Starting phenix.real_space_refine on Fri Jul 3 09:07:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8byi_16326/07_2026/8byi_16326_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8byi_16326/07_2026/8byi_16326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8byi_16326/07_2026/8byi_16326_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8byi_16326/07_2026/8byi_16326_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8byi_16326/07_2026/8byi_16326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8byi_16326/07_2026/8byi_16326.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 85 5.16 5 Na 2 4.78 5 C 8550 2.51 5 N 2075 2.21 5 O 2319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13031 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2548 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2548 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2548 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2548 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2548 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'CPS': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CPS': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'CPS': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CPS': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CPS': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.45, per 1000 atoms: 0.26 Number of scatterers: 13031 At special positions: 0 Unit cell: (91.494, 91.494, 121.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 Na 2 11.00 O 2319 8.00 N 2075 7.00 C 8550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " 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 NAG-ASN " NAG A 501 " - " ASN A 167 " " NAG B 501 " - " ASN B 167 " " NAG C 501 " - " ASN C 167 " " NAG D 501 " - " ASN D 167 " " NAG E 502 " - " ASN E 167 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 476.5 milliseconds 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3070 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 34.1% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 417 through 443 Processing helix chain 'B' and resid 12 through 22 Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 417 through 443 Processing helix chain 'C' and resid 12 through 22 Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 226 through 239 Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 279 through 302 Processing helix chain 'C' and resid 417 through 443 Processing helix chain 'D' and resid 12 through 22 Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 226 through 239 Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 279 through 302 Processing helix chain 'D' and resid 417 through 443 Processing helix chain 'E' and resid 12 through 22 Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 226 through 239 Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 279 through 302 Processing helix chain 'E' and resid 417 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 45 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 39 through 45 current: chain 'A' and resid 59 through 70 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 70 current: chain 'A' and resid 118 through 121 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 126 through 128 current: chain 'A' and resid 185 through 189 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 185 through 189 current: chain 'A' and resid 203 through 216 Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 45 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 39 through 45 current: chain 'B' and resid 59 through 70 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 59 through 70 current: chain 'B' and resid 118 through 121 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 126 through 128 current: chain 'B' and resid 185 through 189 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 185 through 189 current: chain 'B' and resid 203 through 216 Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 45 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 39 through 45 current: chain 'C' and resid 59 through 70 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 59 through 70 current: chain 'C' and resid 118 through 121 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 126 through 128 current: chain 'C' and resid 185 through 189 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 185 through 189 current: chain 'C' and resid 203 through 216 Processing sheet with id=AA4, first strand: chain 'D' and resid 39 through 45 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 39 through 45 current: chain 'D' and resid 59 through 70 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 70 current: chain 'D' and resid 118 through 121 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 126 through 128 current: chain 'D' and resid 185 through 189 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 185 through 189 current: chain 'D' and resid 203 through 216 Processing sheet with id=AA5, first strand: chain 'E' and resid 39 through 45 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 39 through 45 current: chain 'E' and resid 59 through 70 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 59 through 70 current: chain 'E' and resid 118 through 121 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 126 through 