Starting phenix.real_space_refine on Sat Aug 23 16:27:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8byi_16326/08_2025/8byi_16326_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8byi_16326/08_2025/8byi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8byi_16326/08_2025/8byi_16326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8byi_16326/08_2025/8byi_16326.map" model { file = "/net/cci-nas-00/data/ceres_data/8byi_16326/08_2025/8byi_16326_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8byi_16326/08_2025/8byi_16326_trim.cif" } 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-2.0-5787/lib/python3.9/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, 57 Unusual residues: {' NA': 1, 'CPS': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 57 Unusual residues: {' NA': 1, 'CPS': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 3.25, per 1000 atoms: 0.25 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: 0.71 Conformation dependent library (CDL) restraints added in 478.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.25 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: 1.35 Time building geometry restraints manager: 0.98 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.310 Find NCS groups from input model: 0.240 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 aren 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 covalent geometry : bond 0.00858 (13360) covalent geometry : angle 0.72472 (18310) SS BOND : bond 0.00055 ( 5) SS BOND : angle 0.43209 ( 10) hydrogen bonds : bond 0.08947 ( 420) hydrogen bonds : angle 4.46259 ( 1260) link_NAG-ASN : bond 0.00087 ( 5) link_NAG-ASN : angle 0.74129 ( 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 : 0.301 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: 0.7666 (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: 0.1078 time to fit residues: 68.5075 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 : 0.381 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3667 r_free = 0.3667 target = 0.153679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.126977 restraints weight = 17187.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.128131 restraints weight = 20084.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.129006 restraints weight = 15274.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.129633 restraints weight = 12981.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.129856 restraints weight = 11483.707| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13370 Z= 0.132 Angle : 0.560 8.533 18335 Z= 0.284 Chirality : 0.044 0.147 2190 Planarity : 0.004 0.043 2200 Dihedral : 7.103 63.568 2260 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.07 % Allowed : 3.81 % Favored : 96.12 % 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 aren not related in a simple way. whole: 0.96 (0.22), residues: 1580 helix: 2.33 (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 0.020 0.001 TYR B 284 PHE 0.017 0.002 PHE D 289 TRP 0.008 0.001 TRP E 65 HIS 0.008 0.002 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00305 (13360) covalent geometry : angle 0.55994 (18310) SS BOND : bond 0.00133 ( 5) SS BOND : angle 0.42999 ( 10) hydrogen bonds : bond 0.03712 ( 420) hydrogen bonds : angle 4.14081 ( 1260) link_NAG-ASN : bond 0.00052 ( 5) link_NAG-ASN : angle 0.94905 ( 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 363 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 362 time to evaluate : 0.308 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: 0.8187 (tptp) cc_final: 0.7791 (tmmt) REVERT: B 19 LYS cc_start: 0.8096 (tptp) cc_final: 0.7580 (tmmt) REVERT: B 184 GLU cc_start: 0.7073 (pt0) cc_final: 0.6764 (mt-10) REVERT: B 234 PHE cc_start: 0.7253 (t80) cc_final: 0.7009 (t80) REVERT: C 13 ASP cc_start: 0.7698 (p0) cc_final: 0.7383 (m-30) REVERT: C 19 LYS cc_start: 0.8298 (tptp) cc_final: 0.7814 (tmmt) REVERT: C 52 ASP cc_start: 0.7830 (t0) cc_final: 0.7622 (t0) REVERT: C 57 GLU cc_start: 0.7138 (tp30) cc_final: 0.6873 (tp30) REVERT: C 165 SER cc_start: 0.7499 (t) cc_final: 0.7288 (p) REVERT: C 297 LEU cc_start: 0.8788 (tt) cc_final: 0.8545 (tt) REVERT: D 19 LYS cc_start: 0.8215 (tptp) cc_final: 0.7725 (tmmt) REVERT: D 178 TYR cc_start: 0.6028 (p90) cc_final: 0.5713 (p90) REVERT: E 19 LYS cc_start: 0.8349 (tptp) cc_final: 0.7796 (tmmt) REVERT: E 65 TRP cc_start: 0.8892 (p-90) cc_final: 0.8582 (p90) REVERT: E 227 MET cc_start: 0.7706 (ttp) cc_final: 0.6706 (tpt) outliers start: 1 outliers final: 1 residues processed: 362 average time/residue: 0.1005 time to fit residues: 52.8401 Evaluate side-chains 267 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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: 9.9990 chunk 89 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 136 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 186 GLN C 186 GLN C 295 ASN D 68 HIS 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 = 0.3631 r_free = 0.3631 target = 0.151184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.126341 restraints weight = 17315.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.126236 restraints weight = 19404.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.126476 restraints weight = 17356.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.127118 restraints weight = 15731.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.127420 restraints weight = 14059.950| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13370 Z= 0.157 Angle : 0.553 5.377 18335 Z= 0.288 Chirality : 0.045 0.155 2190 Planarity : 0.004 0.040 2200 Dihedral : 5.967 53.213 2260 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.21), residues: 1580 helix: 1.84 (0.22), residues: 520 sheet: 0.06 (0.26), residues: 415 loop : -0.53 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 135 TYR 0.020 0.001 TYR E 284 PHE 0.018 0.002 PHE D 234 TRP 0.011 0.001 TRP C 128 HIS 0.007 0.002 HIS E 442 Details of bonding type rmsd covalent geometry : bond 0.00362 (13360) covalent geometry : angle 0.55254 (18310) SS BOND : bond 0.00253 ( 5) SS BOND : angle 0.51364 ( 10) hydrogen bonds : bond 0.03692 ( 420) hydrogen bonds : angle 4.11386 ( 1260) link_NAG-ASN : bond 0.00127 ( 5) link_NAG-ASN : angle 1.01485 ( 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 314 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.485 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: A 16 ARG cc_start: 0.7378 (ttp-170) cc_final: 0.7085 (ttp80) REVERT: A 19 LYS cc_start: 0.8254 (tptp) cc_final: 0.7783 (tmmt) REVERT: A 297 LEU cc_start: 0.8702 (tt) cc_final: 0.8175 (mt) REVERT: B 17 LEU cc_start: 0.7406 (tt) cc_final: 0.7190 (tt) REVERT: B 19 LYS cc_start: 0.8107 (tptp) cc_final: 0.7660 (tmmt) REVERT: B 56 LYS cc_start: 0.8694 (mttm) cc_final: 0.8133 (mmtp) REVERT: B 184 GLU cc_start: 0.7291 (pt0) cc_final: 0.7011 (mt-10) REVERT: B 234 PHE cc_start: 0.7502 (t80) cc_final: 0.7044 (t80) REVERT: C 16 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7801 (ttp-170) REVERT: C 19 LYS cc_start: 0.8424 (tptp) cc_final: 0.7853 (tmmt) REVERT: D 19 LYS cc_start: 0.8239 (tptp) cc_final: 0.7708 (tmmt) REVERT: D 57 GLU cc_start: 0.7667 (tp30) cc_final: 0.7235 (tp30) REVERT: D 178 TYR cc_start: 0.6097 (p90) cc_final: 0.5825 (p90) REVERT: D 204 ASN cc_start: 0.8108 (t0) cc_final: 0.7483 (p0) REVERT: D 435 ILE cc_start: 0.6946 (mm) cc_final: 0.6453 (mm) REVERT: E 19 LYS cc_start: 0.8347 (tptp) cc_final: 0.7830 (tmmt) REVERT: E 227 MET cc_start: 0.7758 (ttp) cc_final: 0.6755 (tpt) REVERT: E 234 PHE cc_start: 0.7362 (t80) cc_final: 0.7052 (t80) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.0890 time to fit residues: 42.0396 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 : 0.476 ------------------------------------------------------------------------------- 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: 7.9990 chunk 156 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 186 GLN C 186 GLN D 186 GLN D 295 ASN E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.148038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.121535 restraints weight = 17049.