Starting phenix.real_space_refine on Wed Nov 15 12:04:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/11_2023/6v6d_21071.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/11_2023/6v6d_21071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/11_2023/6v6d_21071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/11_2023/6v6d_21071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/11_2023/6v6d_21071.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/11_2023/6v6d_21071.pdb" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7924 2.51 5 N 1778 2.21 5 O 1974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ASP 242": "OD1" <-> "OD2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B ASP 242": "OD1" <-> "OD2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ASP 327": "OD1" <-> "OD2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ASP 242": "OD1" <-> "OD2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ASP 327": "OD1" <-> "OD2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ASP 327": "OD1" <-> "OD2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ASP 242": "OD1" <-> "OD2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E ARG 300": "NH1" <-> "NH2" Residue "E ASP 327": "OD1" <-> "OD2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "F ASP 242": "OD1" <-> "OD2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F ARG 300": "NH1" <-> "NH2" Residue "F ASP 327": "OD1" <-> "OD2" Residue "F GLU 336": "OE1" <-> "OE2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G ARG 217": "NH1" <-> "NH2" Residue "G ASP 242": "OD1" <-> "OD2" Residue "G ARG 254": "NH1" <-> "NH2" Residue "G ARG 300": "NH1" <-> "NH2" Residue "G ASP 327": "OD1" <-> "OD2" Residue "G GLU 336": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 11739 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Chain: "B" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Chain: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Chain: "D" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Chain: "E" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Chain: "F" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Chain: "G" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Time building chain proxies: 6.53, per 1000 atoms: 0.56 Number of scatterers: 11739 At special positions: 0 Unit cell: (110, 110, 94.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1974 8.00 N 1778 7.00 C 7924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 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: 4.66 Conformation dependent library (CDL) restraints added in 2.2 seconds 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 7 sheets defined 71.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.800A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 108 through 139 Proline residue: A 123 - end of helix removed outlier: 3.754A pdb=" N PHE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 208 through 237 removed outlier: 3.574A pdb=" N LEU A 237 " --> pdb=" O TYR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.458A pdb=" N ASN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.716A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.800A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 108 through 139 Proline residue: B 123 - end of helix removed outlier: 3.754A pdb=" N PHE B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Proline residue: B 133 - end of helix Processing helix chain 'B' and resid 208 through 237 removed outlier: 3.575A pdb=" N LEU B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 4.459A pdb=" N ASN B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Proline residue: B 289 - end of helix removed outlier: 3.716A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.799A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 86 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 108 through 139 Proline residue: C 123 - end of helix removed outlier: 3.754A pdb=" N PHE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 130 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Proline residue: C 133 - end of helix Processing helix chain 'C' and resid 208 through 237 removed outlier: 3.574A pdb=" N LEU C 237 " --> pdb=" O TYR C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.457A pdb=" N ASN C 255 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 removed outlier: 3.646A pdb=" N LEU C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Proline residue: C 289 - end of helix removed outlier: 3.716A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.800A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 86 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 108 through 139 Proline residue: D 123 - end of helix removed outlier: 3.754A pdb=" N PHE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 130 " --> pdb=" O PHE D 126 " (cutoff:3.500A) Proline residue: D 133 - end of helix Processing helix chain 'D' and resid 208 through 237 removed outlier: 3.575A pdb=" N LEU D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 4.458A pdb=" N ASN D 255 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Proline residue: D 289 - end of helix removed outlier: 3.716A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.800A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 86 Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 108 through 139 Proline residue: E 123 - end of helix removed outlier: 3.754A pdb=" N PHE E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 130 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Proline residue: E 133 - end of helix Processing helix chain 'E' and resid 208 through 237 removed outlier: 3.574A pdb=" N LEU E 237 " --> pdb=" O TYR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 255 removed outlier: 4.458A pdb=" N ASN E 255 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Proline residue: E 289 - end of helix removed outlier: 