128 current: chain 'E' and resid 185 through 189 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 185 through 189 current: chain 'E' and resid 203 through 216 420 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1975 1.32 - 1.45: 3753 1.45 - 1.58: 7407 1.58 - 1.71: 80 1.71 - 1.84: 145 Bond restraints: 13360 Sorted by residual: bond pdb=" C20 CPS D 502 " pdb=" C9 CPS D 502 " ideal model delta sigma weight residual 1.536 1.381 0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" C20 CPS B 502 " pdb=" C9 CPS B 502 " ideal model delta sigma weight residual 1.536 1.381 0.155 2.00e-02 2.50e+03 6.01e+01 bond pdb=" C20 CPS E 501 " pdb=" C9 CPS E 501 " ideal model delta sigma weight residual 1.536 1.381 0.155 2.00e-02 2.50e+03 5.97e+01 bond pdb=" C20 CPS A 502 " pdb=" C9 CPS A 502 " ideal model delta sigma weight residual 1.536 1.382 0.154 2.00e-02 2.50e+03 5.93e+01 bond pdb=" C20 CPS C 502 " pdb=" C9 CPS C 502 " ideal model delta sigma weight residual 1.536 1.382 0.154 2.00e-02 2.50e+03 5.90e+01 ... (remaining 13355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 18064 2.45 - 4.89: 166 4.89 - 7.34: 35 7.34 - 9.78: 25 9.78 - 12.23: 20 Bond angle restraints: 18310 Sorted by residual: angle pdb=" O1S CPS A 502 " pdb=" S CPS A 502 " pdb=" O3S CPS A 502 " ideal model delta sigma weight residual 113.37 101.14 12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O1S CPS D 502 " pdb=" S CPS D 502 " pdb=" O3S CPS D 502 " ideal model delta sigma weight residual 113.37 101.15 12.22 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O1S CPS B 502 " pdb=" S CPS B 502 " pdb=" O3S CPS B 502 " ideal model delta sigma weight residual 113.37 101.16 12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O1S CPS E 501 " pdb=" S CPS E 501 " pdb=" O3S CPS E 501 " ideal model delta sigma weight residual 113.37 101.21 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O1S CPS C 502 " pdb=" S CPS C 502 " pdb=" O3S CPS C 502 " ideal model delta sigma weight residual 113.37 101.22 12.15 3.00e+00 1.11e-01 1.64e+01 ... (remaining 18305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.11: 7810 19.11 - 38.23: 245 38.23 - 57.34: 70 57.34 - 76.46: 10 76.46 - 95.57: 30 Dihedral angle restraints: 8165 sinusoidal: 3410 harmonic: 4755 Sorted by residual: dihedral pdb=" CA PHE A 145 " pdb=" C PHE A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta harmonic sigma weight residual 180.00 154.46 25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PHE B 145 " pdb=" C PHE B 145 " pdb=" N PRO B 146 " pdb=" CA PRO B 146 " ideal model delta harmonic sigma weight residual 180.00 154.51 25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA PHE E 145 " pdb=" C PHE E 145 " pdb=" N PRO E 146 " pdb=" CA PRO E 146 " ideal model delta harmonic sigma weight residual 180.00 154.54 25.46 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 8162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.700: 2175 0.700 - 1.400: 0 1.400 - 2.099: 10 2.099 - 2.799: 0 2.799 - 3.499: 5 Chirality restraints: 2190 Sorted by residual: chirality pdb=" C18 CPS D 502 " pdb=" C17 CPS D 502 " pdb=" C19 CPS D 502 " pdb=" C6 CPS D 502 " both_signs ideal model delta sigma weight residual False 2.51 -0.99 3.50 2.00e-01 2.50e+01 3.06e+02 chirality pdb=" C18 CPS B 502 " pdb=" C17 CPS B 502 " pdb=" C19 CPS B 502 " pdb=" C6 CPS B 502 " both_signs ideal model delta sigma weight residual False 2.51 -0.99 3.50 2.00e-01 2.50e+01 3.06e+02 chirality pdb=" C18 CPS C 502 " pdb=" C17 CPS C 502 " pdb=" C19 CPS C 502 " pdb=" C6 CPS C 502 " both_signs ideal model delta sigma weight residual False 2.51 -0.99 3.49 2.00e-01 2.50e+01 3.05e+02 ... (remaining 2187 not shown) Planarity restraints: 2205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 145 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO E 146 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 146 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 146 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 145 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO B 146 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 145 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO D 146 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " 0.021 5.00e-02 4.00e+02 ... (remaining 2202 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 197 2.69 - 3.24: 13148 3.24 - 3.79: 20189 3.79 - 4.35: 25900 4.35 - 4.90: 43080 Nonbonded interactions: 102514 Sorted by model distance: nonbonded pdb=" O HOH A 602 " pdb=" O HOH E 601 " model vdw 2.132 3.040 nonbonded pdb=" O HOH D 601 " pdb=" O HOH E 601 " model vdw 2.137 3.040 nonbonded pdb=" O HOH A 602 " pdb=" O HOH D 601 " model vdw 2.137 3.040 nonbonded pdb=" O HOH A 601 " pdb=" O HOH E 602 " model vdw 2.143 3.040 nonbonded pdb=" O HOH C 601 " pdb=" O HOH D 601 " model vdw 2.199 3.040 ... (remaining 102509 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 443) selection = (chain 'B' and resid 11 through 443) selection = (chain 'C' and resid 11 through 443) selection = (chain 'D' and resid 11 through 443) selection = (chain 'E' and resid 11 through 443) } 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 group one per residue 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: 1.000 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.680 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 : 0.009 0.155 13370 Z= 0.429 Angle : 0.725 12.228 18335 Z= 0.289 Chirality : 0.207 3.499 2190 Planarity : 0.003 0.036 2200 Dihedral : 12.071 95.575 5080 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.22), residues: 1580 helix: 4.12 (0.21), residues: 490 sheet: 0.87 (0.29), residues: 365 loop : -0.63 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 111 TYR 0.007 0.001 TYR C 67 PHE 0.008 0.001 PHE B 289 TRP 0.010 0.001 TRP C 70 HIS 0.007 0.001 HIS E 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00858 / 0.43 (13360) covalent geometry : angle 0.72472 / 0.29 (18310) SS BOND : bond 0.00055 / 0.03 ( 5) SS BOND : angle 0.43209 / 0.24 ( 10) hydrogen bonds : bond 0.08947 / 5.89 ( 420) hydrogen bonds : angle 4.46259 / 3.38 ( 1260) link_NAG-ASN : bond 0.00087 / 0.04 ( 5) link_NAG-ASN : angle 0.74129 / 0.46 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.384 Fit side-chains REVERT: A 19 LYS cc_start: 0.8238 (tptp) cc_final: 0.7680 (tmmt) REVERT: A 57 GLU cc_start: 0.7772 (tp30) cc_final: 0.7434 (tp30) REVERT: A 82 TYR cc_start: 0.8317 (m-80) cc_final: 0.8051 (m-80) REVERT: A 170 LEU cc_start: 0.8407 (mt) cc_final: 0.8108 (mm) REVERT: A 178 TYR cc_start: 0.6642 (p90) cc_final: 0.6426 (p90) REVERT: A 234 PHE cc_start: 0.7650 (t80) cc_final: 0.7446 (t80) REVERT: A 237 LEU cc_start: 0.7829 (mt) cc_final: 0.7612 (tp) REVERT: A 279 PRO cc_start: 0.7667 (Cg_endo) cc_final: 0.7403 (Cg_exo) REVERT: A 288 VAL cc_start: 0.8943 (p) cc_final: 0.8694 (p) REVERT: B 11 MET cc_start: 0.6578 (ptp) cc_final: 0.6337 (ptm) REVERT: B 16 ARG cc_start: 0.7336 (ttp-170) cc_final: 0.7023 (ttp80) REVERT: B 34 ASN cc_start: 0.7303 (m-40) cc_final: 0.7082 (m-40) REVERT: B 46 THR cc_start: 0.9261 (m) cc_final: 0.8901 (p) REVERT: B 56 LYS cc_start: 0.8238 (mtmt) cc_final: 0.7920 (mttm) REVERT: B 86 LYS cc_start: 0.7987 (tppt) cc_final: 0.7753 (mmtt) REVERT: B 170 LEU cc_start: 0.8348 (mt) cc_final: 0.8084 (mm) REVERT: B 234 PHE cc_start: 0.7632 (t80) cc_final: 0.7258 (t80) REVERT: B 279 PRO cc_start: 0.7691 (Cg_endo) cc_final: 0.7359 (Cg_exo) REVERT: B 288 VAL cc_start: 0.8937 (p) cc_final: 0.8665 (p) REVERT: C 19 LYS cc_start: 0.8328 (tptp) cc_final: 0.7732 (tmmt) REVERT: C 46 THR cc_start: 0.9133 (m) cc_final: 0.8920 (p) REVERT: C 56 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7841 (mttm) REVERT: C 82 TYR cc_start: 0.8397 (m-80) cc_final: 0.7957 (m-80) REVERT: C 226 ILE cc_start: 0.7894 (mt) cc_final: 0.7495 (mm) REVERT: D 11 MET cc_start: 0.6353 (ptp) cc_final: 0.6124 (ptm) REVERT: D 16 ARG cc_start: 0.7447 (ttp-170) cc_final: 0.7211 (ttp80) REVERT: D 19 LYS cc_start: 0.8269 (tptp) cc_final: 0.7588 (tmmt) REVERT: D 46 THR cc_start: 0.9246 (m) cc_final: 0.9036 (p) REVERT: D 56 LYS cc_start: 0.8216 (mtmt) cc_final: 0.7793 (mttp) REVERT: D 57 GLU cc_start: 0.8007 (tp30) cc_final: 0.7687 (tp30) REVERT: D 61 THR cc_start: 0.7846 (p) cc_final: 0.7632 (p) REVERT: D 170 LEU cc_start: 0.8377 (mt) cc_final: 0.8156 (mm) REVERT: D 279 PRO cc_start: 0.7566 (Cg_endo) cc_final: 0.7144 (Cg_exo) REVERT: E 13 ASP cc_start: 0.8017 (p0) cc_final: 0.7784 (m-30) REVERT: E 19 LYS cc_start: 0.8356 (tptp) cc_final: 0.7774 (tmmt) REVERT: E 56 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7940 (mttm) REVERT: E 82 TYR cc_start: 0.8344 (m-80) cc_final: 0.8035 (m-80) REVERT: E 86 LYS cc_start: 0.7981 (tppt) cc_final: 0.7752 (mmtt) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.0994 time to fit residues: 63.7350 Evaluate side-chains 300 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.0370 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 overall best weight: 1.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 HIS A 186 GLN B 68 HIS B 186 GLN B 295 ASN C 68 HIS C 186 GLN D 186 GLN E 68 HIS E 186 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.155024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.129613 restraints weight = 17205.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.130116 restraints weight = 20688.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.130641 restraints weight = 16595.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.131037 restraints weight = 15043.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.131170 restraints weight = 13139.493| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13370 Z= 0.135 Angle : 0.569 9.118 18335 Z= 0.288 Chirality : 0.044 0.185 2190 Planarity : 0.004 0.043 2200 Dihedral : 7.157 63.317 2260 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.22), residues: 1580 helix: 2.34 (0.22), residues: 515 sheet: 0.52 (0.26), residues: 420 loop : -0.67 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 249 TYR 0.021 0.001 TYR B 284 PHE 0.017 0.002 PHE D 289 TRP 0.008 0.001 TRP E 128 HIS 0.008 0.002 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (13360) covalent geometry : angle 0.56843 / 0.29 (18310) SS BOND : bond 0.00034 / 0.02 ( 5) SS BOND : angle 0.33963 / 0.19 ( 10) hydrogen bonds : bond 0.03741 / 2.53 ( 420) hydrogen bonds : angle 4.13957 / 3.10 ( 1260) link_NAG-ASN : bond 0.00057 / 0.03 ( 5) link_NAG-ASN : angle 0.95169 / 0.58 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8181 (tptp) cc_final: 0.7776 (tmmt) REVERT: B 19 LYS cc_start: 0.8116 (tptp) cc_final: 0.7584 (tmmt) REVERT: B 184 GLU cc_start: 0.7093 (pt0) cc_final: 0.6770 (mt-10) REVERT: B 234 PHE cc_start: 0.7245 (t80) cc_final: 0.7042 (t80) REVERT: C 13 ASP cc_start: 0.7704 (p0) cc_final: 0.7366 (m-30) REVERT: C 16 ARG cc_start: 0.8171 (ttp-110) cc_final: 0.7873 (ttp-170) REVERT: C 19 LYS cc_start: 0.8294 (tptp) cc_final: 0.7802 (tmmt) REVERT: C 52 ASP cc_start: 0.7822 (t0) cc_final: 0.7618 (t0) REVERT: C 165 SER cc_start: 0.7515 (t) cc_final: 0.7303 (p) REVERT: C 297 LEU cc_start: 0.8770 (tt) cc_final: 0.8540 (tt) REVERT: D 19 LYS cc_start: 0.8218 (tptp) cc_final: 0.7721 (tmmt) REVERT: D 178 TYR cc_start: 0.6007 (p90) cc_final: 0.5683 (p90) REVERT: D 227 MET cc_start: 0.8077 (ttp) cc_final: 0.6644 (tpt) REVERT: E 19 LYS cc_start: 0.8350 (tptp) cc_final: 0.7786 (tmmt) REVERT: E 65 TRP cc_start: 0.8886 (p-90) cc_final: 0.8577 (p90) REVERT: E 227 MET cc_start: 0.7692 (ttp) cc_final: 0.6750 (tpt) outliers start: 1 outliers final: 1 residues processed: 365 average time/residue: 0.0912 time to fit residues: 48.9567 Evaluate side-chains 265 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 94 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.0470 chunk 136 optimal weight: 6.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN A 295 ASN B 186 GLN C 186 GLN C 295 ASN D 186 GLN D 295 ASN E 186 GLN E 295 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.153509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.127546 restraints weight = 17178.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.128414 restraints weight = 18133.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.129480 restraints weight = 14493.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.130057 restraints weight = 12623.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.130409 restraints weight = 11106.244| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13370 Z= 0.122 Angle : 0.525 5.310 18335 Z= 0.273 Chirality : 0.044 0.145 2190 Planarity : 0.004 0.040 2200 Dihedral : 5.962 54.912 2260 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.21), residues: 1580 helix: 2.26 (0.23), residues: 495 sheet: 0.40 (0.26), residues: 420 loop : -0.82 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 135 TYR 0.016 0.001 TYR E 284 PHE 0.018 0.002 PHE D 234 TRP 0.007 0.001 TRP D 65 HIS 0.007 0.002 HIS B 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (13360) covalent geometry : angle 0.52468 / 0.27 (18310) SS BOND : bond 0.00150 / 0.09 ( 5) SS BOND : angle 0.40211 / 0.22 ( 10) hydrogen bonds : bond 0.03447 / 2.35 ( 420) hydrogen bonds : angle 4.07777 / 3.01 ( 1260) link_NAG-ASN : bond 0.00141 / 0.08 ( 5) link_NAG-ASN : angle 1.00201 / 0.60 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7328 (ttp-170) cc_final: 0.7061 (ttp80) REVERT: A 19 LYS cc_start: 0.8210 (tptp) cc_final: 0.7712 (tmmt) REVERT: A 254 ILE cc_start: 0.8462 (mm) cc_final: 0.8259 (mm) REVERT: A 297 LEU cc_start: 0.8695 (tt) cc_final: 0.8159 (mt) REVERT: B 17 LEU cc_start: 0.7423 (tt) cc_final: 0.7173 (tt) REVERT: B 19 LYS cc_start: 0.8061 (tptp) cc_final: 0.7592 (tmmt) REVERT: B 56 LYS cc_start: 0.8694 (mttm) cc_final: 0.8285 (mmtt) REVERT: B 184 GLU cc_start: 0.7248 (pt0) cc_final: 0.6898 (mt-10) REVERT: B 234 PHE cc_start: 0.7406 (t80) cc_final: 0.7025 (t80) REVERT: C 13 ASP cc_start: 0.7705 (p0) cc_final: 0.7413 (m-30) REVERT: C 16 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7872 (ttp-170) REVERT: C 19 LYS cc_start: 0.8391 (tptp) cc_final: 0.7792 (tmmt) REVERT: C 56 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8173 (mmtt) REVERT: C 204 ASN cc_start: 0.8095 (t0) cc_final: 0.7334 (p0) REVERT: D 19 LYS cc_start: 0.8231 (tptp) cc_final: 0.7675 (tmmt) REVERT: D 52 ASP cc_start: 0.7711 (p0) cc_final: 0.7486 (t0) REVERT: D 178 TYR cc_start: 0.6022 (p90) cc_final: 0.5752 (p90) REVERT: D 204 ASN cc_start: 0.8044 (t0) cc_final: 0.7402 (p0) REVERT: D 435 ILE cc_start: 0.6881 (mm) cc_final: 0.6346 (mm) REVERT: E 19 LYS cc_start: 0.8286 (tptp) cc_final: 0.7742 (tmmt) REVERT: E 65 TRP cc_start: 0.8885 (p-90) cc_final: 0.8526 (p90) REVERT: E 204 ASN cc_start: 0.8071 (t0) cc_final: 0.7417 (p0) REVERT: E 227 MET cc_start: 0.7694 (ttp) cc_final: 0.6703 (tpt) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.0851 time to fit residues: 43.9483 Evaluate side-chains 269 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 120 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 145 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN B 186 GLN C 186 GLN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 HIS D 186 GLN D 295 ASN E 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.142636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.116418 restraints weight = 17329.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.116490 restraints weight = 17471.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.116481 restraints weight = 14998.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.116714 restraints weight = 14809.