Starting phenix.real_space_refine on Sat Apr 6 09:10:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izd_35862/04_2024/8izd_35862_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izd_35862/04_2024/8izd_35862.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izd_35862/04_2024/8izd_35862_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izd_35862/04_2024/8izd_35862_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izd_35862/04_2024/8izd_35862_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izd_35862/04_2024/8izd_35862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izd_35862/04_2024/8izd_35862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izd_35862/04_2024/8izd_35862_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izd_35862/04_2024/8izd_35862_updated.pdb" } resolution = 3.09 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= -0.001 sd= 0.092 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 P 8 5.49 5 S 40 5.16 5 C 5242 2.51 5 N 1216 2.21 5 O 1300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 25": "NH1" <-> "NH2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B ASP 119": "OD1" <-> "OD2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ASP 122": "OD1" <-> "OD2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 381": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D ASP 119": "OD1" <-> "OD2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 136": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7806 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2670 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1082 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "C" Number of atoms: 2670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2670 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1082 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'6PL': 1, '9NY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6PL:plan-1': 1, '6PL:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'6PL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6PL:plan-1': 1, '6PL:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'6PL': 1, '9NY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6PL:plan-1': 1, '6PL:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'6PL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6PL:plan-1': 1, '6PL:plan-2': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 4.57, per 1000 atoms: 0.59 Number of scatterers: 7806 At special positions: 0 Unit cell: (101.84, 123.28, 99.696, 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 40 16.00 P 8 15.00 O 1300 8.00 N 1216 7.00 C 5242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 102 " - pdb=" SG CYS D 142 " 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: 3.02 Conformation dependent library (CDL) restraints added in 1.3 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 2 sheets defined 61.3% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 85 through 100 Processing helix chain 'A' and resid 110 through 113 No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 131 through 153 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 169 through 195 removed outlier: 3.793A pdb=" N ALA A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 181 " --> pdb=" O MET A 177 " (cutoff:3.500A) Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 204 through 209 removed outlier: 4.081A pdb=" N TYR A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 239 removed outlier: 3.569A pdb=" N GLN A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 Processing helix chain 'A' and resid 272 through 297 Proline residue: A 277 - end of helix removed outlier: 3.806A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 334 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 353 through 383 Processing helix chain 'B' and resid 20 through 46 removed outlier: 3.637A pdb=" N LEU B 31 " --> pdb=" O CYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 85 through 100 Processing helix chain 'C' and resid 110 through 113 No H-bonds generated for 'chain 'C' and resid 110 through 113' Processing helix chain 'C' and resid 131 through 153 Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 169 through 195 removed outlier: 3.793A pdb=" N ALA C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Proline residue: C 188 - end of helix Processing helix chain 'C' and resid 204 through 209 removed outlier: 4.096A pdb=" N TYR C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 239 removed outlier: 3.569A pdb=" N GLN C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 234 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 268 Processing helix chain 'C' and resid 272 through 297 Proline residue: C 277 - end of helix removed outlier: 3.805A pdb=" N LEU C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 334 Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 353 through 383 Processing helix chain 'D' and resid 20 through 46 removed outlier: 3.637A pdb=" N