Starting phenix.real_space_refine on Sun May 11 01:42:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8d_18999/05_2025/8r8d_18999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8d_18999/05_2025/8r8d_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8r8d_18999/05_2025/8r8d_18999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8d_18999/05_2025/8r8d_18999.map" model { file = "/net/cci-nas-00/data/ceres_data/8r8d_18999/05_2025/8r8d_18999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8d_18999/05_2025/8r8d_18999.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 18 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: 18 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: 4.77, per 1000 atoms: 0.68 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: 2.04 Conformation dependent library (CDL) restraints added in 998.0 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: 1.17 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: 2.06 Time building geometry restraints manager: 2.35 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 - 21.36: 4126 21.36 - 42.72: 183 42.72 - 64.08: 39 64.08 - 85.44: 30 85.44 - 106.80: 8 Dihedral angle restraints: 4386 sinusoidal: 1786 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 4383 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.010 Normalize map: mean=0, sd=1: 2.650 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 20.680 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 14.746 106.800 2698 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (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 TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS A 27 PHE 0.011 0.001 PHE E 29 TYR 0.026 0.002 TYR E 112 ARG 0.004 0.000 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.01029 ( 2) link_NAG-ASN : angle 1.47452 ( 6) link_ALPHA1-6 : bond 0.00416 ( 2) link_ALPHA1-6 : angle 1.64345 ( 6) link_BETA1-4 : bond 0.00272 ( 4) link_BETA1-4 : angle 2.44736 ( 12) link_ALPHA1-3 : bond 0.00633 ( 2) link_ALPHA1-3 : angle 1.82879 ( 6) hydrogen bonds : bond 0.22548 ( 236) hydrogen bonds : angle 9.51246 ( 582) link_BETA1-6 : bond 0.00526 ( 2) link_BETA1-6 : angle 2.11748 ( 6) SS BOND : bond 0.00304 ( 16) SS BOND : angle 1.48382 ( 32) covalent geometry : bond 0.00340 ( 7218) covalent geometry : angle 0.66644 ( 9838) *********************** 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 : 0.720 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: 1.2386 time to fit residues: 182.2251 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 : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN I 54 GLN L 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.156321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133781 restraints weight = 6474.053| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.27 r_work: 0.3364 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7246 Z= 0.166 Angle : 0.698 7.261 9906 Z= 0.342 Chirality : 0.047 0.146 1120 Planarity : 0.006 0.040 1248 Dihedral : 8.119 57.294 1234 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.58 % Allowed : 6.34 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.28), residues: 900 helix: -0.99 (0.81), residues: 42 sheet: 0.65 (0.33), residues: 238 loop : 0.07 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS B 241 PHE 0.012 0.001 PHE E 29 TYR 0.020 0.002 TYR E 112 ARG 0.006 0.001 ARG A 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00970 ( 2) link_NAG-ASN : angle 1.84804 ( 6) link_ALPHA1-6 : bond 0.00941 ( 2) link_ALPHA1-6 : angle 1.52554 ( 6) link_BETA1-4 : bond 0.00222 ( 4) link_BETA1-4 : angle 3.03691 ( 12) link_ALPHA1-3 : bond 0.00635 ( 2) link_ALPHA1-3 : angle 1.90149 ( 6) hydrogen bonds : bond 0.03817 ( 236) hydrogen bonds : angle 6.37658 ( 582) link_BETA1-6 : bond 0.00279 ( 2) link_BETA1-6 : angle 1.27562 ( 6) SS BOND : bond 0.00518 ( 16) SS BOND : angle 1.50657 ( 32) covalent geometry : bond 0.00395 ( 7218) covalent geometry : angle 0.68242 ( 9838) *********************** 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 148 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 98 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8609 (ptt180) REVERT: I 83 ASP cc_start: 0.8548 (m-30) cc_final: 0.8308 (m-30) REVERT: H 98 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8607 (ptt180) REVERT: L 83 ASP cc_start: 0.8554 (m-30) cc_final: 0.8308 (m-30) outliers start: 26 outliers final: 15 residues processed: 134 average time/residue: 1.3154 time to fit residues: 184.8675 Evaluate side-chains 130 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 98 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 128 SER 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 3 GLN Chi-restraints excluded: chain H residue 98 ARG 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 L residue 86 ASP 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 58 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN A 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.156553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133980 restraints weight = 6592.608| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.28 r_work: 0.3367 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7246 Z= 0.151 Angle : 0.654 6.997 9906 Z= 0.321 Chirality : 0.046 0.171 1120 Planarity : 0.005 0.038 1248 Dihedral : 7.142 46.817 1234 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.20 % Allowed : 9.50 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.28), residues: 900 helix: -0.89 (0.82), residues: 42 sheet: 0.78 (0.33), residues: 238 loop : 0.11 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.005 0.001 HIS A 57 PHE 0.012 0.002 PHE H 29 TYR 0.012 0.002 TYR H 80 ARG 0.004 0.001 ARG A 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00899 ( 2) link_NAG-ASN : angle 1.64796 ( 6) link_ALPHA1-6 : bond 0.00523 ( 2) link_ALPHA1-6 : angle 1.95932 ( 6) link_BETA1-4 : bond 0.00202 ( 4) link_BETA1-4 : angle 2.62850 ( 12) link_ALPHA1-3 : bond 0.01211 ( 2) link_ALPHA1-3 : angle 1.16332 ( 6) hydrogen bonds : bond 0.03438 ( 236) hydrogen bonds : angle 6.04823 ( 582) link_BETA1-6 : bond 0.00246 ( 2) link_BETA1-6 : angle 1.22535 ( 6) SS BOND : bond 0.00473 ( 16) SS BOND : angle 1.31659 ( 32) covalent geometry : bond 0.00357 ( 7218) covalent geometry : angle 0.64077 ( 9838) *********************** 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 135 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: I 83 ASP cc_start: 0.8573 (m-30) cc_final: 0.8331 (m-30) REVERT: L 83 ASP cc_start: 0.8606 (m-30) cc_final: 0.8364 (m-30) outliers start: 16 outliers final: 13 residues processed: 125 average time/residue: 1.3069 time to fit residues: 171.4242 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 : 0.712 ------------------------------------------------------------------------------- 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 107 ILE Chi-restraints excluded: chain I residue 3 VAL 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 L residue 86 ASP Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 165 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3723 r_free = 0.3723 target = 0.156273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133855 restraints weight = 6531.328| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.26 r_work: 0.3367 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7246 Z= 0.144 Angle : 0.647 7.019 9906 Z= 0.317 Chirality : 0.046 0.177 1120 Planarity : 0.005 0.040 1248 Dihedral : 6.513 38.078 1234 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.89 % Allowed : 10.06 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.28), residues: 900 helix: -0.91 (0.81), residues: 42 sheet: 0.78 (0.33), residues: 240 loop : 0.11 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.005 0.001 HIS B 57 PHE 0.013 0.001 PHE H 29 TYR 0.011 0.002 TYR I 87 ARG 0.005 0.001 ARG A 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00835 ( 2) link_NAG-ASN : angle 1.61405 ( 6) link_ALPHA1-6 : bond 0.00445 ( 2) link_ALPHA1-6 : angle 1.98356 ( 6) link_BETA1-4 : bond 0.00231 ( 4) link_BETA1-4 : angle 2.59437 ( 12) link_ALPHA1-3 : bond 0.01178 ( 2) link_ALPHA1-3 : angle 1.19139 ( 6) hydrogen bonds : bond 0.03150 ( 236) hydrogen bonds : angle 5.84435 ( 582) link_BETA1-6 : bond 0.00217 ( 