Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 13:33:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct2_26978/04_2023/8ct2_26978_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct2_26978/04_2023/8ct2_26978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct2_26978/04_2023/8ct2_26978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct2_26978/04_2023/8ct2_26978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct2_26978/04_2023/8ct2_26978_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct2_26978/04_2023/8ct2_26978_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.169 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 4884 2.51 5 N 1264 2.21 5 O 1296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7464 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "B" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "C" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "A" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG D 234 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG D 234 " occ=0.52 residue: pdb=" N AARG B 234 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 234 " occ=0.50 residue: pdb=" N AARG C 234 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 234 " occ=0.50 residue: pdb=" N AARG A 234 " occ=0.51 ... (20 atoms not shown) pdb=" NH2BARG A 234 " occ=0.49 Time building chain proxies: 7.96, per 1000 atoms: 1.07 Number of scatterers: 7464 At special positions: 0 Unit cell: (88.81, 89.64, 90.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1296 8.00 N 1264 7.00 C 4884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 2.2 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 0 sheets defined 69.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 8 through 32 Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 49 through 71 removed outlier: 5.754A pdb=" N HIS D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 85 Processing helix chain 'D' and resid 91 through 115 Processing helix chain 'D' and resid 135 through 156 Processing helix chain 'D' and resid 168 through 187 removed outlier: 5.736A pdb=" N ASP D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 203 removed outlier: 3.511A pdb=" N SER D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 229 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.676A pdb=" N LYS D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL D 244 " --> pdb=" O ASP D 240 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TRP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 6 No H-bonds generated for 'chain 'B' and resid 4 through 6' Processing helix chain 'B' and resid 8 through 32 Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 49 through 71 removed outlier: 5.931A pdb=" N HIS B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 91 through 115 Processing helix chain 'B' and resid 135 through 156 Processing helix chain 'B' and resid 168 through 187 removed outlier: 5.706A pdb=" N ASP B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TYR B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 203 removed outlier: 3.586A pdb=" N SER B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 229 removed outlier: 3.554A pdb=" N TRP B 213 " --> pdb=" O HIS B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 238 through 247 removed outlier: 4.231A pdb=" N VAL B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TRP B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 6 No H-bonds generated for 'chain 'C' and resid 4 through 6' Processing helix chain 'C' and resid 8 through 32 Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 49 through 71 removed outlier: 6.024A pdb=" N HIS C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 91 through 115 Processing helix chain 'C' and resid 135 through 156 Processing helix chain 'C' and resid 168 through 187 removed outlier: 5.637A pdb=" N ASP C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 203 removed outlier: 3.791A pdb=" N SER C 199 " --> pdb=" O ARG C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 229 Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.728A pdb=" N LYS C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL C 244 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TRP C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 8 through 32 Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 49 through 71 removed outlier: 5.902A pdb=" N HIS A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 91 through 115 Processing helix chain 'A' and resid 135 through 156 Processing helix chain 'A' and resid 168 through 187 removed outlier: 5.609A pdb=" N ASP A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.557A pdb=" N SER A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 229 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.705A pdb=" N LYS A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1404 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: 2.05 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2372 1.34 - 1.46: 1302 1.46 - 1.57: 3918 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 7620 Sorted by residual: bond pdb=" N ASN C 192 " pdb=" CA ASN C 192 " ideal model delta sigma weight residual 1.463 1.450 0.013 8.80e-03 1.29e+04 2.09e+00 bond pdb=" N ASN A 192 " pdb=" CA ASN A 192 " ideal model delta sigma weight residual 1.463 1.451 0.012 8.80e-03 1.29e+04 1.78e+00 bond pdb=" N ASN B 192 " pdb=" CA ASN B 192 " ideal model delta sigma weight residual 1.463 1.452 0.010 8.80e-03 1.29e+04 1.39e+00 bond pdb=" CG LEU D 112 " pdb=" CD2 LEU D 112 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.62e-01 bond pdb=" C ALA C 168 " pdb=" N PRO C 169 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.36e-02 5.41e+03 9.49e-01 ... (remaining 7615 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.35: 205 107.35 - 114.01: 4567 114.01 - 120.68: 3101 120.68 - 127.34: 2443 127.34 - 134.00: 76 Bond angle restraints: 10392 Sorted by residual: angle pdb=" C ILE A 191 " pdb=" N ASN A 192 " pdb=" CA ASN A 192 " ideal model delta sigma weight residual 122.26 126.52 -4.26 1.10e+00 8.26e-01 1.50e+01 angle pdb=" CA CYS D 189 " pdb=" CB CYS D 189 " pdb=" SG CYS D 189 " ideal model delta sigma weight residual 114.40 105.61 8.79 2.30e+00 