3.717A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.800A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 86 Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 108 through 139 Proline residue: F 123 - end of helix removed outlier: 3.754A pdb=" N PHE F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 130 " --> pdb=" O PHE F 126 " (cutoff:3.500A) Proline residue: F 133 - end of helix Processing helix chain 'F' and resid 208 through 237 removed outlier: 3.574A pdb=" N LEU F 237 " --> pdb=" O TYR F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 removed outlier: 4.459A pdb=" N ASN F 255 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Proline residue: F 289 - end of helix removed outlier: 3.716A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 336 removed outlier: 3.726A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.800A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 86 Processing helix chain 'G' and resid 103 through 108 Processing helix chain 'G' and resid 108 through 139 Proline residue: G 123 - end of helix removed outlier: 3.754A pdb=" N PHE G 129 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA G 130 " --> pdb=" O PHE G 126 " (cutoff:3.500A) Proline residue: G 133 - end of helix Processing helix chain 'G' and resid 208 through 237 removed outlier: 3.575A pdb=" N LEU G 237 " --> pdb=" O TYR G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 removed outlier: 4.458A pdb=" N ASN G 255 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU G 286 " --> pdb=" O VAL G 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G 288 " --> pdb=" O TYR G 284 " (cutoff:3.500A) Proline residue: G 289 - end of helix removed outlier: 3.717A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 728 hydrogen bonds defined for protein. 2121 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: 3.18 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3374 1.34 - 1.46: 2809 1.46 - 1.58: 5787 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 12040 Sorted by residual: bond pdb=" N ILE E 41 " pdb=" CA ILE E 41 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.21e-02 6.83e+03 9.11e+00 bond pdb=" N ILE B 41 " pdb=" CA ILE B 41 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.21e-02 6.83e+03 9.03e+00 bond pdb=" N ILE F 41 " pdb=" CA ILE F 41 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.21e-02 6.83e+03 9.03e+00 bond pdb=" N ILE D 41 " pdb=" CA ILE D 41 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.21e-02 6.83e+03 8.88e+00 bond pdb=" N ILE G 41 " pdb=" CA ILE G 41 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.21e-02 6.83e+03 8.85e+00 ... (remaining 12035 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.21: 343 107.21 - 113.91: 6878 113.91 - 120.60: 5162 120.60 - 127.30: 3899 127.30 - 134.00: 140 Bond angle restraints: 16422 Sorted by residual: angle pdb=" N GLY C 61 " pdb=" CA GLY C 61 " pdb=" C GLY C 61 " ideal model delta sigma weight residual 112.73 124.86 -12.13 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N GLY G 61 " pdb=" CA GLY G 61 " pdb=" C GLY G 61 " ideal model delta sigma weight residual 112.73 124.86 -12.13 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N GLY E 61 " pdb=" CA GLY E 61 " pdb=" C GLY E 61 " ideal model delta sigma weight residual 112.73 124.85 -12.12 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N GLY F 61 " pdb=" CA GLY F 61 " pdb=" C GLY F 61 " ideal model delta sigma weight residual 112.73 124.83 -12.10 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N GLY D 61 " pdb=" CA GLY D 61 " pdb=" C GLY D 61 " ideal model delta sigma weight residual 112.73 124.83 -12.10 1.20e+00 6.94e-01 1.02e+02 ... (remaining 16417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 6405 17.09 - 34.18: 581 34.18 - 51.27: 77 51.27 - 68.36: 7 68.36 - 85.45: 7 Dihedral angle restraints: 7077 sinusoidal: 2709 harmonic: 4368 Sorted by residual: dihedral pdb=" C ASP B 35 " pdb=" N ASP B 35 " pdb=" CA ASP B 35 " pdb=" CB ASP B 35 " ideal model delta harmonic sigma weight residual -122.60 -131.85 9.25 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C ASP F 35 " pdb=" N ASP F 35 " pdb=" CA ASP F 35 " pdb=" CB ASP F 35 " ideal model delta harmonic sigma weight residual -122.60 -131.84 9.24 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C ASP A 35 " pdb=" N ASP A 35 " pdb=" CA ASP A 35 " pdb=" CB ASP A 35 " ideal model delta harmonic sigma weight residual -122.60 -131.82 9.22 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 7074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1559 0.057 - 0.114: 308 0.114 - 0.171: 107 0.171 - 0.229: 7 0.229 - 0.286: 14 Chirality restraints: 1995 Sorted by residual: chirality pdb=" CA LEU D 32 " pdb=" N LEU D 32 " pdb=" C LEU D 32 " pdb=" CB LEU D 32 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA LEU C 32 " pdb=" N LEU C 32 " pdb=" C LEU C 32 " pdb=" CB LEU C 32 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA LEU B 32 " pdb=" N LEU B 32 " pdb=" C LEU B 32 " pdb=" CB LEU B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1992 not shown) Planarity restraints: 1953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 132 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.02e+00 pdb=" N PRO E 133 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO E 133 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 133 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 132 " 0.041 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO G 133 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 133 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 133 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 132 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO F 133 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO F 133 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 133 " -0.035 5.00e-02 4.00e+02 ... (remaining 1950 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3326 2.80 - 3.33: 11144 3.33 - 3.85: 18671 3.85 - 4.38: 20454 4.38 - 4.90: 36759 Nonbonded interactions: 90354 Sorted by model distance: nonbonded pdb=" OH TYR E 111 " pdb=" O LEU F 52 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR D 111 " pdb=" O LEU E 52 " model vdw 2.307 2.440 nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.323 2.440 nonbonded pdb=" OH TYR F 111 " pdb=" O LEU G 52 " model vdw 2.325 2.440 nonbonded pdb=" O SER D 241 " pdb=" OG SER D 241 " model vdw 2.350 2.440 ... (remaining 90349 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' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 group one per residue 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: 0.700 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: 0.010 Extract box with map and model: 3.540 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 32.550 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 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 0.053 12040 Z= 0.348 Angle : 0.948 12.128 16422 Z= 0.571 Chirality : 0.058 0.286 1995 Planarity : 0.007 0.061 1953 Dihedral : 13.309 85.452 4179 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % 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: -2.17 (0.20), residues: 1407 helix: -0.43 (0.15), residues: 1001 sheet: -2.75 (0.55), residues: 84 loop : -4.03 (0.18), residues: 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.469 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 outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2866 time to fit residues: 133.9322 Evaluate side-chains 248 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 332 ASN B 106 HIS B 332 ASN C 106 HIS D 106 HIS ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS G 106 HIS ** G 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12040 Z= 0.213 Angle : 0.645 9.288 16422 Z= 0.318 Chirality : 0.040 0.135 1995 Planarity : 0.005 0.049 1953 Dihedral : 4.162 15.352 1554 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.97 % Allowed : 16.55 % Favored : 81.48 % 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: -0.20 (0.22), residues: 1407 helix: 1.03 (0.16), residues: 1008 sheet: -2.50 (0.51), residues: 84 loop : -3.27 (0.22), residues: 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 294 time to evaluate : 1.389 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 outliers start: 26 outliers final: 16 residues processed: 307 average time/residue: 0.2854 time to fit residues: 117.3642 Evaluate side-chains 276 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 260 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1035 time to fit residues: 5.0481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 127 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 ASN E 332 ASN G 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12040 Z= 0.168 Angle : 0.611 9.208 16422 Z= 0.296 Chirality : 0.039 0.135 1995 Planarity : 0.005 0.040 1953 Dihedral : 3.846 13.370 1554 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.83 % Allowed : 19.27 % Favored : 79.89 % 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: 0.57 (0.23), residues: 1407 helix: 1.64 (0.17), residues: 1001 sheet: -2.49 (0.48), residues: 84 loop : -2.98 (0.23), residues: 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 300 time to evaluate : 1.351 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 outliers start: 11 outliers final: 6 residues processed: 305 average time/residue: 0.2773 time to fit residues: 114.5475 Evaluate side-chains 267 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 261 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1077 time to fit residues: 3.0436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 0.1980 chunk 135 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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: 0.8416 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12040 Z= 0.181 Angle : 0.610 9.682 16422 Z= 0.290 Chirality : 0.039 0.133 1995 Planarity : 0.004 0.036 1953 Dihedral : 3.677 12.324 1554 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.66 % Allowed : 20.79 % Favored : 77.55 % 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: 0.84 (0.23), residues: 1407 helix: 1.84 (0.17), residues: 1001 sheet: -2.42 (0.47), residues: 84 loop : -2.84 (0.24), residues: 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 288 time to evaluate : 1.340 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 outliers start: 22 outliers final: 16 residues processed: 294 average time/residue: 0.2845 time to fit residues: 113.5788 Evaluate side-chains 277 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 261 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1009 time to fit residues: 4.8272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 0.0770 chunk 93 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 overall best weight: 0.6286 ------------------------------------------------------------------------------- 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: 0.8399 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12040 Z= 0.160 Angle : 0.599 8.651 16422 Z= 0.285 Chirality : 0.039 0.129 1995 Planarity : 0.004 0.037 1953 Dihedral : 3.576 13.805 1554 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.98 % Allowed : 22.98 % Favored : 76.04 % 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: 1.01 (0.23), residues: 1407 helix: 1.94 (0.17), residues: 1001 sheet: -2.30 (0.46), residues: 84 loop : -2.73 (0.25), residues: 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 296 time to evaluate : 1.384 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 outliers start: 13 outliers final: 10 residues processed: 302 average time/residue: 0.2769 time to fit residues: 113.9188 Evaluate side-chains 291 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 281 time to evaluate : 1.396 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1062 time to fit residues: 3.7925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 