2) link_BETA1-6 : angle 1.25804 ( 6) SS BOND : bond 0.00467 ( 16) SS BOND : angle 1.43174 ( 32) covalent geometry : bond 0.00340 ( 7218) covalent geometry : angle 0.63336 ( 9838) *********************** 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 144 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.722 Fit side-chains REVERT: E 98 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8630 (ptt180) REVERT: I 83 ASP cc_start: 0.8565 (m-30) cc_final: 0.8349 (m-30) REVERT: H 98 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8624 (ptt180) REVERT: L 83 ASP cc_start: 0.8625 (m-30) cc_final: 0.8381 (m-30) outliers start: 21 outliers final: 16 residues processed: 129 average time/residue: 1.2761 time to fit residues: 173.0879 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 : 0.790 ------------------------------------------------------------------------------- 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 E residue 128 SER 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 3 GLN Chi-restraints excluded: chain H residue 98 ARG 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 L residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 165 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.157285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.135083 restraints weight = 6448.930| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.25 r_work: 0.3376 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7246 Z= 0.127 Angle : 0.620 6.839 9906 Z= 0.304 Chirality : 0.045 0.155 1120 Planarity : 0.005 0.040 1248 Dihedral : 5.921 33.386 1234 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.48 % Allowed : 11.16 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.28), residues: 900 helix: -0.88 (0.81), residues: 42 sheet: 0.80 (0.33), residues: 240 loop : 0.11 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.005 0.001 HIS B 57 PHE 0.012 0.001 PHE H 29 TYR 0.013 0.002 TYR H 80 ARG 0.005 0.001 ARG B 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 2) link_NAG-ASN : angle 1.53159 ( 6) link_ALPHA1-6 : bond 0.00388 ( 2) link_ALPHA1-6 : angle 1.84088 ( 6) link_BETA1-4 : bond 0.00224 ( 4) link_BETA1-4 : angle 2.48360 ( 12) link_ALPHA1-3 : bond 0.01250 ( 2) link_ALPHA1-3 : angle 1.25874 ( 6) hydrogen bonds : bond 0.02921 ( 236) hydrogen bonds : angle 5.64848 ( 582) link_BETA1-6 : bond 0.00246 ( 2) link_BETA1-6 : angle 1.23703 ( 6) SS BOND : bond 0.00436 ( 16) SS BOND : angle 1.23945 ( 32) covalent geometry : bond 0.00298 ( 7218) covalent geometry : angle 0.60711 ( 9838) *********************** 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: 18 poor density : 118 time to evaluate : 0.783 Fit side-chains REVERT: B 109 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8061 (tm-30) REVERT: E 98 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8636 (ptt180) REVERT: I 83 ASP cc_start: 0.8587 (m-30) cc_final: 0.8362 (m-30) REVERT: H 98 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8637 (ptt180) REVERT: L 83 ASP cc_start: 0.8602 (m-30) cc_final: 0.8360 (m-30) REVERT: A 109 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7980 (tm-30) outliers start: 18 outliers final: 14 residues processed: 126 average time/residue: 1.2860 time to fit residues: 169.9443 Evaluate side-chains 133 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 E residue 128 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 98 ARG 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 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 80 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3645 r_free = 0.3645 target = 0.144979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120190 restraints weight = 7046.952| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.58 r_work: 0.3275 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 7246 Z= 0.256 Angle : 0.776 8.437 9906 Z= 0.380 Chirality : 0.050 0.153 1120 Planarity : 0.006 0.040 1248 Dihedral : 6.423 30.911 1234 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.03 % Allowed : 11.16 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.27), residues: 900 helix: -1.31 (0.73), residues: 42 