Starting phenix.real_space_refine on Mon Apr 28 08:25:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8d_18999/04_2025/8r8d_18999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8d_18999/04_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_18999/04_2025/8r8d_18999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8d_18999/04_2025/8r8d_18999.map" model { file = "/net/cci-nas-00/data/ceres_data/8r8d_18999/04_2025/8r8d_18999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8d_18999/04_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-5669/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: 4.95, per 1000 atoms: 0.70 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: 1.93 Conformation dependent library (CDL) restraints added in 990.7 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: 0.93 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: 1.97 Time building geometry restraints manager: 2.26 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: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.590 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:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.610 ------------------------------------------------------------------------------- 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 : 0.798 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: 1.2766 time to fit residues: 187.6752 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 : 0.776 ------------------------------------------------------------------------------- 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 : 0.826 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: 0.8307 (m-30) REVERT: H 98 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8607 (ptt180) REVERT: L 83 ASP cc_start: 0.8553 (m-30) cc_final: 0.8308 (m-30) outliers start: 26 outliers final: 15 residues processed: 134 average time/residue: 1.3167 time to fit residues: 185.4241 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 : 1.235 ------------------------------------------------------------------------------- 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: 0.8980 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 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: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.156412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133831 restraints weight = 6592.060| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.28 r_work: 0.3365 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1390 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= 0.153 Angle : 0.656 7.035 9906 Z= 0.322 Chirality : 0.047 0.168 1120 Planarity : 0.005 0.038 1248 Dihedral : 7.185 47.222 1234 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.34 % Allowed : 9.37 % 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: -0.90 (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 0.016 0.002 TRP H 47 HIS 0.005 0.001 HIS B 57 PHE 0.012 0.002 PHE H 29 TYR 0.012 0.002 TYR H 80 ARG 0.005 0.001 ARG A 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00920 ( 2) link_NAG-ASN : angle 1.65422 ( 6) link_ALPHA1-6 : bond 0.00549 ( 2) link_ALPHA1-6 : angle 1.91998 ( 6) link_BETA1-4 : bond 0.00203 ( 4) link_BETA1-4 : angle 2.65205 ( 12) link_ALPHA1-3 : bond 0.01147 ( 2) link_ALPHA1-3 : angle 1.15332 ( 6) hydrogen bonds : bond 0.03464 ( 236) hydrogen bonds : angle 6.06071 ( 582) link_BETA1-6 : bond 0.00246 ( 2) link_BETA1-6 : angle 1.23531 ( 6) SS BOND : bond 0.00479 ( 16) SS BOND : angle 1.31685 ( 32) covalent geometry : bond 0.00364 ( 7218) covalent geometry : angle 0.64349 ( 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 136 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: I 83 ASP cc_start: 0.8563 (m-30) cc_final: 0.8332 (m-30) REVERT: L 83 ASP cc_start: 0.8597 (m-30) cc_final: 0.8353 (m-30) outliers start: 17 outliers final: 14 residues processed: 125 average time/residue: 1.5395 time to fit residues: 201.9730 Evaluate side-chains 129 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 