LEU D 31 " --> pdb=" O CYS D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 91 Processing helix chain 'D' and resid 135 through 141 Processing sheet with id= A, first strand: chain 'B' and resid 53 through 59 removed outlier: 4.649A pdb=" N ALA B 69 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR B 125 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 53 through 59 removed outlier: 4.649A pdb=" N ALA D 69 " --> pdb=" O TYR D 125 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR D 125 " --> pdb=" O ALA D 69 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1260 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: 1.98 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.21: 466 1.21 - 1.40: 3304 1.40 - 1.59: 4214 1.59 - 1.79: 35 1.79 - 1.98: 37 Bond restraints: 8056 Sorted by residual: bond pdb=" C GLY A 127 " pdb=" O GLY A 127 " ideal model delta sigma weight residual 1.234 1.027 0.207 9.80e-03 1.04e+04 4.46e+02 bond pdb=" C GLY C 127 " pdb=" O GLY C 127 " ideal model delta sigma weight residual 1.234 1.027 0.207 9.80e-03 1.04e+04 4.45e+02 bond pdb=" CA HIS C 319 " pdb=" C HIS C 319 " ideal model delta sigma weight residual 1.527 1.284 0.243 1.21e-02 6.83e+03 4.02e+02 bond pdb=" CA HIS A 319 " pdb=" C HIS A 319 " ideal model delta sigma weight residual 1.527 1.284 0.242 1.21e-02 6.83e+03 4.01e+02 bond pdb=" C PHE A 230 " pdb=" O PHE A 230 " ideal model delta sigma weight residual 1.236 1.010 0.226 1.22e-02 6.72e+03 3.42e+02 ... (remaining 8051 not shown) Histogram of bond angle deviations from ideal: 88.62 - 98.43: 72 98.43 - 108.23: 1063 108.23 - 118.04: 4831 118.04 - 127.85: 4783 127.85 - 137.66: 157 Bond angle restraints: 10906 Sorted by residual: angle pdb=" C TYR C 211 " pdb=" N PRO C 212 " pdb=" CA PRO C 212 " ideal model delta sigma weight residual 119.28 97.16 22.12 1.10e+00 8.26e-01 4.04e+02 angle pdb=" C TYR A 211 " pdb=" N PRO A 212 " pdb=" CA PRO A 212 " ideal model delta sigma weight residual 119.28 97.19 22.09 1.10e+00 8.26e-01 4.03e+02 angle pdb=" C ILE C 173 " pdb=" CA ILE C 173 " pdb=" CB ILE C 173 " ideal model delta sigma weight residual 112.22 91.14 21.08 1.38e+00 5.25e-01 2.33e+02 angle pdb=" C ILE A 173 " pdb=" CA ILE A 173 " pdb=" CB ILE A 173 " ideal model delta sigma weight residual 112.22 91.18 21.04 1.38e+00 5.25e-01 2.33e+02 angle pdb=" N PHE C 333 " pdb=" CA PHE C 333 " pdb=" C PHE C 333 " ideal model delta sigma weight residual 111.40 94.19 17.21 1.22e+00 6.72e-01 1.99e+02 ... (remaining 10901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.64: 4046 27.64 - 55.29: 518 55.29 - 82.93: 60 82.93 - 110.57: 12 110.57 - 138.21: 2 Dihedral angle restraints: 4638 sinusoidal: 1974 harmonic: 2664 Sorted by residual: dihedral pdb=" C ILE A 160 " pdb=" N ILE A 160 " pdb=" CA ILE A 160 " pdb=" CB ILE A 160 " ideal model delta harmonic sigma weight residual -122.00 -152.88 30.88 0 2.50e+00 1.60e-01 1.53e+02 dihedral pdb=" C ILE C 160 " pdb=" N ILE C 160 " pdb=" CA ILE C 160 " pdb=" CB ILE C 160 " ideal model delta harmonic sigma weight residual -122.00 -152.87 30.87 0 2.50e+00 1.60e-01 1.52e+02 dihedral pdb=" N ILE A 160 " pdb=" C ILE A 160 " pdb=" CA ILE A 160 " pdb=" CB ILE A 160 " ideal model delta harmonic sigma weight residual 123.40 152.11 -28.71 0 2.50e+00 1.60e-01 1.32e+02 ... (remaining 4635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.255: 894 0.255 - 0.510: 158 0.510 - 0.765: 52 0.765 - 1.019: 34 1.019 - 1.274: 10 Chirality restraints: 1148 Sorted by residual: chirality pdb=" CA PHE C 73 " pdb=" N PHE C 73 " pdb=" C PHE C 73 " pdb=" CB PHE C 73 " both_signs ideal model delta sigma weight residual False 2.51 1.24 1.27 2.00e-01 2.50e+01 4.06e+01 chirality pdb=" CA PHE A 73 " pdb=" N PHE A 73 " pdb=" C PHE A 73 " pdb=" CB PHE A 73 " both_signs ideal model delta sigma weight residual False 2.51 1.24 1.27 2.00e-01 2.50e+01 4.06e+01 chirality pdb=" CA ASN A 250 " pdb=" N ASN A 250 " pdb=" C ASN A 250 " pdb=" CB ASN A 250 " both_signs ideal model delta sigma weight residual False 2.51 1.27 1.24 2.00e-01 2.50e+01 3.86e+01 ... (remaining 1145 not shown) Planarity restraints: 1302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 187 " -0.149 5.00e-02 4.00e+02 2.31e-01 8.54e+01 pdb=" N PRO C 188 " 0.399 5.00e-02 4.00e+02 pdb=" CA PRO C 188 " -0.142 5.00e-02 4.00e+02 pdb=" CD PRO C 188 " -0.108 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 187 " 0.149 5.00e-02 4.00e+02 2.31e-01 8.53e+01 pdb=" N PRO A 188 " -0.399 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.142 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.108 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 302 " -0.043 2.00e-02 2.50e+03 8.36e-02 6.98e+01 pdb=" C LEU C 302 " 0.145 2.00e-02 2.50e+03 pdb=" O LEU C 302 " -0.052 2.00e-02 2.50e+03 pdb=" N ALA C 303 " -0.049 2.00e-02 2.50e+03 ... (remaining 1299 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 98 2.51 - 3.10: 6674 3.10 - 3.70: 11962 3.70 - 4.30: 17171 4.30 - 4.90: 28808 Nonbonded interactions: 