 0.001 HIS B 197 PHE 0.013 0.002 PHE A 419 TYR 0.014 0.002 TYR B 276 ARG 0.001 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 2.137 Fit side-chains REVERT: A 253 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.8042 (m-40) REVERT: B 253 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8075 (m-40) REVERT: C 253 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.8041 (m-40) REVERT: D 253 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8101 (m-40) outliers start: 17 outliers final: 8 residues processed: 211 average time/residue: 3.3676 time to fit residues: 767.7874 Evaluate side-chains 207 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 229 GLN C 229 GLN D 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13780 Z= 0.306 Angle : 0.539 5.439 18700 Z= 0.294 Chirality : 0.038 0.127 2180 Planarity : 0.004 0.035 2276 Dihedral : 3.973 19.975 1988 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.56 % Allowed : 15.29 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.83 (0.20), residues: 1620 helix: 2.63 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.41 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 355 HIS 0.003 0.001 HIS B 197 PHE 0.016 0.002 PHE A 419 TYR 0.015 0.002 TYR B 276 ARG 0.003 0.000 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 2.276 Fit side-chains REVERT: A 249 ILE cc_start: 0.8438 (mm) cc_final: 0.8152 (mm) REVERT: A 253 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8110 (m-40) REVERT: A 310 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8590 (mt-10) REVERT: B 253 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8082 (m-40) REVERT: C 249 ILE cc_start: 0.8460 (mm) cc_final: 0.8175 (mm) REVERT: C 253 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8102 (m-40) REVERT: D 253 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8085 (m-40) outliers start: 23 outliers final: 13 residues processed: 214 average time/residue: 3.3844 time to fit residues: 782.7793 Evaluate side-chains 214 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13780 Z= 0.185 Angle : 0.494 5.911 18700 Z= 0.266 Chirality : 0.036 0.133 2180 Planarity : 0.004 0.034 2276 Dihedral : 3.775 16.936 1988 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.90 % Allowed : 14.67 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.91 (0.20), residues: 1620 helix: 2.71 (0.14), residues: 1192 sheet: None (None), residues: 0 loop : -0.41 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 355 HIS 0.002 0.001 HIS D 197 PHE 0.012 0.001 PHE C 66 TYR 0.013 0.002 TYR A 241 ARG 0.002 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 200 time to evaluate : 2.075 Fit side-chains REVERT: A 249 ILE cc_start: 0.8461 (mm) cc_final: 0.8050 (mm) REVERT: A 253 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.8031 (m-40) REVERT: B 253 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8108 (m-40) REVERT: C 249 ILE cc_start: 0.8460 (mm) cc_final: 0.8068 (mm) REVERT: C 253 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8016 (m-40) REVERT: C 392 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7791 (ttp80) REVERT: D 249 ILE cc_start: 0.8437 (mm) cc_final: 0.8080 (mm) REVERT: D 253 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8072 (m-40) outliers start: 28 outliers final: 15 residues processed: 216 average time/residue: 3.3668 time to fit residues: 785.9045 Evaluate side-chains 218 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 199 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.0870 chunk 17 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- 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: 0.8148 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13780 Z= 0.208 Angle : 0.495 5.604 18700 Z= 0.268 Chirality : 0.036 0.131 2180 Planarity : 0.004 0.033 2276 Dihedral : 3.755 15.549 1988 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.43 % Allowed : 15.08 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.98 (0.20), residues: 1620 helix: 2.72 (0.14), residues: 1216 sheet: None (None), residues: 0 loop : -0.44 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 355 HIS 0.002 0.001 HIS A 197 PHE 0.013 0.001 PHE A 64 TYR 0.013 0.002 TYR D 276 ARG 0.002 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 206 time to evaluate : 2.303 Fit side-chains REVERT: A 249 ILE cc_start: 0.8467 (mm) cc_final: 0.8191 (mm) REVERT: A 253 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8060 (m-40) REVERT: A 392 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7788 (ttp80) REVERT: B 249 ILE cc_start: 0.8484 (mm) cc_final: 0.8240 (mm) REVERT: B 253 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8092 (m-40) REVERT: C 249 ILE cc_start: 0.8457 (mm) cc_final: 0.8059 (mm) REVERT: C 253 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8071 (m-40) REVERT: D 249 ILE cc_start: 0.8412 (mm) cc_final: 0.8046 (mm) REVERT: D 253 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8079 (m-40) outliers start: 21 outliers final: 15 residues processed: 221 average time/residue: 3.4112 time to fit residues: 813.0845 Evaluate side-chains 225 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 206 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.0870 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- 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: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13780 Z= 0.256 Angle : 0.514 5.886 18700 Z= 0.278 Chirality : 0.037 0.129 2180 