3 GLN 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: 0.9980 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 84 optimal weight: 0.0060 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.157062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134550 restraints weight = 6547.778| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.28 r_work: 0.3370 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7246 Z= 0.132 Angle : 0.634 7.054 9906 Z= 0.310 Chirality : 0.046 0.177 1120 Planarity : 0.005 0.041 1248 Dihedral : 6.521 38.836 1234 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.89 % Allowed : 9.92 % Favored : 87.19 % 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: -0.81 (0.83), residues: 42 sheet: 0.79 (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 0.006 0.001 HIS A 57 PHE 0.012 0.001 PHE H 29 TYR 0.010 0.002 TYR E 111 ARG 0.005 0.001 ARG A 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 2) link_NAG-ASN : angle 1.60835 ( 6) link_ALPHA1-6 : bond 0.00359 ( 2) link_ALPHA1-6 : angle 1.95851 ( 6) link_BETA1-4 : bond 0.00247 ( 4) link_BETA1-4 : angle 2.56917 ( 12) link_ALPHA1-3 : bond 0.01265 ( 2) link_ALPHA1-3 : angle 1.27943 ( 6) hydrogen bonds : bond 0.03065 ( 236) hydrogen bonds : angle 5.81332 ( 582) link_BETA1-6 : bond 0.00262 ( 2) link_BETA1-6 : angle 1.22347 ( 6) SS BOND : bond 0.00441 ( 16) SS BOND : angle 1.36924 ( 32) covalent geometry : bond 0.00309 ( 7218) covalent geometry : angle 0.61992 ( 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 143 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.846 Fit side-chains REVERT: E 98 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8626 (ptt180) REVERT: I 83 ASP cc_start: 0.8546 (m-30) cc_final: 0.8336 (m-30) REVERT: H 98 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8621 (ptt180) REVERT: L 83 ASP cc_start: 0.8612 (m-30) cc_final: 0.8373 (m-30) outliers start: 21 outliers final: 15 residues processed: 128 average time/residue: 1.7252 time to fit residues: 231.5963 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 : 0.795 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.157890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135743 restraints weight = 6445.468| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.25 r_work: 0.3386 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7246 Z= 0.119 Angle : 0.613 7.228 9906 Z= 0.300 Chirality : 0.045 0.166 1120 Planarity : 0.005 0.040 1248 Dihedral : 6.052 34.782 1234 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.62 % Allowed : 11.16 % 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 (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: -0.81 (0.82), 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 0.015 0.002 TRP H 47 HIS 0.005 0.001 HIS B 57 PHE 0.011 0.001 PHE E 29 TYR 0.011 0.002 TYR H 80 ARG 0.005 0.001 ARG A 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 2) link_NAG-ASN : angle 1.52029 ( 6) link_ALPHA1-6 : bond 0.00411 ( 2) link_ALPHA1-6 : angle 1.88602 ( 6) link_BETA1-4 : bond 0.00203 ( 4) link_BETA1-4 : angle 2.47637 ( 12) link_ALPHA1-3 : bond 0.01225 ( 2) link_ALPHA1-3 : angle 1.27864 ( 6) hydrogen bonds : bond 0.02895 ( 236) hydrogen bonds : angle 5.64844 ( 582) link_BETA1-6 : bond 0.00282 ( 2) link_BETA1-6 : angle 1.18940 ( 6) SS BOND : bond 0.00417 ( 16) SS BOND : angle 1.17810 ( 32) covalent geometry : bond 0.00276 ( 7218) covalent geometry : angle 0.60096 ( 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 141 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 1.184 Fit side-chains REVERT: B 109 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8026 (tm-30) REVERT: E 98 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8631 (ptt180) REVERT: I 83 ASP cc_start: 0.8589 (m-30) cc_final: 0.8364 (m-30) REVERT: H 98 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8628 (ptt180) REVERT: L 83 ASP cc_start: 0.8542 (m-30) cc_final: 0.8319 (m-30) outliers start: 19 outliers final: 14 residues processed: 130 average time/residue: 2.2095 