1.89e-01 1.46e+01 angle pdb=" C ILE B 191 " pdb=" N ASN B 192 " pdb=" CA ASN B 192 " ideal model delta sigma weight residual 122.26 126.18 -3.92 1.10e+00 8.26e-01 1.27e+01 angle pdb=" C ILE C 191 " pdb=" N ASN C 192 " pdb=" CA ASN C 192 " ideal model delta sigma weight residual 122.26 126.14 -3.88 1.10e+00 8.26e-01 1.24e+01 angle pdb=" C ASP D 158 " pdb=" N ARG D 159 " pdb=" CA ARG D 159 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.99e+00 ... (remaining 10387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4091 17.91 - 35.82: 211 35.82 - 53.73: 38 53.73 - 71.64: 14 71.64 - 89.56: 6 Dihedral angle restraints: 4360 sinusoidal: 1584 harmonic: 2776 Sorted by residual: dihedral pdb=" CA LEU B 182 " pdb=" C LEU B 182 " pdb=" N ALA B 183 " pdb=" CA ALA B 183 " ideal model delta harmonic sigma weight residual -180.00 -156.02 -23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LEU A 182 " pdb=" C LEU A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual 180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU D 182 " pdb=" C LEU D 182 " pdb=" N ALA D 183 " pdb=" CA ALA D 183 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 4357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 892 0.042 - 0.083: 324 0.083 - 0.125: 47 0.125 - 0.166: 4 0.166 - 0.208: 1 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA CYS D 189 " pdb=" N CYS D 189 " pdb=" C CYS D 189 " pdb=" CB CYS D 189 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE D 191 " pdb=" CA ILE D 191 " pdb=" CG1 ILE D 191 " pdb=" CG2 ILE D 191 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CB ILE B 191 " pdb=" CA ILE B 191 " pdb=" CG1 ILE B 191 " pdb=" CG2 ILE B 191 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1265 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 215 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO D 216 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 216 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 216 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 215 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO C 216 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 216 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 216 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 215 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.15e+00 pdb=" N PRO A 216 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " -0.029 5.00e-02 4.00e+02 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 845 2.75 - 3.29: 7753 3.29 - 3.82: 13559 3.82 - 4.36: 16145 4.36 - 4.90: 27434 Nonbonded interactions: 65736 Sorted by model distance: nonbonded pdb=" O CYS B 152 " pdb=" OG1 THR B 156 " model vdw 2.209 2.440 nonbonded pdb=" O CYS C 152 " pdb=" OG1 THR C 156 " model vdw 2.245 2.440 nonbonded pdb=" NZ LYS D 51 " pdb=" OD2 ASP B 185 " model vdw 2.272 2.520 nonbonded pdb=" O ASN A 49 " pdb=" OG SER A 53 " model vdw 2.294 2.440 nonbonded pdb=" OD1 ASN C 127 " pdb=" OG SER C 196 " model vdw 2.300 2.440 ... (remaining 65731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'B' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'C' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'D' and (resid 3 through 233 or resid 235 through 249)) } 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=0.48 max=1.00 mean=0.99 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.940 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 28.280 Find NCS groups from input model: 0.530 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 7620 Z= 0.252 Angle : 0.611 8.785 10392 Z= 0.330 Chirality : 0.041 0.208 1268 Planarity : 0.005 0.054 1272 Dihedral : 12.289 89.556 2592 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.58 % Favored : 97.00 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.26), residues: 980 helix: 1.64 (0.20), residues: 616 sheet: None (None), residues: 0 loop : -0.04 (0.34), residues: 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.859 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 112 average time/residue: 0.1462 time to fit residues: 24.1879 Evaluate side-chains 99 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0686 time to fit residues: 1.8536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN A 88 GLN A 122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 7620 Z= 0.307 Angle : 0.596 8.635 10392 Z= 0.301 Chirality : 0.041 0.202 1268 Planarity : 0.005 0.053 1272 Dihedral : 7.852 56.613 1148 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.48 % Favored : 97.11 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.32 (0.27), residues: 980 helix: 1.56 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.39 (0.35), residues: 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.872 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 101 average time/residue: 0.1657 time to fit residues: 24.3606 Evaluate side-chains 105 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0707 time to fit residues: 2.5408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 0.1980 chunk 72 optimal weight: 10.0000 chunk 59 optimal weight: 0.3980 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN A 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 7620 Z= 0.223 Angle : 0.542 8.046 10392 Z= 0.276 Chirality : 0.040 0.333 1268 Planarity : 0.004 0.051 1272 Dihedral : 7.438 59.473 1148 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.89 % Favored : 96.69 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.57 (0.27), residues: 980 helix: 1.80 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.39 (0.35), residues: 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.843 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 100 average time/residue: 0.1587 time to fit residues: 23.1843 Evaluate side-chains 95 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0706 time to fit residues: 1.3646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 ASN C 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 7620 Z= 0.174 Angle : 0.512 7.486 10392 Z= 0.258 Chirality : 0.038 0.195 1268 Planarity : 0.004 0.050 1272 Dihedral : 7.028 59.264 1148 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.00 % Favored : 96.59 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.89 (0.27), residues: 