Starting phenix.real_space_refine on Wed Jun 11 22:28:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8byi_16326/06_2025/8byi_16326_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8byi_16326/06_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_16326/06_2025/8byi_16326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8byi_16326/06_2025/8byi_16326.map" model { file = "/net/cci-nas-00/data/ceres_data/8byi_16326/06_2025/8byi_16326_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8byi_16326/06_2025/8byi_16326_trim.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.27, per 1000 atoms: 0.63 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: 2.86 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.15 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: 2.92 Time building geometry restraints manager: 3.43 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.090 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.010 0.001 TRP C 70 HIS 0.007 0.001 HIS E 442 PHE 0.008 0.001 PHE B 289 TYR 0.007 0.001 TYR C 67 ARG 0.001 0.000 ARG D 111 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 5) link_NAG-ASN : angle 0.74129 ( 15) hydrogen bonds : bond 0.08947 ( 420) hydrogen bonds : angle 4.46259 ( 1260) SS BOND : bond 0.00055 ( 5) SS BOND : angle 0.43209 ( 10) covalent geometry : bond 0.00858 (13360) covalent geometry : angle 0.72472 (18310) *********************** 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 : 1.409 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: 0.2640 time to fit residues: 166.2023 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 : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.0870 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 93 optimal weight: 30.0000 chunk 145 optimal weight: 3.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.152435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.126947 restraints weight = 17287.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.126982 restraints weight = 20270.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.127417 restraints weight = 17091.294| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13370 Z= 0.167 Angle : 0.585 8.362 18335 Z= 0.299 Chirality : 0.045 0.147 2190 Planarity : 0.004 0.043 2200 Dihedral : 7.048 65.919 2260 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.07 % Allowed : 4.53 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.22), residues: 1580 helix: 2.34 (0.22), residues: 515 sheet: 0.44 (0.26), residues: 420 loop : -0.63 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 128 HIS 0.008 0.002 HIS A 442 PHE 0.017 0.002 PHE D 289 TYR 0.019 0.001 TYR A 284 ARG 0.008 0.001 ARG E 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00041 ( 5) link_NAG-ASN : angle 0.96205 ( 15) hydrogen bonds : bond 0.03804 ( 420) hydrogen bonds : angle 4.12151 ( 1260) SS BOND : bond 0.00149 ( 5) SS BOND : angle 0.48435 ( 10) covalent geometry : bond 0.00377 (13360) covalent geometry : angle 0.58500 (18310) *********************** 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 353 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 352 time to evaluate : 1.393 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: 0.8207 (tptp) cc_final: 0.7806 (tmmt) REVERT: A 180 ILE cc_start: 0.8044 (mm) cc_final: 0.7741 (mt) REVERT: B 19 LYS cc_start: 0.8148 (tptp) cc_final: 0.7680 (tmmt) REVERT: B 184 GLU cc_start: 0.7120 (pt0) cc_final: 0.6766 (mt-10) REVERT: B 234 PHE cc_start: 0.7276 (t80) cc_final: 0.7040 (t80) REVERT: C 13 ASP cc_start: 0.7742 (p0) cc_final: 0.7414 (m-30) REVERT: C 16 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7883 (ttp-170) REVERT: C 19 LYS cc_start: 0.8318 (tptp) cc_final: 0.7844 (tmmt) REVERT: C 57 GLU cc_start: 