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.117412 restraints weight = 13424.695| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13370 Z= 0.263 Angle : 0.658 6.057 18335 Z= 0.342 Chirality : 0.048 0.161 2190 Planarity : 0.005 0.048 2200 Dihedral : 6.561 59.747 2260 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1580 helix: 1.34 (0.22), residues: 525 sheet: -0.39 (0.28), residues: 385 loop : -0.88 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 249 TYR 0.023 0.002 TYR D 284 PHE 0.013 0.003 PHE E 425 TRP 0.015 0.002 TRP A 128 HIS 0.008 0.003 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.26 (13360) covalent geometry : angle 0.65785 / 0.34 (18310) SS BOND : bond 0.00306 / 0.18 ( 5) SS BOND : angle 0.99666 / 0.57 ( 10) hydrogen bonds : bond 0.04206 / 2.82 ( 420) hydrogen bonds : angle 4.16103 / 3.02 ( 1260) link_NAG-ASN : bond 0.00077 / 0.04 ( 5) link_NAG-ASN : angle 0.74241 / 0.46 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7516 (ttp-170) cc_final: 0.7144 (ttp80) REVERT: A 19 LYS cc_start: 0.8311 (tptp) cc_final: 0.7838 (tmmt) REVERT: A 33 GLN cc_start: 0.6765 (tt0) cc_final: 0.6404 (mt0) REVERT: A 52 ASP cc_start: 0.8142 (t0) cc_final: 0.7901 (t0) REVERT: A 115 ASP cc_start: 0.7594 (p0) cc_final: 0.7356 (p0) REVERT: A 153 THR cc_start: 0.8660 (p) cc_final: 0.8379 (t) REVERT: A 169 THR cc_start: 0.8728 (t) cc_final: 0.8485 (p) REVERT: B 19 LYS cc_start: 0.8195 (tptp) cc_final: 0.7776 (tmmt) REVERT: B 56 LYS cc_start: 0.8680 (mttm) cc_final: 0.8319 (mmtm) REVERT: B 234 PHE cc_start: 0.7631 (t80) cc_final: 0.7203 (t80) REVERT: B 439 MET cc_start: 0.6608 (tmm) cc_final: 0.6227 (ttt) REVERT: C 16 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7885 (ttp-170) REVERT: C 19 LYS cc_start: 0.8411 (tptp) cc_final: 0.7897 (tmmt) REVERT: C 56 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8241 (mmtt) REVERT: C 179 MET cc_start: 0.6508 (ttt) cc_final: 0.6227 (ttt) REVERT: C 184 GLU cc_start: 0.7430 (pt0) cc_final: 0.7206 (mt-10) REVERT: D 17 LEU cc_start: 0.7654 (tt) cc_final: 0.7428 (tt) REVERT: D 19 LYS cc_start: 0.8257 (tptp) cc_final: 0.7750 (tmmt) REVERT: D 435 ILE cc_start: 0.7026 (mm) cc_final: 0.5850 (mm) REVERT: E 19 LYS cc_start: 0.8383 (tptp) cc_final: 0.7886 (tmmt) REVERT: E 52 ASP cc_start: 0.7962 (t0) cc_final: 0.7333 (p0) REVERT: E 129 VAL cc_start: 0.8989 (t) cc_final: 0.8712 (p) REVERT: E 227 MET cc_start: 0.8059 (ttp) cc_final: 0.6845 (tpt) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.0907 time to fit residues: 44.1897 Evaluate side-chains 274 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 150 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN A 295 ASN B 186 GLN B 295 ASN C 186 GLN C 295 ASN D 186 GLN D 295 ASN E 186 GLN E 295 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.144393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.117576 restraints weight = 17414.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.118484 restraints weight = 18194.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.119334 restraints weight = 15139.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.119815 restraints weight = 13068.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.120158 restraints weight = 11808.426| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13370 Z= 0.198 Angle : 0.594 5.640 18335 Z= 0.312 Chirality : 0.047 0.198 2190 Planarity : 0.005 0.049 2200 Dihedral : 6.300 53.487 2260 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.36 % Allowed : 3.45 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1580 helix: 1.32 (0.22), residues: 510 sheet: -0.77 (0.27), residues: 385 loop : -0.81 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 249 TYR 0.024 0.002 TYR C 284 PHE 0.017 0.002 PHE D 289 TRP 0.016 0.001 TRP D 185 HIS 0.008 0.003 HIS B 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (13360) covalent geometry : angle 0.59369 / 0.31 (18310) SS BOND : bond 0.00252 / 0.14 ( 5) SS BOND : angle 0.93073 / 0.51 ( 10) hydrogen bonds : bond 0.03889 / 2.59 ( 420) hydrogen bonds : angle 4.09764 / 2.99 ( 1260) link_NAG-ASN : bond 0.00023 / 0.01 ( 5) link_NAG-ASN : angle 0.71021 / 0.42 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 316 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7521 (ttp-170) cc_final: 0.7175 (ttp80) REVERT: A 19 LYS cc_start: 0.8282 (tptp) cc_final: 0.7828 (tmmt) REVERT: A 33 GLN cc_start: 0.6838 (tt0) cc_final: 0.6408 (mt0) REVERT: A 153 THR cc_start: 0.8696 (p) cc_final: 0.8484 (t) REVERT: A 227 MET cc_start: 0.8059 (ttp) cc_final: 0.6416 (tpp) REVERT: B 19 LYS cc_start: 0.8258 (tptp) cc_final: 0.7741 (tmmt) REVERT: B 56 LYS cc_start: 0.8689 (mttm) cc_final: 0.8302 (mmtt) REVERT: B 227 MET cc_start: 0.6524 (tpt) cc_final: 0.6158 (tpp) REVERT: B 234 PHE cc_start: 0.7626 (t80) cc_final: 0.7122 (t80) REVERT: C 16 ARG cc_start: 0.8116 (ttp-110) cc_final: 0.7872 (ttp-170) REVERT: C 19 LYS cc_start: 0.8425 (tptp) cc_final: 0.7834 (tmmt) REVERT: C 56 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8215 (mmtt) REVERT: C 179 MET cc_start: 0.6568 (ttt) cc_final: 0.6328 (ttt) REVERT: C 184 GLU cc_start: 0.7585 (pt0) cc_final: 0.7296 (mt-10) REVERT: D 17 LEU cc_start: 0.7570 (tt) cc_final: 0.7313 (tt) REVERT: D 19 LYS cc_start: 0.8295 (tptp) cc_final: 0.7731 (tmmt) REVERT: D 57 GLU cc_start: 0.7617 (tp30) cc_final: 0.7329 (tp30) REVERT: D 213 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8131 (ttpp) REVERT: D 435 ILE cc_start: 0.7092 (mm) cc_final: 0.6327 (mm) REVERT: E 19 LYS cc_start: 0.8323 (tptp) cc_final: 0.7841 (tmmt) REVERT: E 435 ILE cc_start: 0.6376 (mt) cc_final: 0.5977 (mt) outliers start: 5 outliers final: 4 residues processed: 316 average time/residue: 0.0804 time to fit residues: 38.7937 Evaluate side-chains 267 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 263 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 44 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 51 optimal weight: 0.0000 chunk 134 optimal weight: 0.0670 chunk 91 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 overall best weight: 1.0128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN B 63 ASN B 186 GLN C 186 GLN D 186 GLN E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.146291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.120111 restraints weight = 16910.