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.123020 restraints weight = 13485.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.124475 restraints weight = 11435.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.125194 restraints weight = 10137.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.126014 restraints weight = 9318.927| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13370 Z= 0.146 Angle : 0.542 6.292 18335 Z= 0.280 Chirality : 0.044 0.155 2190 Planarity : 0.004 0.047 2200 Dihedral : 5.677 53.513 2260 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.07 % Allowed : 4.68 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.62 % 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 aren not related in a simple way. whole: 0.23 (0.21), residues: 1580 helix: 1.68 (0.23), residues: 520 sheet: -0.25 (0.27), residues: 385 loop : -0.77 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 249 TYR 0.018 0.001 TYR D 284 PHE 0.011 0.002 PHE D 298 TRP 0.009 0.001 TRP C 128 HIS 0.007 0.002 HIS B 442 Details of bonding type rmsd covalent geometry : bond 0.00340 (13360) covalent geometry : angle 0.54209 (18310) SS BOND : bond 0.00098 ( 5) SS BOND : angle 0.65801 ( 10) hydrogen bonds : bond 0.03448 ( 420) hydrogen bonds : angle 3.89947 ( 1260) link_NAG-ASN : bond 0.00056 ( 5) link_NAG-ASN : angle 0.80167 ( 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 311 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7371 (ttp-170) cc_final: 0.7147 (ttp80) REVERT: A 19 LYS cc_start: 0.8224 (tptp) cc_final: 0.7769 (tmmt) REVERT: A 52 ASP cc_start: 0.7991 (t0) cc_final: 0.7781 (t0) REVERT: A 153 THR cc_start: 0.8651 (p) cc_final: 0.8367 (t) REVERT: B 17 LEU cc_start: 0.7409 (tt) cc_final: 0.7173 (tt) REVERT: B 19 LYS cc_start: 0.8094 (tptp) cc_final: 0.7626 (tmmt) REVERT: B 56 LYS cc_start: 0.8674 (mttm) cc_final: 0.8262 (mmtt) REVERT: C 13 ASP cc_start: 0.7673 (p0) cc_final: 0.7404 (m-30) REVERT: C 16 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7870 (ttp-170) REVERT: C 19 LYS cc_start: 0.8388 (tptp) cc_final: 0.7785 (tmmt) REVERT: C 298 PHE cc_start: 0.7599 (m-80) cc_final: 0.7384 (m-80) REVERT: D 19 LYS cc_start: 0.8230 (tptp) cc_final: 0.7634 (tmmt) REVERT: D 153 THR cc_start: 0.8656 (p) cc_final: 0.8403 (t) REVERT: D 178 TYR cc_start: 0.6022 (p90) cc_final: 0.5669 (p90) REVERT: D 234 PHE cc_start: 0.7617 (t80) cc_final: 0.7396 (t80) REVERT: D 435 ILE cc_start: 0.6948 (mm) cc_final: 0.6544 (mm) REVERT: E 19 LYS cc_start: 0.8300 (tptp) cc_final: 0.7816 (tmmt) REVERT: E 52 ASP cc_start: 0.7857 (t0) cc_final: 0.7610 (p0) REVERT: E 65 TRP cc_start: 0.8846 (p-90) cc_final: 0.8518 (p90) REVERT: E 227 MET cc_start: 0.7833 (ttp) cc_final: 0.6742 (tpt) outliers start: 1 outliers final: 1 residues processed: 310 average time/residue: 0.0924 time to fit residues: 42.6419 Evaluate side-chains 253 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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: 9.9990 chunk 125 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 186 GLN B 295 ASN 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 = 0.3551 r_free = 0.3551 target = 0.144007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.117876 restraints weight = 17352.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.117731 restraints weight = 19182.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.117754 restraints weight = 16437.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.118381 restraints weight = 15197.