0.7219 (tp30) cc_final: 0.6870 (tp30) REVERT: C 108 GLU cc_start: 0.7491 (pt0) cc_final: 0.7251 (pm20) REVERT: D 19 LYS cc_start: 0.8247 (tptp) cc_final: 0.7768 (tmmt) REVERT: D 178 TYR cc_start: 0.6136 (p90) cc_final: 0.5759 (p90) REVERT: D 227 MET cc_start: 0.8148 (ttp) cc_final: 0.6680 (tpt) REVERT: E 19 LYS cc_start: 0.8366 (tptp) cc_final: 0.7831 (tmmt) REVERT: E 227 MET cc_start: 0.7748 (ttp) cc_final: 0.6765 (tpt) REVERT: E 435 ILE cc_start: 0.6666 (mt) cc_final: 0.5528 (mt) outliers start: 1 outliers final: 1 residues processed: 352 average time/residue: 0.2388 time to fit residues: 123.1802 Evaluate side-chains 263 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 125 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 295 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.149569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.123292 restraints weight = 17152.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.124290 restraints weight = 13834.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.125770 restraints weight = 12069.805| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13370 Z= 0.120 Angle : 0.526 5.252 18335 Z= 0.272 Chirality : 0.044 0.148 2190 Planarity : 0.004 0.041 2200 Dihedral : 5.878 59.099 2260 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1580 helix: 1.85 (0.22), residues: 525 sheet: 0.28 (0.25), residues: 420 loop : -0.75 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 65 HIS 0.007 0.002 HIS E 442 PHE 0.020 0.002 PHE D 234 TYR 0.017 0.001 TYR E 284 ARG 0.006 0.001 ARG D 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 5) link_NAG-ASN : angle 0.95376 ( 15) hydrogen bonds : bond 0.03420 ( 420) hydrogen bonds : angle 4.07492 ( 1260) SS BOND : bond 0.00048 ( 5) SS BOND : angle 0.46660 ( 10) covalent geometry : bond 0.00276 (13360) covalent geometry : angle 0.52536 (18310) *********************** 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 326 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7307 (ttp-170) cc_final: 0.7077 (ttp80) REVERT: A 19 LYS cc_start: 0.8233 (tptp) cc_final: 0.7712 (tmmt) REVERT: A 169 THR cc_start: 0.8556 (t) cc_final: 0.8334 (p) REVERT: B 17 LEU cc_start: 0.7337 (tt) cc_final: 0.7135 (tt) REVERT: B 19 LYS cc_start: 0.8141 (tptp) cc_final: 0.7627 (tmmt) REVERT: B 184 GLU cc_start: 0.7270 (pt0) cc_final: 0.6864 (mt-10) REVERT: B 234 PHE cc_start: 0.7546 (t80) cc_final: 0.7100 (t80) REVERT: C 16 ARG cc_start: 0.8087 (ttp-110) cc_final: 0.7796 (ttp-170) REVERT: C 19 LYS cc_start: 0.8395 (tptp) cc_final: 0.7813 (tmmt) REVERT: C 227 MET cc_start: 0.8191 (ttp) cc_final: 0.6270 (tpp) REVERT: D 19 LYS cc_start: 0.8244 (tptp) cc_final: 0.7682 (tmmt) REVERT: D 57 GLU cc_start: 0.7693 (tp30) cc_final: 0.7247 (tp30) REVERT: D 178 TYR cc_start: 0.6054 (p90) cc_final: 0.5721 (p90) REVERT: D 204 ASN cc_start: 0.7999 (t0) cc_final: 0.7417 (p0) REVERT: D 234 PHE cc_start: 0.7468 (t80) cc_final: 0.7229 (t80) REVERT: D 435 ILE cc_start: 0.6832 (mm) cc_final: 0.6331 (mm) REVERT: E 19 LYS cc_start: 0.8328 (tptp) cc_final: 0.7806 (tmmt) REVERT: E 56 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8480 (mmtt) REVERT: E 93 ASP cc_start: 0.7398 (m-30) cc_final: 0.7195 (m-30) REVERT: E 227 MET cc_start: 0.7812 (ttp) cc_final: 0.6675 (tpt) REVERT: E 443 TYR cc_start: 0.4744 (t80) cc_final: 0.4486 (t80) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2524 time to fit residues: 124.4205 Evaluate side-chains 266 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 74 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 = 0.3652 r_free = 0.3652 target = 0.153145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.127089 restraints weight = 16969.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.128183 restraints weight = 14497.