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.121221 restraints weight = 13777.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.122468 restraints weight = 11658.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.123295 restraints weight = 9602.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.123614 restraints weight = 8808.653| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13370 Z= 0.113 Angle : 0.541 7.712 18335 Z= 0.278 Chirality : 0.044 0.174 2190 Planarity : 0.004 0.050 2200 Dihedral : 5.868 51.197 2260 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.15 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.21), residues: 1580 helix: 1.56 (0.23), residues: 510 sheet: -0.37 (0.27), residues: 350 loop : -0.83 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 249 TYR 0.017 0.001 TYR B 284 PHE 0.024 0.002 PHE D 234 TRP 0.007 0.001 TRP A 65 HIS 0.008 0.002 HIS B 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (13360) covalent geometry : angle 0.54051 / 0.28 (18310) SS BOND : bond 0.00064 / 0.03 ( 5) SS BOND : angle 0.68196 / 0.36 ( 10) hydrogen bonds : bond 0.03448 / 2.30 ( 420) hydrogen bonds : angle 3.96981 / 2.88 ( 1260) link_NAG-ASN : bond 0.00111 / 0.06 ( 5) link_NAG-ASN : angle 0.71801 / 0.44 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7436 (ttp-170) cc_final: 0.7124 (ttp80) REVERT: A 19 LYS cc_start: 0.8200 (tptp) cc_final: 0.7758 (tmmt) REVERT: A 153 THR cc_start: 0.8697 (p) cc_final: 0.8475 (t) REVERT: B 19 LYS cc_start: 0.8222 (tptp) cc_final: 0.7692 (tmmt) REVERT: B 56 LYS cc_start: 0.8752 (mttm) cc_final: 0.8314 (mmtt) REVERT: B 227 MET cc_start: 0.6554 (tpt) cc_final: 0.6186 (tpp) REVERT: C 16 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7728 (ttp-170) REVERT: C 19 LYS cc_start: 0.8324 (tptp) cc_final: 0.7762 (tmmt) REVERT: C 56 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8313 (mmtp) REVERT: C 184 GLU cc_start: 0.7514 (pt0) cc_final: 0.7181 (mt-10) REVERT: D 19 LYS cc_start: 0.8177 (tptp) cc_final: 0.7667 (tmmt) REVERT: D 178 TYR cc_start: 0.5985 (p90) cc_final: 0.5584 (p90) REVERT: D 435 ILE cc_start: 0.6980 (mm) cc_final: 0.6763 (mm) REVERT: E 19 LYS cc_start: 0.8283 (tptp) cc_final: 0.7753 (tmmt) REVERT: E 56 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8539 (mmtt) REVERT: E 227 MET cc_start: 0.8100 (ttp) cc_final: 0.6478 (tpp) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.0913 time to fit residues: 45.0958 Evaluate side-chains 254 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 3 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN B 63 ASN B 186 GLN C 186 GLN D 186 GLN E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.147487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.121194 restraints weight = 16897.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.122794 restraints weight = 13200.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.124242 restraints weight = 11075.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.125199 restraints weight = 9774.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.125524 restraints weight = 8911.844| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13370 Z= 0.110 Angle : 0.533 8.040 18335 Z= 0.273 Chirality : 0.043 0.153 2190 Planarity : 0.004 0.047 2200 Dihedral : 5.775 54.040 2260 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.22), residues: 1580 helix: 1.53 (0.23), residues: 515 sheet: -0.33 (0.27), residues: 350 loop : -0.77 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 249 TYR 0.017 0.001 TYR D 284 PHE 0.017 0.002 PHE D 234 TRP 0.009 0.001 TRP B 65 HIS 0.007 0.002 HIS B 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13360) covalent geometry : angle 0.53324 / 0.27 (18310) SS BOND : bond 0.00141 / 0.09 ( 5) SS BOND : angle 0.63052 / 0.36 ( 10) hydrogen bonds : bond 0.03419 / 2.29 ( 420) hydrogen bonds : angle 3.92603 / 2.87 ( 1260) link_NAG-ASN : bond 0.00139 / 0.08 ( 5) link_NAG-ASN : angle 0.73090 / 0.44 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8229 (tptp) cc_final: 0.7773 (tmmt) REVERT: A 435 ILE cc_start: 0.6682 (mm) cc_final: 0.5763 (mt) REVERT: B 19 LYS cc_start: 0.8195 (tptp) cc_final: 0.7670 (tmmt) REVERT: B 56 LYS cc_start: 0.8761 (mttm) cc_final: 0.8361 (mmtt) REVERT: C 16 ARG cc_start: 0.7896 (ttp-110) cc_final: 0.7635 (ttp-170) REVERT: C 19 LYS cc_start: 0.8313 (tptp) cc_final: 0.7743 (tmmt) REVERT: C 56 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8374 (mmtp) REVERT: C 82 TYR cc_start: 0.8380 (m-80) cc_final: 0.8092 (m-80) REVERT: C 184 GLU cc_start: 0.7458 (pt0) cc_final: 0.7213 (mt-10) REVERT: D 19 LYS cc_start: 0.8157 (tptp) cc_final: 0.7625 (tmmt) REVERT: D 178 TYR cc_start: 0.5864 (p90) cc_final: 0.5485 (p90) REVERT: D 435 ILE cc_start: 