Planarity : 0.004 0.034 2276 Dihedral : 3.849 15.875 1988 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.56 % Allowed : 15.76 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.98 (0.20), residues: 1620 helix: 2.75 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.37 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 355 HIS 0.003 0.001 HIS D 197 PHE 0.014 0.002 PHE D 64 TYR 0.014 0.002 TYR B 241 ARG 0.003 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 1.994 Fit side-chains REVERT: A 249 ILE cc_start: 0.8484 (mm) cc_final: 0.8199 (mm) REVERT: A 253 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8048 (m-40) REVERT: A 392 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7791 (ttp80) REVERT: B 249 ILE cc_start: 0.8456 (mm) cc_final: 0.8193 (mm) REVERT: B 253 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8077 (m-40) REVERT: C 249 ILE cc_start: 0.8470 (mm) cc_final: 0.8174 (mm) REVERT: C 253 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8072 (m-40) REVERT: D 249 ILE cc_start: 0.8453 (mm) cc_final: 0.8116 (mm) REVERT: D 253 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.8096 (m-40) outliers start: 23 outliers final: 16 residues processed: 221 average time/residue: 3.3755 time to fit residues: 806.6715 Evaluate side-chains 225 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 205 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 143 optimal weight: 0.0870 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- 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: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 13780 Z= 0.244 Angle : 0.516 5.926 18700 Z= 0.280 Chirality : 0.037 0.130 2180 Planarity : 0.004 0.035 2276 Dihedral : 3.843 15.410 1988 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.43 % Allowed : 15.83 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.96 (0.20), residues: 1620 helix: 2.73 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.36 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 355 HIS 0.003 0.001 HIS B 197 PHE 0.014 0.002 PHE A 419 TYR 0.014 0.002 TYR A 276 ARG 0.003 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 2.080 Fit side-chains REVERT: A 249 ILE cc_start: 0.8492 (mm) cc_final: 0.8206 (mm) REVERT: A 253 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8049 (m-40) REVERT: A 392 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7810 (ttp80) REVERT: B 249 ILE cc_start: 0.8468 (mm) cc_final: 0.8206 (mm) REVERT: B 253 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.8077 (m-40) REVERT: C 249 ILE cc_start: 0.8460 (mm) cc_final: 0.8172 (mm) REVERT: C 253 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8072 (m-40) REVERT: D 249 ILE cc_start: 0.8461 (mm) cc_final: 0.8096 (mm) REVERT: D 253 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8070 (m-40) outliers start: 21 outliers final: 15 residues processed: 220 average time/residue: 3.3882 time to fit residues: 804.8636 Evaluate side-chains 223 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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: 0.8165 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13780 Z= 0.286 Angle : 0.533 6.071 18700 Z= 0.290 Chirality : 0.038 0.128 2180 Planarity : 0.004 0.035 2276 Dihedral : 3.934 15.655 1988 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.29 % Allowed : 16.03 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.88 (0.20), residues: 1620 helix: 2.67 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.38 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 355 HIS 0.003 0.001 HIS B 197 PHE 0.015 0.002 PHE A 419 TYR 0.014 0.002 TYR B 276 ARG 0.003 0.000 ARG C 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 2.023 Fit side-chains REVERT: A 249 ILE cc_start: 0.8513 (mm) cc_final: 0.8235 (mm) REVERT: A 253 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.8133 (m-40) REVERT: A 392 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7796 (ttp80) REVERT: B 249 ILE cc_start: 0.8484 (mm) cc_final: 0.8224 (mm) REVERT: B 253 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8086 (m-40) REVERT: C 249 ILE cc_start: 0.8473 (mm) cc_final: 0.8188 (mm) REVERT: C 253 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8091 (m-40) REVERT: D 249 ILE cc_start: 0.8478 (mm) cc_final: 0.8125 (mm) REVERT: D 253 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8083 (m-40) outliers start: 19 outliers final: 14 residues processed: 213 average time/residue: 3.3191 time to fit residues: 764.7590 Evaluate side-chains 216 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.134168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.100021 restraints weight = 38360.749| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.32 r_work: 0.2945 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13780 Z= 0.243 Angle : 0.521 6.230 18700 Z= 0.283 Chirality : 0.037 0.130 2180 Planarity : 0.004 0.035 2276 Dihedral : 3.871 14.490 1988 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.49 % Allowed : 16.10 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.91 (0.20), residues: 1620 helix: 2.69 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.38 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 355 HIS 0.002 0.001 HIS B 197 PHE 0.014 0.002 PHE A 419 TYR 0.014 0.002 TYR B 276 ARG 0.003 0.000 ARG A 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11718.29 seconds wall clock time: 208 minutes 34.53 seconds (12514.53 seconds total)