time to fit residues: 303.1479 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 : 2.052 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.146164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.121398 restraints weight = 7029.781| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.58 r_work: 0.3290 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 : 0.005 0.061 7246 Z= 0.211 Angle : 0.722 7.907 9906 Z= 0.353 Chirality : 0.049 0.154 1120 Planarity : 0.005 0.041 1248 Dihedral : 6.255 31.678 1234 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.89 % Allowed : 11.29 % 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: 0.13 (0.28), residues: 900 helix: -1.15 (0.75), residues: 42 sheet: 0.70 (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 B 141 HIS 0.004 0.001 HIS A 27 PHE 0.012 0.002 PHE E 29 TYR 0.014 0.002 TYR I 87 ARG 0.005 0.001 ARG A 239 Details of bonding type rmsd link_NAG-ASN : bond 0.01242 ( 2) link_NAG-ASN : angle 1.61800 ( 6) link_ALPHA1-6 : bond 0.00395 ( 2) link_ALPHA1-6 : angle 1.91013 ( 6) link_BETA1-4 : bond 0.00420 ( 4) link_BETA1-4 : angle 2.76428 ( 12) link_ALPHA1-3 : bond 0.01273 ( 2) link_ALPHA1-3 : angle 1.16383 ( 6) hydrogen bonds : bond 0.03431 ( 236) hydrogen bonds : angle 5.97145 ( 582) link_BETA1-6 : bond 0.00028 ( 2) link_BETA1-6 : angle 1.56153 ( 6) SS BOND : bond 0.00635 ( 16) SS BOND : angle 1.59937 ( 32) covalent geometry : bond 0.00509 ( 7218) covalent geometry : angle 0.70814 ( 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 132 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.657 Fit side-chains REVERT: E 98 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8648 (ptt180) REVERT: I 83 ASP cc_start: 0.8628 (m-30) cc_final: 0.8380 (m-30) REVERT: H 98 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8645 (ptt180) REVERT: L 83 ASP cc_start: 0.8595 (m-30) cc_final: 0.8333 (m-30) outliers start: 21 outliers final: 14 residues processed: 122 average time/residue: 1.6348 time to fit residues: 208.3642 Evaluate side-chains 125 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 169 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.148159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123468 restraints weight = 6846.487| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.57 r_work: 0.3313 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7246 Z= 0.160 Angle : 0.670 7.292 9906 Z= 0.329 Chirality : 0.047 0.187 1120 Planarity : 0.005 0.037 1248 Dihedral : 5.979 30.177 1234 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.17 % Allowed : 11.98 % 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 (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: 0.17 (0.28), residues: 900 helix: -1.02 (0.78), residues: 42 sheet: 0.74 (0.33), residues: 240 loop : -0.00 (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 0.002 PHE H 29 TYR 0.012 0.002 TYR H 80 ARG 0.005 0.001 ARG B 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00880 ( 2) link_NAG-ASN : angle 1.49873 ( 6) link_ALPHA1-6 : bond 0.00332 ( 2) link_ALPHA1-6 : angle 1.78197 ( 6) link_BETA1-4 : bond 0.00308 ( 4) link_BETA1-4 : angle 2.61366 ( 12) link_ALPHA1-3 : bond 0.01253 ( 2) link_ALPHA1-3 : angle 1.09594 ( 6) hydrogen bonds : bond 0.03088 ( 236) hydrogen bonds : angle 5.79464 ( 582) link_BETA1-6 : bond 0.00120 ( 2) link_BETA1-6 : angle 1.43652 ( 6) SS BOND : bond 0.00513 ( 16) SS BOND : angle 2.12007 ( 32) covalent geometry : bond 0.00384 ( 7218) covalent geometry : angle 0.65066 ( 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 139 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.807 Fit side-chains REVERT: E 98 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8652 (ptt180) REVERT: I 83 ASP cc_start: 0.8608 (m-30) cc_final: 0.8350 (m-30) REVERT: H 98 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8649 (ptt180) REVERT: L 83 ASP cc_start: 0.8601 (m-30) cc_final: 0.8342 (m-30) outliers start: 23 outliers final: 17 residues processed: 126 average time/residue: 1.5222 time to fit residues: 201.1827 