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.118717 restraints weight = 13707.161| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13370 Z= 0.212 Angle : 0.606 8.153 18335 Z= 0.316 Chirality : 0.046 0.151 2190 Planarity : 0.005 0.045 2200 Dihedral : 5.955 50.920 2260 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.14 % Allowed : 3.67 % 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 aren not related in a simple way. whole: 0.06 (0.21), residues: 1580 helix: 1.58 (0.23), residues: 515 sheet: -0.62 (0.28), residues: 385 loop : -0.69 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 249 TYR 0.019 0.002 TYR A 284 PHE 0.014 0.002 PHE E 289 TRP 0.010 0.001 TRP C 65 HIS 0.007 0.003 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00499 (13360) covalent geometry : angle 0.60554 (18310) SS BOND : bond 0.00174 ( 5) SS BOND : angle 0.93000 ( 10) hydrogen bonds : bond 0.03859 ( 420) hydrogen bonds : angle 4.05409 ( 1260) link_NAG-ASN : bond 0.00034 ( 5) link_NAG-ASN : angle 0.79438 ( 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 306 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 0.486 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: 0.7165 (ttp80) REVERT: A 19 LYS cc_start: 0.8263 (tptp) cc_final: 0.7814 (tmmt) REVERT: A 153 THR cc_start: 0.8664 (p) cc_final: 0.8447 (t) REVERT: B 19 LYS cc_start: 0.8268 (tptp) cc_final: 0.7749 (tmmt) REVERT: B 56 LYS cc_start: 0.8680 (mttm) cc_final: 0.8247 (mmtt) REVERT: C 16 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7871 (ttp-170) REVERT: C 19 LYS cc_start: 0.8430 (tptp) cc_final: 0.7812 (tmmt) REVERT: C 56 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8614 (mmtt) REVERT: C 213 LYS cc_start: 0.7940 (ttpp) cc_final: 0.7665 (ttpp) REVERT: D 19 LYS cc_start: 0.8229 (tptp) cc_final: 0.7718 (tmmt) REVERT: D 57 GLU cc_start: 0.7753 (tp30) cc_final: 0.7373 (tp30) REVERT: D 435 ILE cc_start: 0.7017 (mm) cc_final: 0.5953 (mm) REVERT: E 19 LYS cc_start: 0.8328 (tptp) cc_final: 0.7817 (tmmt) REVERT: E 27 THR cc_start: 0.8630 (p) cc_final: 0.8420 (t) REVERT: E 227 MET cc_start: 0.8087 (ttp) cc_final: 0.6871 (tpt) outliers start: 2 outliers final: 1 residues processed: 304 average time/residue: 0.0923 time to fit residues: 42.7201 Evaluate side-chains 257 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 51 optimal weight: 0.0020 chunk 134 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 63 ASN B 186 GLN C 186 GLN D 186 GLN E 186 GLN E 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.146350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.120069 restraints weight = 17082.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.120483 restraints weight = 17910.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.120467 restraints weight = 15582.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.120827 restraints weight = 14213.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.121125 restraints weight = 13136.091| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13370 Z= 0.130 Angle : 0.555 7.931 18335 Z= 0.284 Chirality : 0.044 0.212 2190 Planarity : 0.004 0.049 2200 Dihedral : 5.871 54.826 2260 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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 : 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 aren not related in a simple way. whole: 0.08 (0.21), residues: 1580 helix: 1.52 (0.23), residues: 510 sheet: -0.38 (0.27), residues: 350 loop : -0.75 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 249 TYR 0.018 0.001 TYR E 284 PHE 0.016 0.002 PHE D 289 TRP 0.008 0.001 TRP E 185 HIS 0.007 0.002 HIS B 442 Details of bonding type rmsd covalent geometry : bond 0.00299 (13360) covalent geometry : angle 0.55456 (18310) SS BOND : bond 0.00114 ( 5) SS BOND : angle 0.84228 ( 10) hydrogen bonds : bond 0.03568 ( 420) hydrogen bonds : angle 4.01128 ( 1260) link_NAG-ASN : bond 0.00102 ( 5) link_NAG-ASN : angle 0.75116 ( 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 