sheet: 0.53 (0.32), residues: 254 loop : -0.04 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 141 HIS 0.006 0.001 HIS B 27 PHE 0.013 0.002 PHE H 29 TYR 0.016 0.003 TYR B 117 ARG 0.005 0.001 ARG B 239 Details of bonding type rmsd link_NAG-ASN : bond 0.01432 ( 2) link_NAG-ASN : angle 1.68054 ( 6) link_ALPHA1-6 : bond 0.00411 ( 2) link_ALPHA1-6 : angle 1.94232 ( 6) link_BETA1-4 : bond 0.00456 ( 4) link_BETA1-4 : angle 2.89904 ( 12) link_ALPHA1-3 : bond 0.01197 ( 2) link_ALPHA1-3 : angle 1.03386 ( 6) hydrogen bonds : bond 0.03670 ( 236) hydrogen bonds : angle 6.13991 ( 582) link_BETA1-6 : bond 0.00210 ( 2) link_BETA1-6 : angle 1.70667 ( 6) SS BOND : bond 0.00719 ( 16) SS BOND : angle 1.75170 ( 32) covalent geometry : bond 0.00623 ( 7218) covalent geometry : angle 0.76150 ( 9838) *********************** 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 131 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.729 Fit side-chains REVERT: E 98 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8659 (ptt180) REVERT: I 83 ASP cc_start: 0.8635 (m-30) cc_final: 0.8356 (m-30) REVERT: H 98 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8651 (ptt180) REVERT: L 83 ASP cc_start: 0.8651 (m-30) cc_final: 0.8358 (m-30) outliers start: 22 outliers final: 16 residues processed: 123 average time/residue: 1.2653 time to fit residues: 163.4597 Evaluate side-chains 123 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 E residue 128 SER 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 3 GLN Chi-restraints excluded: chain H residue 98 ARG 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 L residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 169 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 67 optimal weight: 0.8980 chunk 4 optimal weight: 0.0770 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3710 r_free = 0.3710 target = 0.150780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126295 restraints weight = 6825.416| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.56 r_work: 0.3338 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7246 Z= 0.109 Angle : 0.607 6.605 9906 Z= 0.300 Chirality : 0.045 0.183 1120 Planarity : 0.005 0.036 1248 Dihedral : 5.709 29.201 1234 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.89 % Allowed : 12.12 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.28), residues: 900 helix: -0.80 (0.81), residues: 42 sheet: 0.81 (0.33), residues: 240 loop : 0.02 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.005 0.001 HIS B 57 PHE 0.013 0.001 PHE H 29 TYR 0.012 0.001 TYR H 80 ARG 0.005 0.001 ARG B 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 2) link_NAG-ASN : angle 1.46985 ( 6) link_ALPHA1-6 : bond 0.00361 ( 2) link_ALPHA1-6 : angle 1.69817 ( 6) link_BETA1-4 : bond 0.00175 ( 4) link_BETA1-4 : angle 2.49150 ( 12) link_ALPHA1-3 : bond 0.01251 ( 2) link_ALPHA1-3 : angle 1.09251 ( 6) hydrogen bonds : bond 0.02723 ( 236) hydrogen bonds : angle 5.62175 ( 582) link_BETA1-6 : bond 0.00295 ( 2) link_BETA1-6 : angle 1.22083 ( 6) SS BOND : bond 0.00400 ( 16) SS BOND : angle 1.63794 ( 32) covalent geometry : bond 0.00247 ( 7218) covalent geometry : angle 0.59128 ( 9838) *********************** 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 143 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.711 Fit side-chains REVERT: B 109 GLU cc_start: 0.7059 (mp0) cc_final: 0.6805 (mp0) REVERT: E 98 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8646 (ptt180) REVERT: I 83 ASP cc_start: 0.8585 (m-30) cc_final: 0.8357 (m-30) REVERT: H 98 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8642 (ptt180) REVERT: L 83 ASP cc_start: 0.8577 (m-30) cc_final: 0.8322 (m-30) outliers start: 21 outliers final: 14 residues processed: 131 average time/residue: 1.2172 time to fit residues: 167.8695 Evaluate side-chains 136 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 E residue 128 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 128 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 87 optimal weight: 0.1980 chunk 28 optimal weight: 0.1980 chunk 10 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126102 