Starting phenix.real_space_refine on Thu Jul 2 06:29:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8r8d_18999/07_2026/8r8d_18999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8d_18999/07_2026/8r8d_18999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r8d_18999/07_2026/8r8d_18999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8d_18999/07_2026/8r8d_18999.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r8d_18999/07_2026/8r8d_18999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8d_18999/07_2026/8r8d_18999.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8r8d_18999/07_2026/8r8d_18999.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8r8d_18999/07_2026/8r8d_18999.cif" } resolution = 2.6 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 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= 0.059 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 38 5.16 5 C 4452 2.51 5 N 1192 2.21 5 O 1380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7062 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1664 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 209} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "I" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 798 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "H" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 798 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1664 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 209} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 1.15, per 1000 atoms: 0.16 Number of scatterers: 7062 At special positions: 0 Unit cell: (128.115, 84.315, 86.505, 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 38 16.00 O 1380 8.00 N 1192 7.00 C 4452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 58 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 58 " distance=2.04 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA D 3 " - " MAN D 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG C 1 " - " FUC C 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG D 1 " - " FUC D 6 " NAG-ASN " NAG C 1 " - " ASN B 74 " " NAG D 1 " - " ASN A 74 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 350.7 milliseconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1640 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 14 sheets defined 9.0% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.873A pdb=" N GLN B 60 " --> pdb=" O HIS B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 60D through 63 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.823A pdb=" N ILE B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 242 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.593A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.795A pdb=" N GLU I 84 " --> pdb=" O SER I 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.594A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.796A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.874A pdb=" N GLN A 60 " --> pdb=" O HIS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 60D through 63 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.823A pdb=" N ILE A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 234 through 242 Processing sheet with id=AA1, first strand: chain 'B' and resid 20 through 21 removed outlier: 3.661A pdb=" N ALA B 139 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 199 " --> pdb=" O GLN B 210 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE B 213 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR B 229 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS B 182 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 30 through 37 removed outlier: 6.549A pdb=" N TRP B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 87 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 7 removed outlier: 