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.129677 restraints weight = 12457.220| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13370 Z= 0.100 Angle : 0.503 5.509 18335 Z= 0.258 Chirality : 0.043 0.141 2190 Planarity : 0.004 0.046 2200 Dihedral : 5.368 55.967 2260 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1580 helix: 1.86 (0.23), residues: 520 sheet: 0.18 (0.25), residues: 420 loop : -0.86 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 65 HIS 0.007 0.002 HIS B 442 PHE 0.015 0.001 PHE D 234 TYR 0.015 0.001 TYR D 284 ARG 0.003 0.000 ARG E 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 5) link_NAG-ASN : angle 0.83500 ( 15) hydrogen bonds : bond 0.03167 ( 420) hydrogen bonds : angle 3.90536 ( 1260) SS BOND : bond 0.00095 ( 5) SS BOND : angle 0.36307 ( 10) covalent geometry : bond 0.00224 (13360) covalent geometry : angle 0.50229 (18310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7290 (ttp-170) cc_final: 0.7038 (ttp80) REVERT: A 19 LYS cc_start: 0.8167 (tptp) cc_final: 0.7721 (tmmt) REVERT: A 169 THR cc_start: 0.8607 (t) cc_final: 0.8389 (p) REVERT: B 17 LEU cc_start: 0.7256 (tt) cc_final: 0.7038 (tt) REVERT: B 19 LYS cc_start: 0.8132 (tptp) cc_final: 0.7587 (tmmt) REVERT: B 169 THR cc_start: 0.8533 (t) cc_final: 0.8323 (p) REVERT: B 184 GLU cc_start: 0.7254 (pt0) cc_final: 0.6867 (mt-10) REVERT: B 234 PHE cc_start: 0.7578 (t80) cc_final: 0.7099 (t80) REVERT: B 298 PHE cc_start: 0.7711 (m-80) cc_final: 0.7491 (m-80) REVERT: C 13 ASP cc_start: 0.7630 (p0) cc_final: 0.7341 (m-30) REVERT: C 19 LYS cc_start: 0.8380 (tptp) cc_final: 0.7758 (tmmt) REVERT: C 56 LYS cc_start: 0.8839 (mmtp) cc_final: 0.8591 (mmtp) REVERT: C 298 PHE cc_start: 0.7646 (m-80) cc_final: 0.7421 (m-80) REVERT: D 19 LYS cc_start: 0.8149 (tptp) cc_final: 0.7597 (tmmt) REVERT: D 178 TYR cc_start: 0.6185 (p90) cc_final: 0.5874 (p90) REVERT: D 435 ILE cc_start: 0.6881 (mm) cc_final: 0.6526 (mt) REVERT: E 19 LYS cc_start: 0.8232 (tptp) cc_final: 0.7720 (tmmt) REVERT: E 65 TRP cc_start: 0.8893 (p-90) cc_final: 0.8557 (p90) REVERT: E 204 ASN cc_start: 0.8121 (t0) cc_final: 0.7401 (p0) REVERT: E 227 MET cc_start: 0.7825 (ttp) cc_final: 0.6795 (tpt) REVERT: E 443 TYR cc_start: 0.4688 (t80) cc_final: 0.4371 (t80) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2155 time to fit residues: 106.4035 Evaluate side-chains 263 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 86 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 C 186 GLN D 186 GLN E 186 GLN E 295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.139854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.113519 restraints weight = 17626.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.113560 restraints weight = 17840.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.114051 restraints weight = 14948.255| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 13370 Z= 0.315 Angle : 0.728 9.673 18335 Z= 0.376 Chirality : 0.051 0.161 2190 Planarity : 0.006 0.045 2200 Dihedral : 6.836 52.032 2260 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1580 helix: 1.13 (0.22), residues: 515 sheet: -0.87 (0.28), residues: 385 loop : -0.86 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 128 HIS 0.010 0.004 HIS E 68 PHE 0.018 0.003 PHE B 73 TYR 0.020 0.002 TYR E 284 ARG 0.006 0.001 ARG E 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 5) link_NAG-ASN : angle 0.82348 ( 15) hydrogen bonds : bond 0.04644 ( 420) hydrogen bonds : angle 4.37363 ( 1260) SS BOND : bond 0.00303 ( 5) SS BOND : angle 1.18476 ( 10) covalent geometry : bond 0.00737 (13360) covalent geometry : angle 0.72756 (18310) *********************** 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 317 