309 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7525 (ttp-170) cc_final: 0.7186 (ttp80) REVERT: A 19 LYS cc_start: 0.8272 (tptp) cc_final: 0.7790 (tmmt) REVERT: A 153 THR cc_start: 0.8687 (p) cc_final: 0.8462 (t) REVERT: A 297 LEU cc_start: 0.8754 (tt) cc_final: 0.8110 (mt) REVERT: A 435 ILE cc_start: 0.6740 (mm) cc_final: 0.6223 (mt) REVERT: B 19 LYS cc_start: 0.8216 (tptp) cc_final: 0.7668 (tmmt) REVERT: B 56 LYS cc_start: 0.8754 (mttm) cc_final: 0.8279 (mmtt) REVERT: B 227 MET cc_start: 0.6605 (tpt) cc_final: 0.6125 (tpp) REVERT: C 16 ARG cc_start: 0.8036 (ttp-110) cc_final: 0.7818 (ttp-170) REVERT: C 19 LYS cc_start: 0.8396 (tptp) cc_final: 0.7776 (tmmt) REVERT: C 56 LYS cc_start: 0.8851 (mmtp) cc_final: 0.8603 (mmtt) REVERT: C 213 LYS cc_start: 0.7928 (ttpp) cc_final: 0.7677 (ttpp) REVERT: D 19 LYS cc_start: 0.8176 (tptp) cc_final: 0.7686 (tmmt) REVERT: D 56 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8405 (mmtt) REVERT: D 435 ILE cc_start: 0.7042 (mm) cc_final: 0.6326 (mm) REVERT: E 19 LYS cc_start: 0.8335 (tptp) cc_final: 0.7804 (tmmt) REVERT: E 227 MET cc_start: 0.8068 (ttp) cc_final: 0.6908 (tpt) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.0852 time to fit residues: 40.3599 Evaluate side-chains 253 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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: 9.9990 chunk 121 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 105 optimal weight: 0.0870 chunk 40 optimal weight: 4.9990 overall best weight: 1.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3591 r_free = 0.3591 target = 0.147653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.122634 restraints weight = 16985.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.122910 restraints weight = 14099.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.124503 restraints weight = 12287.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.125151 restraints weight = 10098.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.125164 restraints weight = 9301.812| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13370 Z= 0.137 Angle : 0.560 8.382 18335 Z= 0.288 Chirality : 0.044 0.193 2190 Planarity : 0.004 0.046 2200 Dihedral : 5.795 52.803 2260 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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 : 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 aren not related in a simple way. whole: 0.08 (0.22), residues: 1580 helix: 1.55 (0.23), residues: 510 sheet: -0.43 (0.27), residues: 350 loop : -0.73 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 249 TYR 0.018 0.001 TYR B 284 PHE 0.016 0.002 PHE D 73 TRP 0.008 0.001 TRP C 65 HIS 0.007 0.002 HIS B 442 Details of bonding type rmsd covalent geometry : bond 0.00317 (13360) covalent geometry : angle 0.55969 (18310) SS BOND : bond 0.00168 ( 5) SS BOND : angle 0.81412 ( 10) hydrogen bonds : bond 0.03515 ( 420) hydrogen bonds : angle 4.02782 ( 1260) link_NAG-ASN : bond 0.00098 ( 5) link_NAG-ASN : angle 0.76989 ( 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 297 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7392 (ttp-170) cc_final: 0.7124 (ttp80) REVERT: A 19 LYS cc_start: 0.8211 (tptp) cc_final: 0.7748 (tmmt) REVERT: A 153 THR cc_start: 0.8723 (p) cc_final: 0.8506 (t) REVERT: A 297 LEU cc_start: 0.8808 (tt) cc_final: 0.8236 (mt) REVERT: A 435 ILE cc_start: 0.6708 (mm) cc_final: 0.6159 (mm) REVERT: B 17 LEU cc_start: 0.7291 (tt) cc_final: 0.7060 (tt) REVERT: B 19 LYS cc_start: 0.8141 (tptp) cc_final: 0.7674 (tmmt) REVERT: B 56 LYS cc_start: 0.8769 (mttm) cc_final: 0.8297 (mmtt) REVERT: B 227 MET cc_start: 0.6587 (tpt) cc_final: 0.6088 (tpp) REVERT: C 16 ARG cc_start: 0.8022 (ttp-110) cc_final: 0.7788 (ttp-170) REVERT: C 19 LYS cc_start: 0.8342 (tptp) cc_final: 0.7784 (tmmt) REVERT: C 213 LYS cc_start: 0.7906 (ttpp) cc_final: 0.7673 (ttpp) REVERT: D 19 