5.887A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.807A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.300A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 9 through 12 removed outlier: 4.009A pdb=" N ASP I 93 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 removed outlier: 5.887A pdb=" N GLY H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.805A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.300A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 removed outlier: 4.011A pdb=" N ASP L 93 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ARG L 97 " --> pdb=" O ASP L 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'A' and resid 20 through 21 removed outlier: 3.661A pdb=" N ALA A 139 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 199 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 213 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR A 229 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS A 182 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 30 through 37 removed outlier: 6.550A pdb=" N TRP A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 87 " --> pdb=" O ARG A 107 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 582 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: 0.88 Time building geometry restraints manager: 0.57 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: 2258 1.34 - 1.46: 1767 1.46 - 1.58: 3149 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 7218 Sorted by residual: bond pdb=" C5 FUC C 6 " pdb=" O5 FUC C 6 " ideal model delta sigma weight residual 1.423 1.458 -0.035 2.00e-02 2.50e+03 3.05e+00 bond pdb=" C5 FUC D 6 " pdb=" O5 FUC D 6 " ideal model delta sigma weight residual 1.423 1.458 -0.035 2.00e-02 2.50e+03 3.05e+00 bond pdb=" C5 MAN D 5 " pdb=" O5 MAN D 5 " ideal model delta sigma weight residual 1.418 1.445 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C5 MAN C 5 " pdb=" O5 MAN C 5 " ideal model delta sigma weight residual 1.418 1.445 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 MAN C 5 " pdb=" C2 MAN C 5 " ideal model delta sigma weight residual 1.526 1.552 -0.026 2.00e-02 2.50e+03 1.64e+00 ... (remaining 7213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 9566 1.72 - 3.44: 226 3.44 - 5.16: 28 5.16 - 6.88: 14 6.88 - 8.60: 4 Bond angle restraints: 9838 Sorted by residual: angle pdb=" C SER L 51 " pdb=" N ASN L 52 " pdb=" CA ASN L 52 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C SER I 51 " pdb=" N ASN I 52 " pdb=" CA ASN I 52 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 angle pdb=" N ARG H 67 " pdb=" CA ARG H 67 " pdb=" C ARG H 67 " ideal model delta sigma weight residual 114.04 111.26 2.78 1.24e+00 6.50e-01 5.03e+00 angle pdb=" N ARG E 67 " pdb=" CA ARG E 67 " pdb=" C ARG E 67 " ideal model delta sigma weight residual 114.04 111.29 2.75 1.24e+00 6.50e-01 4.93e+00 angle pdb=" C3 BMA C 3 " pdb=" C2 BMA C 3 " pdb=" O2 BMA C 3 " ideal model delta sigma weight residual 112.95 106.62 6.33 3.00e+00 1.11e-01 4.46e+00 ... (remaining 9833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 3903 16.21 - 32.43: 241 32.43 - 48.64: 62 48.64 - 64.85: 14 64.85 - 81.06: 18 Dihedral angle restraints: 4238 sinusoidal: 1638 harmonic: 2600 Sorted by residual: dihedral pdb=" CB CYS A 168 " pdb=" SG CYS A 168 " pdb=" SG CYS A 182 " pdb=" CB CYS A 182 " ideal model delta sinusoidal sigma weight residual 93.00 158.90 -65.90 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS B 168 " pdb=" SG CYS B 168 " pdb=" SG CYS B 182 " pdb=" CB CYS B 182 " ideal model delta sinusoidal sigma weight residual 93.00 158.90 -65.90 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " pdb=" SG CYS A 58 " pdb=" CB CYS A 58 " ideal model delta sinusoidal sigma weight residual 93.00 150.14 -57.14 1 1.00e+01 1.00e-02 4.39e+01 ... (remaining 4235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 917 0.057 - 0.114: 171 0.114 - 0.170: 30 0.170 - 0.227: 0 0.227 - 0.284: 2 