64713 Sorted by model distance: nonbonded pdb=" O ASP C 248 " pdb=" N ASN C 250 " model vdw 1.908 2.520 nonbonded pdb=" O ASP A 248 " pdb=" N ASN A 250 " model vdw 1.908 2.520 nonbonded pdb=" OD2 ASP C 132 " pdb=" OH TYR C 267 " model vdw 2.026 2.440 nonbonded pdb=" OD2 ASP A 132 " pdb=" OH TYR A 267 " model vdw 2.027 2.440 nonbonded pdb=" CD2 LEU C 323 " pdb=" NE2 GLN C 365 " model vdw 2.047 3.540 ... (remaining 64708 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.930 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.350 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.053 0.284 8056 Z= 3.395 Angle : 3.295 25.562 10906 Z= 2.039 Chirality : 0.278 1.274 1148 Planarity : 0.019 0.231 1302 Dihedral : 22.397 138.214 2918 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 43.97 Ramachandran Plot: Outliers : 2.48 % Allowed : 10.27 % Favored : 87.25 % Rotamer: Outliers : 22.08 % Allowed : 12.90 % Favored : 65.01 % Cbeta Deviations : 15.69 % 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: -4.20 (0.24), residues: 886 helix: -2.38 (0.19), residues: 536 sheet: -0.55 (0.72), residues: 58 loop : -3.80 (0.28), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.012 TRP D 50 HIS 0.050 0.006 HIS D 117 PHE 0.048 0.010 PHE A 307 TYR 0.058 0.007 TYR A 139 ARG 0.014 0.001 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 134 time to evaluate : 0.841 Fit side-chains REVERT: A 78 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7225 (mm) REVERT: A 168 HIS cc_start: 0.5498 (OUTLIER) cc_final: 0.4562 (t-90) REVERT: A 169 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.5841 (mtp-110) REVERT: A 171 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7709 (tmmt) REVERT: A 209 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7442 (mtm110) REVERT: A 224 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8476 (m-80) REVERT: A 246 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7330 (ttp80) REVERT: A 304 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7005 (t80) REVERT: A 384 TRP cc_start: 0.4130 (OUTLIER) cc_final: 0.3822 (t60) REVERT: B 38 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: C 76 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.4430 (tpt170) REVERT: C 78 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6969 (mm) REVERT: C 168 HIS cc_start: 0.5550 (OUTLIER) cc_final: 0.4533 (t-90) REVERT: C 169 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.5945 (mtp-110) REVERT: C 170 ILE cc_start: 0.7673 (tt) cc_final: 0.7451 (tt) REVERT: C 171 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7627 (tmmt) REVERT: C 207 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.9174 (mtp) REVERT: C 209 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7433 (mtm110) REVERT: C 224 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: C 304 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7023 (t80) REVERT: C 384 TRP cc_start: 0.4044 (OUTLIER) cc_final: 0.3724 (t60) REVERT: D 38 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7615 (mp0) outliers start: 178 outliers final: 113 residues processed: 275 average time/residue: 0.2103 time to fit residues: 76.7621 Evaluate side-chains 249 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 115 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 384 TRP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 80 TYR Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 384 TRP Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 131 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS A 124 ASN A 256 HIS ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN B 95 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS C 124 ASN C 256 HIS ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8056 Z= 0.262 Angle : 0.745 6.969 10906 Z= 0.394 Chirality : 0.049 0.177 1148 Planarity : 0.007 0.099 1302 Dihedral : 20.312 175.511 1509 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.32 % Favored : 93.00 % Rotamer: Outliers : 13.28 % Allowed : 17.62 % Favored : 69.11 % 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: -2.23 (0.26), residues: 886 helix: -0.65 (0.21), residues: 534 sheet: -1.24 (0.68), residues: 60 loop : -2.99 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 231 HIS 0.010 0.002 HIS A 111 PHE 0.016 0.002 PHE A 181 TYR 0.027 0.002 TYR A 139 ARG 0.005 0.001 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 106 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7761 (ptmt) REVERT: A 148 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7080 (mm-30) REVERT: A 164 VAL cc_start: 0.7233 (OUTLIER) cc_final: 0.7018 (p) REVERT: A 168 HIS cc_start: 0.5532 (OUTLIER) cc_final: 0.4728 (t-90) REVERT: A 176 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6945 (mp-120) REVERT: A 224 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7033 (m-80) REVERT: A 244 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6488 (pttt) REVERT: A 249 HIS cc_start: 0.6389 (OUTLIER) cc_final: 