Evaluate side-chains 132 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 3 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.147528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122823 restraints weight = 6959.321| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.58 r_work: 0.3306 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7246 Z= 0.190 Angle : 0.714 8.557 9906 Z= 0.352 Chirality : 0.048 0.177 1120 Planarity : 0.005 0.042 1248 Dihedral : 6.053 29.185 1234 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.03 % Allowed : 12.40 % 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: 0.12 (0.27), residues: 900 helix: -1.11 (0.76), residues: 42 sheet: 0.71 (0.33), residues: 240 loop : -0.04 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.004 0.001 HIS A 27 PHE 0.012 0.002 PHE E 29 TYR 0.012 0.002 TYR L 87 ARG 0.007 0.001 ARG A 107 Details of bonding type rmsd link_NAG-ASN : bond 0.01039 ( 2) link_NAG-ASN : angle 1.51871 ( 6) link_ALPHA1-6 : bond 0.00421 ( 2) link_ALPHA1-6 : angle 1.78488 ( 6) link_BETA1-4 : bond 0.00378 ( 4) link_BETA1-4 : angle 2.71777 ( 12) link_ALPHA1-3 : bond 0.01160 ( 2) link_ALPHA1-3 : angle 0.96176 ( 6) hydrogen bonds : bond 0.03202 ( 236) hydrogen bonds : angle 5.87130 ( 582) link_BETA1-6 : bond 0.00003 ( 2) link_BETA1-6 : angle 1.49367 ( 6) SS BOND : bond 0.00667 ( 16) SS BOND : angle 2.81457 ( 32) covalent geometry : bond 0.00456 ( 7218) covalent geometry : angle 0.68799 ( 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 141 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.815 Fit side-chains REVERT: E 98 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8655 (ptt180) REVERT: I 83 ASP cc_start: 0.8610 (m-30) cc_final: 0.8362 (m-30) REVERT: H 98 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8652 (ptt180) REVERT: L 83 ASP cc_start: 0.8608 (m-30) cc_final: 0.8357 (m-30) outliers start: 22 outliers final: 17 residues processed: 127 average time/residue: 1.3318 time to fit residues: 177.4762 Evaluate side-chains 137 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 3 VAL 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 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 29 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 chunk 73 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.148931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124277 restraints weight = 6991.366| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.58 r_work: 0.3324 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7246 Z= 0.151 Angle : 0.664 7.221 9906 Z= 0.327 Chirality : 0.046 0.162 1120 Planarity : 0.005 0.045 1248 Dihedral : 5.825 27.996 1234 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.03 % Allowed : 13.09 % Favored : 83.88 % 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: 0.19 (0.28), residues: 900 helix: -0.93 (0.79), residues: 42 sheet: 0.73 (0.33), residues: 240 loop : 0.02 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 47 HIS 0.005 0.001 HIS B 57 PHE 0.013 0.001 PHE E 29 TYR 0.012 0.002 TYR E 80 ARG 0.007 0.001 ARG A 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 2) link_NAG-ASN : angle 1.48995 ( 6) link_ALPHA1-6 : bond 0.00373 ( 2) link_ALPHA1-6 : angle 1.70254 ( 6) link_BETA1-4 : bond 0.00296 ( 4) link_BETA1-4 : angle 2.61563 ( 12) link_ALPHA1-3 : bond 0.01222 ( 2) link_ALPHA1-3 : angle 0.96242 ( 6) hydrogen bonds : bond 0.02948 ( 236) hydrogen bonds : angle 5.72892 ( 582) link_BETA1-6 : bond 0.00158 ( 2) link_BETA1-6 : angle 1.39500 ( 6) SS BOND : bond 0.00572 ( 16) SS BOND : angle 2.31563 ( 32) covalent geometry : bond 0.00359 ( 7218) covalent geometry : angle 0.64268 ( 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 141 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.932 Fit side-chains REVERT: B 50 CYS cc_start: 0.7207 (OUTLIER) cc_final: 0.5656 (m) REVERT: E 98 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8653 (ptt180) REVERT: I 83 ASP cc_start: 0.8598 (m-30) cc_final: 0.8352 (m-30) REVERT: H 98 