LYS cc_start: 0.8157 (tptp) cc_final: 0.7655 (tmmt) REVERT: D 56 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8313 (mmtt) REVERT: D 57 GLU cc_start: 0.7639 (tp30) cc_final: 0.7331 (tp30) REVERT: D 178 TYR cc_start: 0.5936 (p90) cc_final: 0.5555 (p90) REVERT: D 234 PHE cc_start: 0.7521 (t80) cc_final: 0.7234 (t80) REVERT: D 435 ILE cc_start: 0.6971 (mm) cc_final: 0.6209 (mm) REVERT: E 19 LYS cc_start: 0.8278 (tptp) cc_final: 0.7728 (tmmt) REVERT: E 56 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8642 (mmtt) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.0872 time to fit residues: 39.3289 Evaluate side-chains 250 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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: 1.9990 chunk 83 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3563 r_free = 0.3563 target = 0.145260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.117046 restraints weight = 17490.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.117346 restraints weight = 19236.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.117702 restraints weight = 16161.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.118316 restraints weight = 14774.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.118494 restraints weight = 13159.213| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13370 Z= 0.191 Angle : 0.611 8.317 18335 Z= 0.313 Chirality : 0.046 0.264 2190 Planarity : 0.005 0.046 2200 Dihedral : 6.130 57.411 2260 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.07 % Allowed : 1.94 % Favored : 97.99 % 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 aren not related in a simple way. whole: -0.19 (0.22), residues: 1580 helix: 1.24 (0.23), residues: 510 sheet: -0.81 (0.28), residues: 340 loop : -0.70 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 249 TYR 0.025 0.002 TYR A 284 PHE 0.016 0.002 PHE C 73 TRP 0.009 0.001 TRP E 185 HIS 0.007 0.003 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00448 (13360) covalent geometry : angle 0.61036 (18310) SS BOND : bond 0.00187 ( 5) SS BOND : angle 0.93362 ( 10) hydrogen bonds : bond 0.03976 ( 420) hydrogen bonds : angle 4.19760 ( 1260) link_NAG-ASN : bond 0.00031 ( 5) link_NAG-ASN : angle 0.79074 ( 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: 1 poor density : 292 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7554 (ttp-170) cc_final: 0.7210 (ttp80) REVERT: A 19 LYS cc_start: 0.8275 (tptp) cc_final: 0.7844 (tmmt) REVERT: A 115 ASP cc_start: 0.7536 (p0) cc_final: 0.7291 (p0) REVERT: A 297 LEU cc_start: 0.8794 (tt) cc_final: 0.8176 (mt) REVERT: A 435 ILE cc_start: 0.6908 (mm) cc_final: 0.6121 (mm) REVERT: B 19 LYS cc_start: 0.8215 (tptp) cc_final: 0.7738 (tmmt) REVERT: B 56 LYS cc_start: 0.8768 (mttm) cc_final: 0.8398 (mmtm) REVERT: C 16 ARG cc_start: 0.8137 (ttp-110) cc_final: 0.7881 (ttp-170) REVERT: C 19 LYS cc_start: 0.8412 (tptp) cc_final: 0.7852 (tmmt) REVERT: C 56 LYS cc_start: 0.9069 (tppt) cc_final: 0.8756 (mmtt) REVERT: C 184 GLU cc_start: 0.7589 (pt0) cc_final: 0.7206 (mt-10) REVERT: C 213 LYS cc_start: 0.7954 (ttpp) cc_final: 0.7713 (ttpp) REVERT: D 19 LYS cc_start: 0.8263 (tptp) cc_final: 0.7709 (tmmt) REVERT: D 178 TYR cc_start: 0.6048 (p90) cc_final: 0.5626 (p90) REVERT: D 234 PHE cc_start: 0.7522 (t80) cc_final: 0.7235 (t80) REVERT: D 435 ILE cc_start: 0.7107 (mm) cc_final: 0.5943 (mm) REVERT: E 19 LYS cc_start: 0.8308 (tptp) cc_final: 0.7845 (tmmt) REVERT: E 56 LYS cc_start: 0.8874 (mmtm) cc_final: 0.8275 (mptt) REVERT: E 213 LYS cc_start: 0.8020 (ttpp) cc_final: 0.7743 (ttpp) REVERT: E 227 MET cc_start: 0.8233 (ttp) cc_final: 0.6685 (tpp) outliers start: 1 outliers final: 1 residues processed: 292 average time/residue: 0.1040 time to fit residues: 45.9930 Evaluate side-chains 240 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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: 5.9990 chunk 117 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 151 optimal weight: 0.3980 chunk 116 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3597 r_free = 0.3597 target = 0.148417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.120563 restraints weight = 17406.