0.6078 (t-90) REVERT: A 304 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6564 (t80) REVERT: A 332 GLN cc_start: 0.8244 (mt0) cc_final: 0.8001 (mt0) REVERT: B 38 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: C 106 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7762 (ptmt) REVERT: C 148 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7073 (mm-30) REVERT: C 168 HIS cc_start: 0.5549 (OUTLIER) cc_final: 0.4698 (t-90) REVERT: C 176 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6913 (mp-120) REVERT: C 199 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7448 (tt) REVERT: C 224 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7011 (m-80) REVERT: C 244 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6398 (pttt) REVERT: C 249 HIS cc_start: 0.6521 (OUTLIER) cc_final: 0.6109 (t-90) REVERT: C 304 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6590 (t80) REVERT: D 38 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: D 139 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7366 (mt0) outliers start: 107 outliers final: 56 residues processed: 194 average time/residue: 0.1895 time to fit residues: 50.1110 Evaluate side-chains 169 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 94 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 139 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS B 95 ASN B 117 HIS C 319 HIS D 117 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8056 Z= 0.248 Angle : 0.648 7.099 10906 Z= 0.341 Chirality : 0.046 0.167 1148 Planarity : 0.006 0.078 1302 Dihedral : 17.711 179.147 1347 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.09 % Favored : 93.34 % Rotamer: Outliers : 8.56 % Allowed : 22.46 % Favored : 68.98 % 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: -1.10 (0.27), residues: 886 helix: 0.29 (0.21), residues: 540 sheet: -1.13 (0.70), residues: 60 loop : -2.59 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 231 HIS 0.005 0.001 HIS C 319 PHE 0.017 0.002 PHE A 145 TYR 0.027 0.001 TYR C 139 ARG 0.003 0.001 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 106 time to evaluate : 0.896 Fit side-chains REVERT: A 106 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7810 (ptmt) REVERT: A 168 HIS cc_start: 0.5583 (OUTLIER) cc_final: 0.4745 (t-90) REVERT: A 176 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6813 (mp-120) REVERT: A 200 TRP cc_start: 0.7928 (t-100) cc_final: 0.7623 (t-100) REVERT: A 224 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: A 244 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6555 (pttt) REVERT: A 260 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8222 (mt) REVERT: B 38 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: C 91 LEU cc_start: 0.7292 (pp) cc_final: 0.7048 (mp) REVERT: C 106 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7806 (ptmt) REVERT: C 140 MET cc_start: 0.7830 (mtp) cc_final: 0.7615 (mtm) REVERT: C 160 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6572 (pt) REVERT: C 168 HIS cc_start: 0.5497 (OUTLIER) cc_final: 0.4642 (t-90) REVERT: C 176 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6747 (mp-120) REVERT: C 224 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.6958 (m-80) REVERT: C 237 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8167 (mp) REVERT: C 260 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8198 (mt) REVERT: D 38 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7414 (tt0) outliers start: 69 outliers final: 39 residues processed: 161 average time/residue: 0.2051 time to fit residues: 44.8518 Evaluate side-chains 156 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 102 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8056 Z= 0.272 Angle : 0.637 7.390 10906 Z= 0.333 Chirality : 0.045 0.159 1148 Planarity : 0.006 0.071 1302 Dihedral : 16.916 179.032 1306 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.88 % Favored : 92.55 % Rotamer: Outliers : 9.68 % Allowed : 20.60 % Favored : 69.73 % 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: -0.73 (0.27), residues: 886 helix: 0.55 (0.21), residues: 552 sheet: -0.92 (0.72), residues: 60 loop : -2.52 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 231 HIS 0.004 0.001 HIS C 319 PHE 0.013 0.002 PHE A 145 TYR 0.024 0.001 TYR C 139 ARG 0.005 0.001 ARG C 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 104 time to evaluate : 0.901 Fit side-chains REVERT: A 91 LEU cc_start: 0.7377 (pp) cc_final: 0.7155 (mp) REVERT: A 106 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7795 (ptmt) REVERT: A 148 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7242 (mm-30) REVERT: A 168 HIS cc_start: 0.5696 (OUTLIER) cc_final: 0.4760 (t-90) REVERT: A 176 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6716 (mp-120) REVERT: A 200 TRP cc_start: 0.7996 (t-100) cc_final: 0.7721 (t-100) REVERT: A 224 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7005 (m-80) REVERT: A 244 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6615 (ptmt) REVERT: A 246 ARG cc_start: 0.6169 (OUTLIER) cc_final: 0.5895 (mmm160) REVERT: B 38 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: C 106 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7827 (ptmt) REVERT: C 112 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7186 (ptm160) REVERT: C 148 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7209 (mm-30) REVERT: C 168 HIS cc_start: 0.5697 (OUTLIER) cc_final: 0.4498 (t70) REVERT: C 176 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6695 (mp-120) REVERT: C 224 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7011 (m-80) REVERT: C 237 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8141 (mp) REVERT: D 38 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: D 139 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7359 (mt0) outliers start: 78 outliers final: 47 residues processed: 167 average time/residue: 0.1854 time to fit residues: 42.6186 Evaluate side-chains 159 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 97 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 139 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8056 Z= 0.190 Angle : 0.580 7.300 10906 Z= 0.302 Chirality : 0.043 0.174 1148 Planarity : 0.005 0.066 1302 Dihedral : 16.191 179.205 1298 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.53 % Favored : 94.02 % Rotamer: Outliers : 8.68 % Allowed : 21.22 % Favored : 70.10 % 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: -0.33 (0.28), residues: 886 helix: 0.85 (0.21), residues: 550 sheet: -0.77 (0.73), residues: 60 loop : -2.29 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 231 HIS 0.005 0.001 HIS A 319 PHE 0.012 0.001 PHE A 145 TYR 0.027 0.001 TYR C 182 ARG 0.008 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 108 time to evaluate : 0.860 Fit side-chains REVERT: A 106 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7787 (ptmt) REVERT: A 112 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7426 (ptm160) REVERT: A 148 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7304 (mm-30) REVERT: A 168 HIS cc_start: 0.5738 (OUTLIER) cc_final: 0.4680 (t-90) REVERT: A 176 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6640 (mp10) REVERT: A 224 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: A 237 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8096 (mp) REVERT: A 244 LYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6384 (pttt) REVERT: B 38 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: C 106 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7753 (ptmt) REVERT: C 112 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7408 (ptm160) REVERT: C 148 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7172 (mm-30) REVERT: C 176 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6618 (mp10) REVERT: C 224 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7057 (m-80) REVERT: C 237 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8054 (mp) REVERT: D 38 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: D 139 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7313 (mt0) outliers start: 70 outliers final: 37 residues processed: 169 average time/residue: 0.1878 time to fit residues: 43.7616 Evaluate side-chains 152 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 100 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 139 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 0.0040 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 0.1980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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: 0.7619 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8056 Z= 0.187 Angle : 0.565 5.975 10906 Z= 0.292 Chirality : 0.043 0.133 1148 Planarity : 0.005 0.065 1302 Dihedral : 15.708 179.789 1286 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.87 % Favored : 93.91 % Rotamer: Outliers : 8.44 % Allowed : 21.34 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.11 (0.28), residues: 886 helix: 0.97 (0.21), residues: 554 sheet: -0.16 (0.79), residues: 54 loop : -2.21 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 231 HIS 0.005 0.001 HIS A 319 PHE 0.011 0.001 PHE C 333 TYR 0.023 0.001 TYR A 139 ARG 0.004 0.001 ARG C 209 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 106 time to evaluate : 0.860 Fit side-chains REVERT: A 106 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7775 (ptmt) REVERT: A 112 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7497 (ptm160) REVERT: A 148 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7223 (mm-30) REVERT: A 168 HIS cc_start: 0.5807 (OUTLIER) cc_final: 0.4686 (t-90) REVERT: A 176 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6605 (mp10) REVERT: A 224 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: A 244 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6769 (ptmt) REVERT: B 38 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: C 106 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7737 (ptmt) REVERT: C 112 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7521 (ptm160) REVERT: C 148 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7187 (mm-30) REVERT: C 168 HIS cc_start: 0.5624 (OUTLIER) cc_final: 0.4537 (t-90) REVERT: C 176 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6596 (mp10) REVERT: C 224 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.6993 (m-80) REVERT: C 237 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8112 (mp) REVERT: D 38 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: D 139 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7402 (mt0) outliers start: 68 outliers final: 41 residues processed: 163 average time/residue: 0.2001 time to fit residues: 44.8674 Evaluate side-chains 157 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 101 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 139 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.0040 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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: 0.7659 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8056 Z= 0.247 Angle : 0.592 6.441 10906 Z= 0.305 Chirality : 0.044 0.144 1148 Planarity : 0.005 0.066 1302 Dihedral : 15.888 179.146 1286 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.76 % Favored : 94.13 % Rotamer: Outliers : 8.44 % Allowed : 21.34 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.09 (0.28), residues: 886 helix: 0.95 (0.21), residues: 558 sheet: -0.54 (0.79), residues: 56 loop : -2.08 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 231 HIS 0.005 0.001 HIS A 319 PHE 0.012 0.001 PHE A 135 TYR 0.022 0.001 TYR A 182 ARG 0.003 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 103 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7814 (ptmt) REVERT: A 112 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7585 (ptm160) REVERT: A 148 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7247 (mm-30) REVERT: A 168 HIS cc_start: 0.6020 (OUTLIER) cc_final: 0.4777 (t-90) REVERT: A 176 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6584 (mp10) REVERT: A 224 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.6913 (m-80) REVERT: A 237 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8114 (mp) REVERT: B 38 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: B 86 LYS cc_start: 0.8456 (ttpp) cc_final: 0.8210 (ttmt) REVERT: C 73 PHE cc_start: 0.3446 (OUTLIER) cc_final: 0.3008 (t80) REVERT: C 106 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7741 (ptmt) REVERT: C 112 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7639 (ptm160) REVERT: C 176 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6364 (mp10) REVERT: C 224 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.6914 (m-80) REVERT: C 237 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8048 (mp) REVERT: D 38 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: D 139 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7436 (mt0) outliers start: 68 outliers final: 46 residues processed: 158 average time/residue: 0.1856 time to fit residues: 40.5044 Evaluate side-chains 159 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 98 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 139 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7611 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8056 Z= 0.186 Angle : 0.542 5.941 10906 Z= 0.281 Chirality : 0.042 0.137 1148 Planarity : 0.005 0.064 1302 Dihedral : 15.393 179.978 1286 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 7.44 % Allowed : 21.71 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.02 (0.28), residues: 886 helix: 1.02 (0.21), residues: 570 sheet: -0.12 (0.78), residues: 54 loop : -2.21 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 231 HIS 0.005 0.001 HIS A 319 PHE 0.010 0.001 PHE A 333 TYR 0.023 0.001 TYR A 139 ARG 0.004 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 100 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7818 (ptmt) REVERT: A 112 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7537 (ptm160) REVERT: A 168 HIS cc_start: 0.5951 (OUTLIER) cc_final: 0.4950 (t-90) REVERT: A 176 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6240 (mp10) REVERT: A 224 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.6788 (m-80) REVERT: A 237 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7988 (mp) REVERT: B 38 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: B 86 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8227 (ttmt) REVERT: C 112 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7557 (ptm160) REVERT: C 176 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6157 (mp10) REVERT: C 224 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: D 38 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: D 139 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7396 (mt0) outliers start: 60 outliers final: 37 residues processed: 148 average time/residue: 