restraints weight = 6964.743| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.57 r_work: 0.3342 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7246 Z= 0.124 Angle : 0.624 6.936 9906 Z= 0.307 Chirality : 0.045 0.152 1120 Planarity : 0.005 0.037 1248 Dihedral : 5.610 28.222 1234 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.89 % Allowed : 12.53 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.28), residues: 900 helix: -0.78 (0.80), residues: 42 sheet: 0.77 (0.33), residues: 240 loop : 0.08 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.006 0.001 HIS A 57 PHE 0.013 0.001 PHE H 29 TYR 0.015 0.002 TYR H 112 ARG 0.007 0.001 ARG A 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00668 ( 2) link_NAG-ASN : angle 1.46321 ( 6) link_ALPHA1-6 : bond 0.00401 ( 2) link_ALPHA1-6 : angle 1.66469 ( 6) link_BETA1-4 : bond 0.00242 ( 4) link_BETA1-4 : angle 2.52245 ( 12) link_ALPHA1-3 : bond 0.01198 ( 2) link_ALPHA1-3 : angle 1.02728 ( 6) hydrogen bonds : bond 0.02666 ( 236) hydrogen bonds : angle 5.53997 ( 582) link_BETA1-6 : bond 0.00262 ( 2) link_BETA1-6 : angle 1.24456 ( 6) SS BOND : bond 0.00515 ( 16) SS BOND : angle 2.03493 ( 32) covalent geometry : bond 0.00287 ( 7218) covalent geometry : angle 0.60540 ( 9838) *********************** 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 146 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.773 Fit side-chains REVERT: E 98 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8645 (ptt180) REVERT: I 83 ASP cc_start: 0.8573 (m-30) cc_final: 0.8341 (m-30) REVERT: H 98 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8642 (ptt180) REVERT: L 83 ASP cc_start: 0.8571 (m-30) cc_final: 0.8322 (m-30) outliers start: 21 outliers final: 12 residues processed: 133 average time/residue: 1.3028 time to fit residues: 182.1924 Evaluate side-chains 135 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 E residue 128 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 50 CYS 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 29 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN I 54 GLN L 54 GLN A 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121512 restraints weight = 7006.757| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.58 r_work: 0.3291 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 7246 Z= 0.240 Angle : 0.769 8.282 9906 Z= 0.378 Chirality : 0.050 0.185 1120 Planarity : 0.006 0.043 1248 Dihedral : 6.117 27.013 1234 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.62 % Allowed : 13.77 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.27), residues: 900 helix: -1.10 (0.75), residues: 42 sheet: 0.64 (0.33), residues: 240 loop : -0.03 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 141 HIS 0.005 0.001 HIS B 27 PHE 0.012 0.002 PHE E 29 TYR 0.019 0.003 TYR H 112 ARG 0.006 0.001 ARG A 239 Details of bonding type rmsd link_NAG-ASN : bond 0.01338 ( 2) link_NAG-ASN : angle 1.60314 ( 6) link_ALPHA1-6 : bond 0.00436 ( 2) link_ALPHA1-6 : angle 1.78162 ( 6) link_BETA1-4 : bond 0.00433 ( 4) link_BETA1-4 : angle 2.87411 ( 12) link_ALPHA1-3 : bond 0.01178 ( 2) link_ALPHA1-3 : angle 0.87677 ( 6) hydrogen bonds : bond 0.03445 ( 236) hydrogen bonds : angle 5.97655 ( 582) link_BETA1-6 : bond 0.00139 ( 2) link_BETA1-6 : angle 1.70632 ( 6) SS BOND : bond 0.00749 ( 16) SS BOND : angle 2.76012 ( 32) covalent geometry : bond 0.00582 ( 7218) covalent geometry : angle 0.74439 ( 9838) *********************** 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 136 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.800 Fit side-chains REVERT: E 43 LYS cc_start: 0.8131 (mptt) cc_final: 0.7922 (mptt) REVERT: E 98 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8662 (ptt180) REVERT: I 83 ASP cc_start: 0.8627 (m-30) cc_final: 0.8360 (m-30) REVERT: H 98 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8653 (ptt180) REVERT: L 83 ASP cc_start: 0.8645 (m-30) cc_final: 0.8361 (m-30) outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 1.2894 time to fit residues: 170.3839 Evaluate side-chains 132 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 3 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 