Chirality restraints: 1120 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 1117 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 48 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 49 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 48 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO B 49 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 115 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO A 116 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " -0.025 5.00e-02 4.00e+02 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1068 2.77 - 3.30: 6362 3.30 - 3.83: 12223 3.83 - 4.37: 15300 4.37 - 4.90: 25681 Nonbonded interactions: 60634 Sorted by model distance: nonbonded pdb=" O PRO A 60C" pdb=" OH TYR A 88 " model vdw 2.232 3.040 nonbonded pdb=" O PRO B 60C" pdb=" OH TYR B 88 " model vdw 2.232 3.040 nonbonded pdb=" O PRO E 41 " pdb=" NZ LYS E 43 " model vdw 2.256 3.120 nonbonded pdb=" O PRO H 41 " pdb=" NZ LYS H 43 " model vdw 2.256 3.120 nonbonded pdb=" O ARG A 24 " pdb=" NH1 ARG A 24 " model vdw 2.287 3.120 ... (remaining 60629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'C' 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: 1.350 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.003 0.035 7246 Z= 0.155 Angle : 0.681 8.596 9906 Z= 0.318 Chirality : 0.047 0.284 1120 Planarity : 0.005 0.059 1248 Dihedral : 12.682 81.065 2550 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.28), residues: 900 helix: -1.32 (0.75), residues: 42 sheet: 0.41 (0.34), residues: 252 loop : 0.10 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 98 TYR 0.026 0.002 TYR E 112 PHE 0.011 0.001 PHE E 29 TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 7218) covalent geometry : angle 0.66644 / 0.31 ( 9838) SS BOND : bond 0.00304 / 0.20 ( 16) SS BOND : angle 1.48382 / 1.01 ( 32) hydrogen bonds : bond 0.22548 / 15.78 ( 236) hydrogen bonds : angle 9.51246 / 6.65 ( 582) link_ALPHA1-3 : bond 0.00633 / 0.32 ( 2) link_ALPHA1-3 : angle 1.82879 / 0.92 ( 6) link_ALPHA1-6 : bond 0.00416 / 0.21 ( 2) link_ALPHA1-6 : angle 1.64345 / 0.84 ( 6) link_BETA1-4 : bond 0.00272 / 0.12 ( 4) link_BETA1-4 : angle 2.44736 / 1.42 ( 12) link_BETA1-6 : bond 0.00526 / 0.26 ( 2) link_BETA1-6 : angle 2.11748 / 1.01 ( 6) link_NAG-ASN : bond 0.01029 / 0.52 ( 2) link_NAG-ASN : angle 1.47452 / 0.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.8124 (tt0) cc_final: 0.7478 (tp30) REVERT: I 83 ASP cc_start: 0.8661 (m-30) cc_final: 0.8346 (m-30) REVERT: L 83 ASP cc_start: 0.8676 (m-30) cc_final: 0.8364 (m-30) REVERT: A 71 GLU cc_start: 0.8131 (tt0) cc_final: 0.7473 (tp30) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.4583 time to fit residues: 67.3607 Evaluate side-chains 120 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0050 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 54 GLN L 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.157485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.135022 restraints weight = 6534.521| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.28 r_work: 0.3374 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.003 0.038 7246 Z= 0.146 Angle : 0.653 6.869 9906 Z= 0.325 Chirality : 0.046 0.147 1120 Planarity : 0.005 0.039 1248 Dihedral : 4.876 19.587 1086 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.31 % Allowed : 6.34 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.28), residues: 900 helix: -0.92 (0.82), residues: 42 sheet: 0.65 (0.33), residues: 238 loop : 0.10 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 239 TYR 0.019 0.002 TYR E 112 PHE 0.012 0.001 PHE E 29 TRP 0.014 0.002 TRP H 47 HIS 0.003 0.001 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 7218) covalent geometry : angle 0.64123 / 0.32 ( 9838) SS BOND : bond 0.00472 / 0.29 ( 16) SS BOND : angle 1.45889 / 1.00 ( 32) hydrogen bonds : bond 0.03813 / 2.63 ( 236) hydrogen bonds : angle 6.47690 / 4.60 ( 582) link_ALPHA1-3 : bond 0.00471 / 0.24 ( 2) link_ALPHA1-3 : angle 1.39359 / 0.72 ( 6) link_ALPHA1-6 : bond 0.00548 / 0.27 ( 2) link_ALPHA1-6 : angle 1.36798 / 0.74 ( 6) link_BETA1-4 : bond 0.00205 / 0.10 ( 4) link_BETA1-4 : angle 2.35989 / 1.41 ( 12) link_BETA1-6 : bond 0.00319 / 0.16 ( 2) link_BETA1-6 : angle 1.16008 / 0.57 ( 6) link_NAG-ASN : bond 0.00872 / 0.44 ( 2) link_NAG-ASN : angle 1.75274 / 0.