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8651 (ptt180) REVERT: L 83 ASP cc_start: 0.8598 (m-30) cc_final: 0.8349 (m-30) REVERT: A 50 CYS cc_start: 0.7265 (OUTLIER) cc_final: 0.5724 (m) outliers start: 22 outliers final: 15 residues processed: 127 average time/residue: 2.1233 time to fit residues: 280.6463 Evaluate side-chains 137 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 3 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 0.7980 chunk 54 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 85 optimal weight: 0.1980 chunk 81 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.150254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125970 restraints weight = 7105.776| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.56 r_work: 0.3344 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.003 0.030 7246 Z= 0.114 Angle : 0.612 7.112 9906 Z= 0.302 Chirality : 0.045 0.153 1120 Planarity : 0.005 0.042 1248 Dihedral : 5.538 26.924 1234 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.89 % Allowed : 13.09 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.28), residues: 900 helix: -0.83 (0.80), residues: 42 sheet: 0.74 (0.33), residues: 240 loop : 0.10 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.005 0.001 HIS A 57 PHE 0.013 0.001 PHE H 29 TYR 0.016 0.001 TYR E 112 ARG 0.006 0.001 ARG B 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 2) link_NAG-ASN : angle 1.47469 ( 6) link_ALPHA1-6 : bond 0.00420 ( 2) link_ALPHA1-6 : angle 1.64656 ( 6) link_BETA1-4 : bond 0.00199 ( 4) link_BETA1-4 : angle 2.51547 ( 12) link_ALPHA1-3 : bond 0.01231 ( 2) link_ALPHA1-3 : angle 1.01459 ( 6) hydrogen bonds : bond 0.02668 ( 236) hydrogen bonds : angle 5.53395 ( 582) link_BETA1-6 : bond 0.00267 ( 2) link_BETA1-6 : angle 1.21786 ( 6) SS BOND : bond 0.00470 ( 16) SS BOND : angle 1.70748 ( 32) covalent geometry : bond 0.00261 ( 7218) covalent geometry : angle 0.59588 ( 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 147 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.086 Fit side-chains REVERT: E 98 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8644 (ptt180) REVERT: I 83 ASP cc_start: 0.8575 (m-30) cc_final: 0.8323 (m-30) REVERT: H 98 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8644 (ptt180) REVERT: L 83 ASP cc_start: 0.8577 (m-30) cc_final: 0.8344 (m-30) outliers start: 21 outliers final: 15 residues processed: 133 average time/residue: 1.9147 time to fit residues: 267.7101 Evaluate side-chains 137 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 3 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.0070 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126557 restraints weight = 6896.906| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.57 r_work: 0.3345 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7246 Z= 0.117 Angle : 0.615 7.292 9906 Z= 0.303 Chirality : 0.045 0.151 1120 Planarity : 0.005 0.042 1248 Dihedral : 5.409 25.914 1234 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.48 % Allowed : 13.77 % Favored : 83.75 % 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: -1.35 (0.70), residues: 50 sheet: 0.83 (0.33), residues: 236 loop : 0.08 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 HIS 0.006 0.001 HIS B 57 PHE 0.013 0.001 PHE E 29 TYR 0.017 0.002 TYR H 112 ARG 0.007 0.001 ARG B 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 2) link_NAG-ASN : angle 1.44010 ( 6) link_ALPHA1-6 : bond 0.00373 ( 2) link_ALPHA1-6 : angle 1.62497 ( 6) link_BETA1-4 : bond 0.00220 ( 4) link_BETA1-4 : angle 2.50417 ( 12) link_ALPHA1-3 : bond 0.01200 ( 2) link_ALPHA1-3 : angle 1.00327 ( 6) hydrogen bonds : bond 0.02629 ( 236) hydrogen bonds : angle 5.49009 ( 582) link_BETA1-6 : bond 0.00282 ( 2) link_BETA1-6 : angle 1.21383 ( 6) SS BOND : bond 0.00453 ( 16) SS BOND : angle 1.58342 ( 32) covalent geometry : bond 0.00273 ( 7218) covalent geometry : angle 0.60100 ( 9838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7543.22 seconds wall clock time: 137 minutes 17.70 seconds (8237.70 seconds total)