85 optimal weight: 0.0980 chunk 81 optimal weight: 0.7980 chunk 56 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN I 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 = 0.3667 r_free = 0.3667 target = 0.146670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121718 restraints weight = 7108.124| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.60 r_work: 0.3293 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 7246 Z= 0.243 Angle : 1.309 59.188 9906 Z= 0.755 Chirality : 0.048 0.168 1120 Planarity : 0.006 0.044 1248 Dihedral : 6.098 26.886 1234 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.48 % Allowed : 13.50 % Favored : 84.02 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.27), residues: 900 helix: -1.12 (0.75), residues: 42 sheet: 0.62 (0.33), residues: 240 loop : -0.04 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 141 HIS 0.005 0.001 HIS B 57 PHE 0.011 0.002 PHE E 29 TYR 0.016 0.002 TYR H 112 ARG 0.005 0.001 ARG A 239 Details of bonding type rmsd link_NAG-ASN : bond 0.01041 ( 2) link_NAG-ASN : angle 1.60966 ( 6) link_ALPHA1-6 : bond 0.00332 ( 2) link_ALPHA1-6 : angle 1.82332 ( 6) link_BETA1-4 : bond 0.00452 ( 4) link_BETA1-4 : angle 2.85222 ( 12) link_ALPHA1-3 : bond 0.01141 ( 2) link_ALPHA1-3 : angle 0.91701 ( 6) hydrogen bonds : bond 0.03391 ( 236) hydrogen bonds : angle 5.96381 ( 582) link_BETA1-6 : bond 0.00011 ( 2) link_BETA1-6 : angle 1.62502 ( 6) SS BOND : bond 0.00625 ( 16) SS BOND : angle 2.72209 ( 32) covalent geometry : bond 0.00548 ( 7218) covalent geometry : angle 1.29791 ( 9838) ********************** 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 135 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.766 Fit side-chains REVERT: E 43 LYS cc_start: 0.8131 (mptt) cc_final: 0.7916 (mptt) REVERT: E 98 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8658 (ptt180) REVERT: I 83 ASP cc_start: 0.8630 (m-30) cc_final: 0.8364 (m-30) REVERT: H 98 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8644 (ptt180) REVERT: L 83 ASP cc_start: 0.8642 (m-30) cc_final: 0.8356 (m-30) REVERT: A 50 CYS cc_start: 0.7340 (OUTLIER) cc_final: 0.5766 (m) outliers start: 18 outliers final: 10 residues processed: 124 average time/residue: 1.2563 time to fit residues: 164.3096 Evaluate side-chains 128 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 57 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 153 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 80 optimal weight: 0.4980 chunk 18 optimal weight: 0.3980 chunk 51 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 overall best weight: 0.2436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 GLN ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121966 restraints weight = 6942.627| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.57 r_work: 0.3296 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 7246 Z= 0.242 Angle : 1.309 59.200 9906 Z= 0.755 Chirality : 0.048 0.168 1120 Planarity : 0.006 0.044 1248 Dihedral : 6.098 26.886 1234 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.79 % Allowed : 14.19 % Favored : 84.02 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.27), residues: 900 helix: -1.12 (0.75), residues: 42 sheet: 0.62 (0.33), residues: 240 loop : -0.04 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 141 HIS 0.005 0.001 HIS B 57 PHE 0.011 0.002 PHE E 29 TYR 0.016 0.002 TYR H 112 ARG 0.005 0.001 ARG A 239 Details of bonding type rmsd link_NAG-ASN : bond 0.01040 ( 2) link_NAG-ASN : angle 1.60966 ( 6) link_ALPHA1-6 : bond 0.00331 ( 2) link_ALPHA1-6 : angle 1.82279 ( 6) link_BETA1-4 : bond 0.00453 ( 4) link_BETA1-4 : angle 2.85219 ( 12) link_ALPHA1-3 : bond 0.01141 ( 2) link_ALPHA1-3 : angle 0.91711 ( 6) hydrogen bonds : bond 0.03391 ( 236) hydrogen bonds : angle 5.96380 ( 582) link_BETA1-6 : bond 0.00010 ( 2) link_BETA1-6 : angle 1.62507 ( 6) SS BOND : bond 0.00625 ( 16) SS BOND : angle 2.72191 ( 32) covalent geometry : bond 0.00547 ( 7218) covalent geometry : angle 1.29787 ( 9838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5683.08 seconds wall clock time: 98 minutes 31.60 seconds (5911.60 seconds total)