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.8848 (tt0) cc_final: 0.7408 (tp30) REVERT: E 98 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8576 (ptt180) REVERT: I 83 ASP cc_start: 0.8550 (m-30) cc_final: 0.8304 (m-30) REVERT: L 83 ASP cc_start: 0.8557 (m-30) cc_final: 0.8310 (m-30) REVERT: A 71 GLU cc_start: 0.8850 (tt0) cc_final: 0.7464 (tp30) outliers start: 24 outliers final: 9 residues processed: 136 average time/residue: 0.4619 time to fit residues: 65.9377 Evaluate side-chains 130 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 153 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121674 restraints weight = 7005.294| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.60 r_work: 0.3296 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7246 Z= 0.202 Angle : 0.709 7.680 9906 Z= 0.350 Chirality : 0.048 0.147 1120 Planarity : 0.005 0.040 1248 Dihedral : 5.168 23.327 1086 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.62 % Allowed : 9.37 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 900 helix: -1.05 (0.79), residues: 42 sheet: 0.75 (0.33), residues: 238 loop : 0.03 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 239 TYR 0.015 0.002 TYR B 117 PHE 0.012 0.002 PHE H 29 TRP 0.017 0.002 TRP H 47 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.20 ( 7218) covalent geometry : angle 0.69611 / 0.35 ( 9838) SS BOND : bond 0.00597 / 0.37 ( 16) SS BOND : angle 1.59183 / 1.10 ( 32) hydrogen bonds : bond 0.03803 / 2.63 ( 236) hydrogen bonds : angle 6.21464 / 4.44 ( 582) link_ALPHA1-3 : bond 0.00586 / 0.29 ( 2) link_ALPHA1-3 : angle 1.58114 / 0.83 ( 6) link_ALPHA1-6 : bond 0.00583 / 0.29 ( 2) link_ALPHA1-6 : angle 1.25376 / 0.69 ( 6) link_BETA1-4 : bond 0.00350 / 0.16 ( 4) link_BETA1-4 : angle 2.47376 / 1.47 ( 12) link_BETA1-6 : bond 0.00128 / 0.06 ( 2) link_BETA1-6 : angle 1.34991 / 0.65 ( 6) link_NAG-ASN : bond 0.01361 / 0.68 ( 2) link_NAG-ASN : angle 1.79273 / 0.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.174 Fit side-chains REVERT: E 43 LYS cc_start: 0.8030 (mptt) cc_final: 0.7721 (mptt) REVERT: E 98 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8618 (ptt180) REVERT: I 83 ASP cc_start: 0.8646 (m-30) cc_final: 0.8389 (m-30) REVERT: H 98 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8647 (ptt180) REVERT: L 83 ASP cc_start: 0.8651 (m-30) cc_final: 0.8397 (m-30) outliers start: 19 outliers final: 13 residues processed: 126 average time/residue: 0.5034 time to fit residues: 66.4726 Evaluate side-chains 129 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 153 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 54 GLN L 54 GLN A 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.146149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121108 restraints weight = 7037.178| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.60 r_work: 0.3290 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7246 Z= 0.205 Angle : 0.709 7.758 9906 Z= 0.351 Chirality : 0.048 0.151 1120 Planarity : 0.005 0.040 1248 Dihedral : 5.226 24.169 1086 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.44 % Allowed : 9.92 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.27), residues: 900 helix: -1.06 (0.78), residues: 42 sheet: 0.72 (0.33), residues: 238 loop : -0.03 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 239 TYR 0.012 0.002 TYR H 114 PHE 0.014 0.002 PHE H 29 TRP 0.017 0.002 TRP H 47 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.20 ( 7218) covalent geometry : angle 0.69641 / 0.35 ( 9838) SS BOND : bond 0.00604 / 0.38 ( 16) SS BOND : angle 1.64685 / 1.13 ( 32) hydrogen bonds : bond 0.03545 / 2.45 ( 236) hydrogen bonds : angle 6.15125 / 4.41 ( 582) link_ALPHA1-3 : bond 0.00573 / 0.29 ( 2) link_ALPHA1-3 : angle 1.56675 / 0.81 ( 6) link_ALPHA1-6 : bond 0.00547 / 0.28 ( 2) link_ALPHA1-6 : angle 1.26503 / 0.69 ( 6) link_BETA1-4 : bond 0.00324 / 0.15 ( 4) link_BETA1-4 : angle 2.48448 / 1.48 ( 12) link_BETA1-6 : bond 0.00054 / 0.03 ( 2) link_BETA1-6 : angle 1.42412 / 0.65 ( 6) link_NAG-ASN : bond 0.01138 / 0.57 ( 2) link_NAG-ASN : angle 1.63295 / 0.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.264 Fit side-chains REVERT: B 186 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: E 39 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8719 (mm-40) REVERT: E 98 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8635 (ptt180) REVERT: I 83 ASP cc_start: 0.8643 (m-30) cc_final: 0.8364 (m-30) REVERT: H 98 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8657 (ptt180) REVERT: L 83 ASP cc_start: 0.8607 (m-30) cc_final: 0.8343 (m-30) REVERT: A 186 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7160 (mp0) outliers start: 25 outliers final: 11 residues processed: 125 average time/residue: 0.5493 time to fit residues: 71.6928 Evaluate side-chains 130 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 186 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123817 restraints weight = 7037.176| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.58 r_work: 0.3317 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7246 Z= 0.138 Angle : 0.628 7.011 9906 Z= 0.311 Chirality : 0.045 0.150 1120 Planarity : 0.005 0.039 1248 Dihedral : 4.918 21.901 1086 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.34 % Allowed : 11.43 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.28), residues: 900 helix: -0.86 (0.80), residues: 42 sheet: 0.74 (0.33), residues: 240 loop : 0.01 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 239 TYR 0.011 0.002 TYR E 80 PHE 0.014 0.001 PHE H 29 TRP 0.017 0.002 TRP H 47 HIS 0.005 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7218) covalent geometry : angle 0.61705 / 0.31 ( 9838) SS BOND : bond 0.00464 / 0.29 ( 16) SS BOND : angle 1.28114 / 0.89 ( 32) hydrogen bonds : bond 0.03017 / 2.05 ( 236) hydrogen bonds : angle 5.81505 / 4.15 ( 582) link_ALPHA1-3 : bond 0.00634 / 0.32 ( 2) link_ALPHA1-3 : angle 1.45634 / 0.73 ( 6) link_ALPHA1-6 : bond 0.00564 / 0.28 ( 2) link_ALPHA1-6 : angle 1.31670 / 0.71 ( 6) link_BETA1-4 : bond 0.00193 / 0.09 ( 4) link_BETA1-4 : angle 2.27173 / 1.36 ( 12) link_BETA1-6 : bond 0.00172 / 0.09 ( 2) link_BETA1-6 : angle 1.24722 / 0.56 ( 6) link_NAG-ASN : bond 0.00736 / 0.37 ( 2) link_NAG-ASN : angle 1.44888 / 0.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.164 Fit side-chains REVERT: E 39 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8632 (mm-40) REVERT: E 98 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8621 (ptt180) REVERT: I 83 ASP cc_start: 0.8619 (m-30) cc_final: 0.8371 (m-30) REVERT: H 98 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8671 (ptt180) REVERT: L 83 ASP cc_start: 0.8634 (m-30) cc_final: 0.8380 (m-30) REVERT: A 109 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7962 (tm-30) outliers start: 17 outliers final: 11 residues processed: 126 average time/residue: 0.4915 time to fit residues: 64.9369 Evaluate side-chains 127 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 165 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 54 GLN L 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.149221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124674 restraints weight = 7088.186| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.58 r_work: 0.3321 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7246 Z= 0.125 Angle : 0.606 6.928 9906 Z= 0.300 Chirality : 0.044 0.150 1120 Planarity : 0.005 0.039 1248 Dihedral : 4.778 21.515 1086 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.48 % Allowed : 11.85 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.28), residues: 900 helix: -0.86 (0.79), residues: 42 sheet: 0.73 (0.33), residues: 240 loop : 0.05 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 239 TYR 0.010 0.002 TYR H 111 PHE 0.014 0.001 PHE H 29 TRP 0.016 0.002 TRP H 47 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 7218) covalent geometry : angle 0.59585 / 0.30 ( 9838) SS BOND : bond 0.00438 / 0.27 ( 16) SS BOND : angle 1.20213 / 0.84 ( 32) hydrogen bonds : bond 0.02860 / 1.94 ( 236) hydrogen bonds : angle 5.65506 / 4.04 ( 582) link_ALPHA1-3 : bond 0.00625 / 0.31 ( 2) link_ALPHA1-3 : angle 1.46030 / 0.73 ( 6) link_ALPHA1-6 : bond 0.00535 / 0.27 ( 2) link_ALPHA1-6 : angle 1.33414 / 0.71 ( 6) link_BETA1-4 : bond 0.00187 / 0.09 ( 4) link_BETA1-4 : angle 2.21783 / 1.32 ( 12) link_BETA1-6 : bond 0.00221 / 0.11 ( 2) link_BETA1-6 : angle 1.18693 / 0.54 ( 6) link_NAG-ASN : bond 0.00636 / 0.32 ( 2) link_NAG-ASN : angle 1.41533 / 0.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.177 Fit side-chains REVERT: E 98 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8602 (ptt180) REVERT: I 83 ASP cc_start: 0.8608 (m-30) cc_final: 0.8362 (m-30) REVERT: H 98 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8663 (ptt180) REVERT: L 83 ASP cc_start: 0.8590 (m-30) cc_final: 0.8347 (m-30) REVERT: A 109 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7982 (tm-30) outliers start: 18 outliers final: 11 residues processed: 125 average time/residue: 0.5419 time to fit residues: 71.1582 Evaluate side-chains 129 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 165 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 77 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.149298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124821 restraints weight = 6921.877| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.56 r_work: 0.3327 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7246 Z= 0.142 Angle : 0.634 7.141 9906 Z= 0.313 Chirality : 0.045 0.181 1120 Planarity : 0.005 0.037 1248 Dihedral : 4.855 22.493 1086 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.48 % Allowed : 12.67 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.28), residues: 900 helix: -0.92 (0.78), residues: 42 sheet: 0.79 (0.33), residues: 240 loop : 0.04 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 239 TYR 0.012 0.002 TYR H 80 PHE 0.013 0.001 PHE H 29 TRP 0.015 0.002 TRP E 47 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 7218) covalent geometry : angle 0.61703 / 0.31 ( 9838) SS BOND : bond 0.00482 / 0.30 ( 16) SS BOND : angle 1.98246 / 1.34 ( 32) hydrogen bonds : bond 0.02920 / 1.99 ( 236) hydrogen bonds : angle 5.65247 / 4.04 ( 582) link_ALPHA1-3 : bond 0.00605 / 0.30 ( 2) link_ALPHA1-3 : angle 1.48041 / 0.74 ( 6) link_ALPHA1-6 : bond 0.00549 / 0.28 ( 2) link_ALPHA1-6 : angle 1.33219 / 0.71 ( 6) link_BETA1-4 : bond 0.00186 / 0.08 ( 4) link_BETA1-4 : angle 2.28584 / 1.36 ( 12) link_BETA1-6 : bond 0.00165 / 0.08 ( 2) link_BETA1-6 : angle 1.24832 / 0.56 ( 6) link_NAG-ASN : bond 0.00670 / 0.34 ( 2) link_NAG-ASN : angle 1.43971 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.166 Fit side-chains REVERT: E 98 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8613 (ptt180) REVERT: I 83 ASP cc_start: 0.8615 (m-30) cc_final: 0.8344 (m-30) REVERT: H 98 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8654 (ptt180) REVERT: L 83 ASP cc_start: 0.8595 (m-30) cc_final: 0.8361 (m-30) outliers start: 18 outliers final: 13 residues processed: 129 average time/residue: 0.5355 time to fit residues: 72.5119 Evaluate side-chains 136 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 165 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 