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.121357 restraints weight = 16401.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.121174 restraints weight = 14537.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.121571 restraints weight = 13473.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.121900 restraints weight = 12376.140| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13370 Z= 0.109 Angle : 0.565 7.646 18335 Z= 0.285 Chirality : 0.044 0.247 2190 Planarity : 0.004 0.046 2200 Dihedral : 5.857 58.273 2260 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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 aren not related in a simple way. whole: -0.09 (0.21), residues: 1580 helix: 1.40 (0.23), residues: 510 sheet: -0.63 (0.27), residues: 350 loop : -0.76 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 249 TYR 0.020 0.001 TYR A 443 PHE 0.025 0.002 PHE C 289 TRP 0.007 0.001 TRP E 185 HIS 0.007 0.002 HIS B 442 Details of bonding type rmsd covalent geometry : bond 0.00245 (13360) covalent geometry : angle 0.56430 (18310) SS BOND : bond 0.00102 ( 5) SS BOND : angle 0.81107 ( 10) hydrogen bonds : bond 0.03418 ( 420) hydrogen bonds : angle 4.05781 ( 1260) link_NAG-ASN : bond 0.00124 ( 5) link_NAG-ASN : angle 0.80073 ( 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 300 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7525 (ttp-170) cc_final: 0.7166 (ttp80) REVERT: A 19 LYS cc_start: 0.8203 (tptp) cc_final: 0.7745 (tmmt) REVERT: A 52 ASP cc_start: 0.8129 (t0) cc_final: 0.7904 (t0) REVERT: B 17 LEU cc_start: 0.7204 (tt) cc_final: 0.6936 (tt) REVERT: B 19 LYS cc_start: 0.8189 (tptp) cc_final: 0.7652 (tmmt) REVERT: B 56 LYS cc_start: 0.8756 (mttm) cc_final: 0.8398 (mmtt) REVERT: B 227 MET cc_start: 0.8769 (ttp) cc_final: 0.6742 (tpt) REVERT: C 16 ARG cc_start: 0.8062 (ttp-110) cc_final: 0.7493 (ttp-170) REVERT: C 19 LYS cc_start: 0.8292 (tptp) cc_final: 0.7712 (tmmt) REVERT: C 56 LYS cc_start: 0.9059 (tppt) cc_final: 0.8618 (mmtt) REVERT: C 184 GLU cc_start: 0.7575 (pt0) cc_final: 0.7050 (mt-10) REVERT: C 213 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7683 (ttpp) REVERT: D 19 LYS cc_start: 0.8131 (tptp) cc_final: 0.7550 (tmmt) REVERT: D 178 TYR cc_start: 0.5958 (p90) cc_final: 0.5617 (p90) REVERT: D 234 PHE cc_start: 0.7505 (t80) cc_final: 0.7098 (t80) REVERT: D 435 ILE cc_start: 0.7001 (mm) cc_final: 0.5984 (mm) REVERT: E 19 LYS cc_start: 0.8280 (tptp) cc_final: 0.7694 (tmmt) REVERT: E 227 MET cc_start: 0.8229 (ttp) cc_final: 0.6602 (tpp) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.1072 time to fit residues: 48.2262 Evaluate side-chains 250 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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: 1.9990 chunk 97 optimal weight: 0.0970 chunk 36 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 102 optimal weight: 0.1980 chunk 156 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3592 r_free = 0.3592 target = 0.147844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.119539 restraints weight = 17397.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.120651 restraints weight = 14222.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.122035 restraints weight = 12317.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.122913 restraints weight = 10123.