0.6990 (mm) cc_final: 0.6732 (mm) REVERT: E 19 LYS cc_start: 0.8213 (tptp) cc_final: 0.7704 (tmmt) REVERT: E 56 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8351 (mmtt) REVERT: E 73 PHE cc_start: 0.7813 (p90) cc_final: 0.7576 (p90) REVERT: E 227 MET cc_start: 0.8062 (ttp) cc_final: 0.6510 (tpp) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.0827 time to fit residues: 38.8105 Evaluate side-chains 244 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 54 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 78 optimal weight: 0.1980 chunk 68 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN B 63 ASN B 186 GLN C 186 GLN C 295 ASN D 186 GLN E 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.146208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.119996 restraints weight = 17038.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.121412 restraints weight = 17473.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.121447 restraints weight = 14367.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.122029 restraints weight = 13233.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.122307 restraints weight = 11911.923| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13370 Z= 0.145 Angle : 0.569 8.088 18335 Z= 0.290 Chirality : 0.045 0.230 2190 Planarity : 0.005 0.046 2200 Dihedral : 5.954 59.532 2260 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.22), residues: 1580 helix: 1.56 (0.23), residues: 510 sheet: -0.53 (0.27), residues: 350 loop : -0.80 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 16 TYR 0.019 0.001 TYR A 284 PHE 0.031 0.002 PHE C 289 TRP 0.008 0.001 TRP E 65 HIS 0.007 0.002 HIS B 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (13360) covalent geometry : angle 0.56905 / 0.29 (18310) SS BOND : bond 0.00143 / 0.09 ( 5) SS BOND : angle 0.82907 / 0.46 ( 10) hydrogen bonds : bond 0.03585 / 2.40 ( 420) hydrogen bonds : angle 3.99256 / 2.91 ( 1260) link_NAG-ASN : bond 0.00067 / 0.04 ( 5) link_NAG-ASN : angle 0.79103 / 0.48 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8227 (tptp) cc_final: 0.7791 (tmmt) REVERT: A 115 ASP cc_start: 0.7590 (p0) cc_final: 0.7296 (p0) REVERT: A 435 ILE cc_start: 0.6651 (mm) cc_final: 0.5898 (mm) REVERT: B 19 LYS cc_start: 0.8252 (tptp) cc_final: 0.7713 (tmmt) REVERT: B 56 LYS cc_start: 0.8802 (mttm) cc_final: 0.8326 (mmtt) REVERT: B 227 MET cc_start: 0.8702 (ttp) cc_final: 0.6688 (tpt) REVERT: C 16 ARG cc_start: 0.7995 (ttp-110) cc_final: 0.7744 (ttp-170) REVERT: C 19 LYS cc_start: 0.8327 (tptp) cc_final: 0.7771 (tmmt) REVERT: C 56 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8252 (mmtt) REVERT: C 184 GLU cc_start: 0.7568 (pt0) cc_final: 0.7201 (mt-10) REVERT: C 250 ILE cc_start: 0.7708 (pt) cc_final: 0.7421 (pt) REVERT: D 19 LYS cc_start: 0.8155 (tptp) cc_final: 0.7627 (tmmt) REVERT: D 178 TYR cc_start: 0.5975 (p90) cc_final: 0.5558 (p90) REVERT: D 435 ILE cc_start: 0.7173 (mm) cc_final: 0.6053 (mm) REVERT: E 19 LYS cc_start: 0.8252 (tptp) cc_final: 0.7719 (tmmt) REVERT: E 56 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8373 (mmtt) REVERT: E 169 THR cc_start: 0.8742 (t) cc_final: 0.8433 (p) REVERT: E 227 MET cc_start: 0.8237 (ttp) cc_final: 0.6596 (tpp) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.0789 time to fit residues: 35.5871 Evaluate side-chains 245 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 85 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 93 optimal weight: 0.0970 chunk 151 optimal weight: 0.0470 chunk 116 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.9478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN A 295 ASN B 63 ASN B 186 GLN C 186 GLN D 186 GLN E 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.148187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.119698 restraints weight = 17367.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.121804 restraints weight = 13563.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.122300 restraints weight = 11353.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.123046 restraints weight = 10078.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.123628 restraints weight = 9271.913| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13370 Z= 0.115 Angle : 0.564 7.733 18335 Z= 0.286 Chirality : 0.044 0.173 2190 Planarity : 0.005 0.046 2200 Dihedral : 5.887 59.875 2260 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1580 helix: 1.49 (0.23), residues: 510 sheet: -0.63 (0.28), residues: 320 loop : -0.94 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 249 TYR 0.017 0.001 TYR A 443 PHE 0.026 0.002 PHE A 289 TRP 0.007 0.001 TRP E 65 HIS 0.007 0.002 HIS B 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (13360) covalent geometry : angle 0.56352 / 0.29 (18310) SS BOND : bond 0.00150 / 0.09 ( 5) SS BOND : angle 0.77765 / 0.43 ( 10) hydrogen bonds : bond 0.03496 / 2.34 ( 420) hydrogen bonds : angle 4.01257 / 2.93 ( 1260) link_NAG-ASN : bond 0.00127 / 0.07 ( 5) link_NAG-ASN : angle 0.74965 / 0.45 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8175 (tptp) cc_final: 0.7735 (tmmt) REVERT: A 115 ASP cc_start: 0.7546 (p0) cc_final: 0.7232 (p0) REVERT: B 19 LYS cc_start: 0.8201 (tptp) cc_final: 0.7663 (tmmt) REVERT: B 56 LYS cc_start: 0.8850 (mttm) cc_final: 0.8413 (mmtt) REVERT: B 227 MET cc_start: 0.8717 (ttp) cc_final: 0.6570 (tpt) REVERT: C 16 ARG cc_start: 0.7975 (ttp-110) cc_final: 0.7732 (ttp-170) REVERT: C 19 LYS cc_start: 0.8330 (tptp) cc_final: 0.7683 (tmmt) REVERT: C 56 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8233 (mmtt) REVERT: C 127 MET cc_start: 0.8012 (mtt) cc_final: 0.7680 (mtt) REVERT: C 184 GLU cc_start: 0.7585 (pt0) cc_final: 0.7170 (mt-10) REVERT: D 19 LYS cc_start: 0.8164 (tptp) cc_final: 0.7595 (tmmt) REVERT: D 178 TYR cc_start: 0.5795 (p90) cc_final: 0.5430 (p90) REVERT: D 234 PHE cc_start: 0.7454 (t80) cc_final: 0.6956 (t80) REVERT: D 435 ILE cc_start: 0.7017 (mm) cc_final: 0.5878 (mm) REVERT: E 19 LYS cc_start: 0.8272 (tptp) cc_final: 0.7706 (tmmt) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.0845 time to fit residues: 37.5348 Evaluate side-chains 244 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 76 optimal weight: 6.9990 chunk 97 optimal weight: 0.0010 chunk 36 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN B 63 ASN B 186 GLN C 186 GLN D 186 GLN E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.149293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.123050 restraints weight = 17071.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.123512 restraints weight = 17088.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.123821 restraints weight = 14082.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.123905 restraints weight = 13968.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.124217 restraints weight = 12620.425| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13370 Z= 0.115 Angle : 0.567 7.196 18335 Z= 0.287 Chirality : 0.044 0.185 2190 Planarity : 0.005 0.046 2200 Dihedral : 5.922 60.587 2260 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.21), residues: 1580 helix: 1.52 (0.23), residues: 510 sheet: -0.67 (0.28), residues: 320 loop : -0.91 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 249 TYR 0.019 0.001 TYR A 284 PHE 0.024 0.002 PHE A 73 TRP 0.011 0.001 TRP B 128 HIS 0.007 0.002 HIS B 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (13360) covalent geometry : angle 0.56639 / 0.29 (18310) SS BOND : bond 0.00144 / 0.08 ( 5) SS BOND : angle 0.83582 / 0.47 ( 10) hydrogen bonds : bond 0.03474 / 2.31 ( 420) hydrogen bonds : angle 3.98197 / 2.91 ( 1260) link_NAG-ASN : bond 0.00115 / 0.07 ( 5) link_NAG-ASN : angle 0.78847 / 0.47 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8206 (tptp) cc_final: 0.7776 (tmmt) REVERT: A 115 ASP cc_start: 0.7537 (p0) cc_final: 0.7212 (p0) REVERT: B 19 LYS cc_start: 0.8240 (tptp) cc_final: 0.7677 (tmmt) REVERT: B 56 LYS cc_start: 0.8842 (mttm) cc_final: 0.8450 (mmtt) REVERT: B 179 MET cc_start: 0.6616 (ttt) cc_final: 0.6373 (ttt) REVERT: C 16 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7671 (ttp-170) REVERT: C 19 LYS cc_start: 0.8322 (tptp) cc_final: 0.7744 (tmmt) REVERT: C 56 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8315 (mmtt) REVERT: C 115 ASP cc_start: 0.7465 (p0) cc_final: 0.7178 (p0) REVERT: C 184 GLU cc_start: 0.7556 (pt0) cc_final: 0.7156 (mt-10) REVERT: D 19 LYS cc_start: 0.8150 (tptp) cc_final: 0.7610 (tmmt) REVERT: D 178 TYR cc_start: 0.5783 (p90) cc_final: 0.5433 (p90) REVERT: D 234 PHE cc_start: 0.7380 (t80) cc_final: 0.6886 (t80) REVERT: D 298 PHE cc_start: 0.7556 (m-80) cc_final: 0.6836 (m-80) REVERT: D 435 ILE cc_start: 0.7102 (mm) cc_final: 0.5971 (mm) REVERT: E 19 LYS cc_start: 0.8218 (tptp) cc_final: 0.7712 (tmmt) REVERT: E 56 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8360 (mmtt) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.0835 time to fit residues: 37.1031 Evaluate side-chains 239 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 119 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 0.0170 chunk 113 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN B 63 ASN C 186 GLN D 186 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.148828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.120082 restraints weight = 17247.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.122117 restraints weight = 13561.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.122423 restraints weight = 12118.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.123407 restraints weight = 10734.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.123854 restraints weight = 9443.345| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13370 Z= 0.111 Angle : 0.565 7.094 18335 Z= 0.287 Chirality : 0.044 0.243 2190 Planarity : 0.005 0.047 2200 Dihedral : 5.960 60.196 2260 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.21), residues: 1580 helix: 1.54 (0.23), residues: 510 sheet: -0.72 (0.26), residues: 390 loop : -0.87 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 16 TYR 0.019 0.001 TYR D 443 PHE 0.020 0.002 PHE A 289 TRP 0.007 0.001 TRP E 65 HIS 0.007 0.002 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (13360) covalent geometry : angle 0.56501 / 0.29 (18310) SS BOND : bond 0.00129 / 0.07 ( 5) SS BOND : angle 0.80797 / 0.45 ( 10) hydrogen bonds : bond 0.03411 / 2.26 ( 420) hydrogen bonds : angle 3.99771 / 2.92 ( 1260) link_NAG-ASN : bond 0.00130 / 0.07 ( 5) link_NAG-ASN : angle 0.78848 / 0.47 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1663.41 seconds wall clock time: 29 minutes 34.08 seconds (1774.08 seconds total)