980 helix: 2.07 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.31 (0.35), residues: 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.805 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 94 average time/residue: 0.1688 time to fit residues: 23.0515 Evaluate side-chains 97 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0718 time to fit residues: 1.6233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 7620 Z= 0.232 Angle : 0.541 7.966 10392 Z= 0.274 Chirality : 0.040 0.299 1268 Planarity : 0.004 0.049 1272 Dihedral : 7.199 58.506 1148 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.48 % Favored : 97.11 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.75 (0.27), residues: 980 helix: 1.96 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.36 (0.36), residues: 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.819 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 92 average time/residue: 0.1698 time to fit residues: 22.6158 Evaluate side-chains 90 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.824 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0741 time to fit residues: 1.3802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7620 Z= 0.275 Angle : 0.564 8.173 10392 Z= 0.285 Chirality : 0.040 0.211 1268 Planarity : 0.004 0.049 1272 Dihedral : 7.483 58.737 1148 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.48 % Favored : 97.11 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.57 (0.27), residues: 980 helix: 1.82 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.43 (0.35), residues: 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.868 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 94 average time/residue: 0.1660 time to fit residues: 22.7718 Evaluate side-chains 97 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0702 time to fit residues: 1.9648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 0.0970 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 55 optimal weight: 0.1980 overall best weight: 1.0580 ------------------------------------------------------------------------------- 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: 0.8269 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7620 Z= 0.160 Angle : 0.500 7.545 10392 Z= 0.253 Chirality : 0.037 0.185 1268 Planarity : 0.004 0.049 1272 Dihedral : 6.897 59.090 1148 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.89 % Favored : 96.69 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.96 (0.27), residues: 980 helix: 2.15 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.34 (0.35), residues: 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.873 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 92 average time/residue: 0.1654 time to fit residues: 22.1546 Evaluate side-chains 91 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0754 time to fit residues: 1.3582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 63 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 0.0040 chunk 80 optimal weight: 5.9990 overall best weight: 2.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7620 Z= 0.284 Angle : 0.575 8.177 10392 Z= 0.289 Chirality : 0.041 0.324 1268 Planarity : 0.004 0.049 1272 Dihedral : 7.461 59.738 1148 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.48 % Favored : 97.11 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.60 (0.27), residues: 980 helix: 1.85 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.45 (0.35), residues: 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.827 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 91 average time/residue: 0.1652 time to fit residues: 21.8389 Evaluate side-chains 93 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0724 time to fit residues: 1.5099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 7620 Z= 0.145 Angle : 0.497 8.273 10392 Z= 0.252 Chirality : 0.037 0.199 1268 Planarity : 0.004 0.048 1272 Dihedral : 6.834 59.708 1148 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.89 % Favored : 96.69 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.08 (0.27), residues: 980 helix: 2.27 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.35 (0.35), residues: 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.740 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 91 average time/residue: 0.1652 time to fit residues: 21.8579 Evaluate side-chains 93 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0728 time to fit residues: 1.4245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 63 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8240 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 7620 Z= 0.141 Angle : 0.494 8.485 10392 Z= 0.249 Chirality : 0.037 0.178 1268 Planarity : 0.004 0.048 1272 Dihedral : 6.607 59.789 1148 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.38 % Favored : 97.21 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.27), residues: 980 helix: 2.38 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.27 (0.36), residues: 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.835 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 0.1686 time to fit residues: 22.0094 Evaluate side-chains 86 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0716 time to fit residues: 1.3376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 0.0040 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN C 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.130404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.105581 restraints weight = 30757.483| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.96 r_work: 0.2878 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7620 Z= 0.206 Angle : 0.528 8.454 10392 Z= 0.266 Chirality : 0.038 0.187 1268 Planarity : 0.004 0.049 1272 Dihedral : 6.820 59.594 1148 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.79 % Favored : 96.80 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.03 (0.27), residues: 980 helix: 2.21 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -0.33 (0.36), residues: 340 =============================================================================== Job complete usr+sys time: 1837.09 seconds wall clock time: 33 minutes 51.72 seconds (2031.72 seconds total)