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.123142 restraints weight = 9299.242| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13370 Z= 0.114 Angle : 0.572 7.471 18335 Z= 0.288 Chirality : 0.044 0.248 2190 Planarity : 0.004 0.048 2200 Dihedral : 5.887 60.032 2260 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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 aren not related in a simple way. whole: -0.08 (0.21), residues: 1580 helix: 1.42 (0.23), residues: 510 sheet: -0.63 (0.27), residues: 350 loop : -0.77 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 249 TYR 0.021 0.001 TYR B 284 PHE 0.023 0.002 PHE C 289 TRP 0.006 0.001 TRP B 128 HIS 0.007 0.002 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00262 (13360) covalent geometry : angle 0.57178 (18310) SS BOND : bond 0.00153 ( 5) SS BOND : angle 0.82532 ( 10) hydrogen bonds : bond 0.03406 ( 420) hydrogen bonds : angle 4.05901 ( 1260) link_NAG-ASN : bond 0.00114 ( 5) link_NAG-ASN : angle 0.79394 ( 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 289 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8168 (tptp) cc_final: 0.7721 (tmmt) REVERT: A 52 ASP cc_start: 0.8120 (t0) cc_final: 0.7898 (t0) REVERT: A 115 ASP cc_start: 0.7551 (p0) cc_final: 0.7289 (p0) REVERT: A 297 LEU cc_start: 0.8882 (tt) cc_final: 0.8256 (mt) REVERT: B 17 LEU cc_start: 0.7323 (tt) cc_final: 0.7086 (tt) REVERT: B 19 LYS cc_start: 0.8216 (tptp) cc_final: 0.7649 (tmmt) REVERT: C 16 ARG cc_start: 0.8027 (ttp-110) cc_final: 0.7491 (ttp-170) REVERT: C 19 LYS cc_start: 0.8302 (tptp) cc_final: 0.7687 (tmmt) REVERT: C 56 LYS cc_start: 0.9096 (tppt) cc_final: 0.8642 (mmtt) REVERT: C 184 GLU cc_start: 0.7593 (pt0) cc_final: 0.7140 (mt-10) REVERT: C 213 LYS cc_start: 0.7936 (ttpp) cc_final: 0.7696 (ttpp) REVERT: D 19 LYS cc_start: 0.8149 (tptp) cc_final: 0.7575 (tmmt) REVERT: D 178 TYR cc_start: 0.5877 (p90) cc_final: 0.5512 (p90) REVERT: D 234 PHE cc_start: 0.7512 (t80) cc_final: 0.7170 (t80) REVERT: D 435 ILE cc_start: 0.6933 (mm) cc_final: 0.5811 (mm) REVERT: E 19 LYS cc_start: 0.8227 (tptp) cc_final: 0.7660 (tmmt) REVERT: E 169 THR cc_start: 0.8719 (t) cc_final: 0.8387 (p) REVERT: E 227 MET cc_start: 0.8249 (ttp) cc_final: 0.6618 (tpp) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1051 time to fit residues: 46.2703 Evaluate side-chains 237 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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: 0.0870 chunk 137 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 97 optimal weight: 0.0030 chunk 39 optimal weight: 0.0070 chunk 113 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3614 r_free = 0.3614 target = 0.149808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.121856 restraints weight = 17302.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.121869 restraints weight = 16388.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.122717 restraints weight = 13801.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.123123 restraints weight = 12473.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.123522 restraints weight = 11414.136| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13370 Z= 0.102 Angle : 0.561 6.840 18335 Z= 0.282 Chirality : 0.044 0.229 2190 Planarity : 0.004 0.046 2200 Dihedral : 5.814 59.249 2260 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.07 % Allowed : 0.50 % Favored : 99.42 % 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 aren not related in a simple way. whole: 0.00 (0.21), residues: 1580 helix: 1.50 (0.23), residues: 510 sheet: -0.52 (0.26), residues: 350 loop : -0.76 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 16 TYR 0.020 0.001 TYR A 284 PHE 0.023 0.002 PHE B 73 TRP 0.007 0.001 TRP A 185 HIS 0.008 0.001 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.00229 (13360) covalent geometry : angle 0.56097 (18310) SS BOND : bond 0.00119 ( 5) SS BOND : angle 0.74073 ( 10) hydrogen bonds : bond 0.03305 ( 420) hydrogen bonds : angle 4.06075 ( 1260) link_NAG-ASN : bond 0.00167 ( 5) link_NAG-ASN : angle 0.80566 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1777.15 seconds wall clock time: 31 minutes 32.87 seconds (1892.87 seconds total)