54 GLN L 54 GLN A 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124852 restraints weight = 7012.494| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.58 r_work: 0.3330 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7246 Z= 0.144 Angle : 0.641 7.219 9906 Z= 0.318 Chirality : 0.045 0.150 1120 Planarity : 0.005 0.042 1248 Dihedral : 4.940 22.731 1086 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.48 % Allowed : 12.81 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 900 helix: -0.90 (0.78), residues: 42 sheet: 0.75 (0.33), residues: 240 loop : 0.03 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 239 TYR 0.010 0.002 TYR E 111 PHE 0.013 0.001 PHE H 29 TRP 0.016 0.002 TRP H 47 HIS 0.005 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 7218) covalent geometry : angle 0.62099 / 0.31 ( 9838) SS BOND : bond 0.00549 / 0.34 ( 16) SS BOND : angle 2.32484 / 1.57 ( 32) hydrogen bonds : bond 0.02872 / 1.96 ( 236) hydrogen bonds : angle 5.63663 / 4.03 ( 582) link_ALPHA1-3 : bond 0.00645 / 0.32 ( 2) link_ALPHA1-3 : angle 1.48359 / 0.74 ( 6) link_ALPHA1-6 : bond 0.00493 / 0.25 ( 2) link_ALPHA1-6 : angle 1.31320 / 0.70 ( 6) link_BETA1-4 : bond 0.00198 / 0.09 ( 4) link_BETA1-4 : angle 2.27089 / 1.35 ( 12) link_BETA1-6 : bond 0.00149 / 0.07 ( 2) link_BETA1-6 : angle 1.25627 / 0.56 ( 6) link_NAG-ASN : bond 0.00683 / 0.34 ( 2) link_NAG-ASN : angle 1.42750 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.246 Fit side-chains REVERT: E 98 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8614 (ptt180) REVERT: I 83 ASP cc_start: 0.8610 (m-30) cc_final: 0.8335 (m-30) REVERT: H 98 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8650 (ptt180) REVERT: L 83 ASP cc_start: 0.8597 (m-30) cc_final: 0.8340 (m-30) outliers start: 18 outliers final: 12 residues processed: 124 average time/residue: 0.5484 time to fit residues: 71.6480 Evaluate side-chains 132 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 153 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 54 GLN L 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.148846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124120 restraints weight = 7027.881| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.58 r_work: 0.3320 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7246 Z= 0.162 Angle : 0.665 7.357 9906 Z= 0.329 Chirality : 0.046 0.159 1120 Planarity : 0.005 0.046 1248 Dihedral : 5.002 23.828 1086 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.48 % Allowed : 13.36 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.27), residues: 900 helix: -0.96 (0.78), residues: 42 sheet: 0.75 (0.33), residues: 240 loop : 0.02 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 239 TYR 0.013 0.002 TYR H 80 PHE 0.013 0.002 PHE H 29 TRP 0.015 0.002 TRP H 47 HIS 0.005 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 7218) covalent geometry : angle 0.64525 / 0.32 ( 9838) SS BOND : bond 0.00598 / 0.38 ( 16) SS BOND : angle 2.27937 / 1.54 ( 32) hydrogen bonds : bond 0.03005 / 2.05 ( 236) hydrogen bonds : angle 5.69312 / 4.07 ( 582) link_ALPHA1-3 : bond 0.00616 / 0.31 ( 2) link_ALPHA1-3 : angle 1.49520 / 0.75 ( 6) link_ALPHA1-6 : bond 0.00539 / 0.27 ( 2) link_ALPHA1-6 : angle 1.32059 / 0.71 ( 6) link_BETA1-4 : bond 0.00229 / 0.10 ( 4) link_BETA1-4 : angle 2.33438 / 1.39 ( 12) link_BETA1-6 : bond 0.00046 / 0.02 ( 2) link_BETA1-6 : angle 1.33184 / 0.59 ( 6) link_NAG-ASN : bond 0.00766 / 0.38 ( 2) link_NAG-ASN : angle 1.44817 / 0.