0.1864 time to fit residues: 38.4977 Evaluate side-chains 148 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 99 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 139 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7630 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8056 Z= 0.209 Angle : 0.579 10.787 10906 Z= 0.294 Chirality : 0.043 0.138 1148 Planarity : 0.005 0.064 1302 Dihedral : 15.263 179.949 1275 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 6.70 % Allowed : 21.71 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.09 (0.28), residues: 886 helix: 1.05 (0.21), residues: 570 sheet: -0.03 (0.78), residues: 54 loop : -2.17 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.005 0.001 HIS A 319 PHE 0.011 0.001 PHE C 223 TYR 0.022 0.001 TYR A 139 ARG 0.003 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 98 time to evaluate : 0.880 Fit side-chains REVERT: A 112 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7537 (ptm160) REVERT: A 168 HIS cc_start: 0.5854 (OUTLIER) cc_final: 0.5067 (t-90) REVERT: A 176 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6295 (mp10) REVERT: A 224 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.6880 (m-80) REVERT: A 237 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8027 (mp) REVERT: B 38 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: B 86 LYS cc_start: 0.8534 (ttpp) cc_final: 0.8273 (ttmt) REVERT: C 112 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7570 (ptm160) REVERT: C 176 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6283 (mp10) REVERT: C 224 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: D 38 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: D 139 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7407 (mt0) outliers start: 54 outliers final: 38 residues processed: 141 average time/residue: 0.1937 time to fit residues: 37.4703 Evaluate side-chains 146 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 97 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 139 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 0.0970 chunk 87 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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: 0.7613 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8056 Z= 0.194 Angle : 0.563 10.088 10906 Z= 0.286 Chirality : 0.043 0.132 1148 Planarity : 0.005 0.064 1302 Dihedral : 14.984 179.772 1266 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 6.33 % Allowed : 21.84 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.18 (0.28), residues: 886 helix: 1.12 (0.21), residues: 570 sheet: 0.08 (0.78), residues: 54 loop : -2.11 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 200 HIS 0.004 0.001 HIS A 319 PHE 0.011 0.001 PHE C 223 TYR 0.022 0.001 TYR A 139 ARG 0.003 0.000 ARG C 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 101 time to evaluate : 1.205 Fit side-chains REVERT: A 112 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7568 (ptm160) REVERT: A 176 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6141 (mp10) REVERT: A 224 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: B 38 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: B 86 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8276 (ttmt) REVERT: C 112 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8083 (ptp-110) REVERT: C 176 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6134 (mp10) REVERT: C 224 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.6785 (m-80) REVERT: D 38 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: D 139 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7404 (mt0) outliers start: 51 outliers final: 38 residues processed: 140 average time/residue: 0.2080 time to fit residues: 40.2723 Evaluate side-chains 147 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 100 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 108 ASN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 139 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.0000 chunk 3 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.161551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132298 restraints weight = 9266.526| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.08 r_work: 0.3413 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8056 Z= 0.174 Angle : 0.549 10.232 10906 Z= 0.279 Chirality : 0.042 0.130 1148 Planarity : 0.005 0.064 1302 Dihedral : 14.729 179.636 1260 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 5.71 % Allowed : 22.58 % Favored : 71.71 % 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: 0.29 (0.28), residues: 886 helix: 1.19 (0.21), residues: 572 sheet: 0.11 (0.78), residues: 54 loop : -2.07 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.004 0.001 HIS A 319 PHE 0.012 0.001 PHE A 223 TYR 0.023 0.001 TYR A 139 ARG 0.003 0.000 ARG A 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1907.41 seconds wall clock time: 35 minutes 40.07 seconds (2140.07 seconds total)