0.4980 chunk 135 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12040 Z= 0.192 Angle : 0.612 8.640 16422 Z= 0.293 Chirality : 0.039 0.130 1995 Planarity : 0.004 0.036 1953 Dihedral : 3.536 11.042 1554 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.89 % Allowed : 23.58 % Favored : 74.53 % 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: 1.13 (0.23), residues: 1407 helix: 1.99 (0.17), residues: 1008 sheet: -2.17 (0.48), residues: 84 loop : -2.67 (0.26), residues: 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 291 time to evaluate : 1.247 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 outliers start: 25 outliers final: 19 residues processed: 299 average time/residue: 0.2757 time to fit residues: 111.2538 Evaluate side-chains 296 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 277 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1005 time to fit residues: 5.2045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 134 optimal weight: 0.0970 chunk 84 optimal weight: 0.0030 chunk 82 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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: 0.8377 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12040 Z= 0.157 Angle : 0.602 8.426 16422 Z= 0.288 Chirality : 0.039 0.130 1995 Planarity : 0.004 0.037 1953 Dihedral : 3.415 11.658 1554 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.83 % Allowed : 23.96 % Favored : 75.21 % 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: 1.28 (0.23), residues: 1407 helix: 2.02 (0.17), residues: 1015 sheet: -1.99 (0.48), residues: 84 loop : -2.43 (0.27), residues: 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 299 time to evaluate : 1.496 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 outliers start: 11 outliers final: 9 residues processed: 301 average time/residue: 0.2801 time to fit residues: 114.5005 Evaluate side-chains 270 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 261 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1042 time to fit residues: 3.5454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 0.0020 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12040 Z= 0.187 Angle : 0.626 8.717 16422 Z= 0.300 Chirality : 0.039 0.130 1995 Planarity : 0.004 0.035 1953 Dihedral : 3.461 11.754 1554 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.21 % Allowed : 25.77 % Favored : 73.02 % 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: 1.37 (0.23), residues: 1407 helix: 2.05 (0.17), residues: 1008 sheet: -1.63 (0.51), residues: 84 loop : -2.26 (0.28), residues: 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 288 time to evaluate : 1.222 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 outliers start: 16 outliers final: 11 residues processed: 296 average time/residue: 0.2765 time to fit residues: 110.1792 Evaluate side-chains 278 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 267 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1095 time to fit residues: 4.0832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 75 optimal weight: 0.0010 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 0.0870 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN B 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12040 Z= 0.169 Angle : 0.627 8.858 16422 Z= 0.301 Chirality : 0.039 0.132 1995 Planarity : 0.004 0.037 1953 Dihedral : 3.432 12.465 1554 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.83 % Allowed : 26.61 % Favored : 72.56 % 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: 1.49 (0.23), residues: 1407 helix: 2.04 (0.17), residues: 1015 sheet: -1.42 (0.52), residues: 84 loop : -1.98 (0.30), residues: 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 283 time to evaluate : 1.213 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 outliers start: 11 outliers final: 9 residues processed: 287 average time/residue: 0.2898 time to fit residues: 111.5152 Evaluate side-chains 282 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 273 time to evaluate : 1.393 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1006 time to fit residues: 3.3751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12040 Z= 0.221 Angle : 0.660 9.124 16422 Z= 0.317 Chirality : 0.040 0.132 1995 Planarity : 0.004 0.034 1953 Dihedral : 3.555 11.116 1554 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.60 % Allowed : 26.53 % Favored : 72.86 % 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: 1.46 (0.23), residues: 1407 helix: 2.04 (0.17), residues: 1008 sheet: -1.24 (0.53), residues: 84 loop : -2.02 (0.30), residues: 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 271 time to evaluate : 1.444 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 outliers start: 8 outliers final: 5 residues processed: 273 average time/residue: 0.3011 time to fit residues: 109.4609 Evaluate side-chains 259 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 254 time to evaluate : 1.393 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1206 time to fit residues: 3.0189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.0670 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.090241 restraints weight = 19443.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.092538 restraints weight = 10521.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.093898 restraints weight = 7483.844| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12040 Z= 0.184 Angle : 0.643 9.082 16422 Z= 0.309 Chirality : 0.040 0.129 1995 Planarity : 0.004 0.035 1953 Dihedral : 3.490 11.422 1554 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.30 % Allowed : 27.66 % Favored : 72.03 % 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: 1.50 (0.23), residues: 1407 helix: 2.00 (0.17), residues: 1015 sheet: -1.19 (0.53), residues: 84 loop : -1.87 (0.30), residues: 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2656.24 seconds wall clock time: 48 minutes 46.61 seconds (2926.61 seconds total)