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.192 Fit side-chains REVERT: E 98 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8625 (ptt180) REVERT: I 83 ASP cc_start: 0.8621 (m-30) cc_final: 0.8356 (m-30) REVERT: H 98 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8656 (ptt180) REVERT: L 83 ASP cc_start: 0.8601 (m-30) cc_final: 0.8355 (m-30) outliers start: 18 outliers final: 14 residues processed: 129 average time/residue: 0.5049 time to fit residues: 68.4690 Evaluate side-chains 137 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 169 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 54 GLN L 54 GLN A 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122254 restraints weight = 6964.197| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.56 r_work: 0.3297 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7246 Z= 0.208 Angle : 0.724 7.948 9906 Z= 0.358 Chirality : 0.048 0.160 1120 Planarity : 0.005 0.045 1248 Dihedral : 5.301 26.030 1086 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.62 % Allowed : 12.95 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.27), residues: 900 helix: -1.03 (0.77), residues: 42 sheet: 0.66 (0.33), residues: 240 loop : -0.06 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 239 TYR 0.016 0.002 TYR B 117 PHE 0.013 0.002 PHE H 29 TRP 0.016 0.002 TRP A 141 HIS 0.005 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 ( 7218) covalent geometry : angle 0.70478 / 0.35 ( 9838) SS BOND : bond 0.00664 / 0.42 ( 16) SS BOND : angle 2.34988 / 1.59 ( 32) hydrogen bonds : bond 0.03329 / 2.30 ( 236) hydrogen bonds : angle 5.93602 / 4.25 ( 582) link_ALPHA1-3 : bond 0.00615 / 0.31 ( 2) link_ALPHA1-3 : angle 1.55145 / 0.77 ( 6) link_ALPHA1-6 : bond 0.00549 / 0.28 ( 2) link_ALPHA1-6 : angle 1.28862 / 0.70 ( 6) link_BETA1-4 : bond 0.00397 / 0.18 ( 4) link_BETA1-4 : angle 2.50379 / 1.49 ( 12) link_BETA1-6 : bond 0.00115 / 0.06 ( 2) link_BETA1-6 : angle 1.54348 / 0.68 ( 6) link_NAG-ASN : bond 0.01044 / 0.52 ( 2) link_NAG-ASN : angle 1.52521 / 0.75 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.183 Fit side-chains REVERT: E 98 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8643 (ptt180) REVERT: I 83 ASP cc_start: 0.8649 (m-30) cc_final: 0.8362 (m-30) REVERT: H 98 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8669 (ptt180) REVERT: L 83 ASP cc_start: 0.8626 (m-30) cc_final: 0.8360 (m-30) outliers start: 19 outliers final: 17 residues processed: 129 average time/residue: 0.4863 time to fit residues: 65.9546 Evaluate side-chains 135 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 2 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 83 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 54 GLN L 54 GLN A 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121887 restraints weight = 6924.982| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.59 r_work: 0.3301 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 7246 Z= 0.196 Angle : 1.067 59.116 9906 Z= 0.593 Chirality : 0.048 0.241 1120 Planarity : 0.005 0.046 1248 Dihedral : 5.290 26.101 1086 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.17 % Allowed : 12.53 % Favored : 84.30 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.27), residues: 900 helix: -1.05 (0.76), residues: 42 sheet: 0.65 (0.33), residues: 240 loop : -0.06 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 239 TYR 0.014 0.002 TYR E 111 PHE 0.012 0.002 PHE H 29 TRP 0.016 0.002 TRP A 141 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 ( 7218) covalent geometry : angle 1.05582 / 0.59 ( 9838) SS BOND : bond 0.00576 / 0.36 ( 16) SS BOND : angle 2.32617 / 1.57 ( 32) hydrogen bonds : bond 0.03288 / 2.26 ( 236) hydrogen bonds : angle 5.92964 / 4.25 ( 582) link_ALPHA1-3 : bond 0.00612 / 0.31 ( 2) link_ALPHA1-3 : angle 1.57229 / 0.78 ( 6) link_ALPHA1-6 : bond 0.00566 / 0.28 ( 2) link_ALPHA1-6 : angle 1.29756 / 0.70 ( 6) link_BETA1-4 : bond 0.00381 / 0.16 ( 4) link_BETA1-4 : angle 2.49907 / 1.48 ( 12) link_BETA1-6 : bond 0.00113 / 0.06 ( 2) link_BETA1-6 : angle 1.54014 / 0.67 ( 6) link_NAG-ASN : bond 0.00834 / 0.42 ( 2) link_NAG-ASN : angle 1.51895 / 0.73 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2371.68 seconds wall clock time: 41 minutes 8.49 seconds (2468.49 seconds total)