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7575 (ttp-170) cc_final: 0.7242 (ttp80) REVERT: A 19 LYS cc_start: 0.8316 (tptp) cc_final: 0.7899 (tmmt) REVERT: A 33 GLN cc_start: 0.6914 (tt0) cc_final: 0.6515 (mt0) REVERT: A 169 THR cc_start: 0.8764 (t) cc_final: 0.8450 (p) REVERT: B 19 LYS cc_start: 0.8309 (tptp) cc_final: 0.7864 (tmmt) REVERT: B 234 PHE cc_start: 0.7635 (t80) cc_final: 0.7279 (t80) REVERT: B 271 MET cc_start: 0.8111 (tpt) cc_final: 0.7876 (tpt) REVERT: C 19 LYS cc_start: 0.8449 (tptp) cc_final: 0.7954 (tmmt) REVERT: C 56 LYS cc_start: 0.8835 (mmtp) cc_final: 0.8503 (mmtp) REVERT: C 179 MET cc_start: 0.6365 (ttt) cc_final: 0.6059 (ttt) REVERT: C 184 GLU cc_start: 0.7581 (pt0) cc_final: 0.7357 (mt-10) REVERT: C 213 LYS cc_start: 0.7980 (ttpp) cc_final: 0.7775 (ttpp) REVERT: D 19 LYS cc_start: 0.8255 (tptp) cc_final: 0.7768 (tmmt) REVERT: D 271 MET cc_start: 0.8013 (tpp) cc_final: 0.7394 (tpp) REVERT: E 19 LYS cc_start: 0.8362 (tptp) cc_final: 0.7845 (tmmt) REVERT: E 27 THR cc_start: 0.8649 (p) cc_final: 0.8434 (t) REVERT: E 227 MET cc_start: 0.8315 (ttp) cc_final: 0.6704 (tpp) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2305 time to fit residues: 107.7768 Evaluate side-chains 258 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 157 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 110 optimal weight: 0.0070 chunk 119 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3576 r_free = 0.3576 target = 0.146226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.120374 restraints weight = 17414.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.121198 restraints weight = 14258.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.121424 restraints weight = 12394.603| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13370 Z= 0.141 Angle : 0.572 7.281 18335 Z= 0.294 Chirality : 0.045 0.199 2190 Planarity : 0.005 0.050 2200 Dihedral : 6.192 52.879 2260 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.07 % Allowed : 1.37 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1580 helix: 1.33 (0.23), residues: 515 sheet: -0.64 (0.27), residues: 345 loop : -0.97 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.007 0.002 HIS D 442 PHE 0.017 0.002 PHE E 289 TYR 0.023 0.002 TYR B 284 ARG 0.003 0.000 ARG E 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00055 ( 5) link_NAG-ASN : angle 0.69994 ( 15) hydrogen bonds : bond 0.03745 ( 420) hydrogen bonds : angle 4.17390 ( 1260) SS BOND : bond 0.00119 ( 5) SS BOND : angle 0.86383 ( 10) covalent geometry : bond 0.00326 (13360) covalent geometry : angle 0.57176 (18310) *********************** 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 314 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 1.617 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: 0.7413 (ttp-170) cc_final: 0.7112 (ttp80) REVERT: A 19 LYS cc_start: 0.8252 (tptp) cc_final: 0.7810 (tmmt) REVERT: A 153 THR cc_start: 0.8760 (p) cc_final: 0.8552 (t) REVERT: A 435 ILE cc_start: 0.6667 (mm) cc_final: 0.6089 (mm) REVERT: B 17 LEU cc_start: 0.7262 (tt) cc_final: 0.7001 (tt) REVERT: B 19 LYS cc_start: 0.8224 (tptp) cc_final: 0.7709 (tmmt) REVERT: B 227 MET cc_start: 0.6733 (tpt) cc_final: 0.6193 (tpp) REVERT: C 19 LYS cc_start: 0.8415 (tptp) cc_final: 0.7836 (tmmt) REVERT: C 56 LYS cc_start: 0.8782 (mmtp) cc_final: 0.8485 (mmtt) REVERT: C 178 TYR cc_start: 0.6330 (p90) cc_final: 0.5948 (p90) REVERT: C 213 LYS cc_start: 0.7914 (ttpp) cc_final: 0.7662 (ttpp) REVERT: C 227 MET cc_start: 0.8149 (ttm) cc_final: 0.6389 (tpt) REVERT: D 19 LYS cc_start: 0.8192 (tptp) cc_final: 0.7684 (tmmt) REVERT: D 271 MET cc_start: 0.8028 (tpp) cc_final: 0.7456 (tpp) REVERT: D 435 ILE cc_start: 0.6990 (mm) cc_final: 0.6667 (mm) REVERT: E 19 LYS cc_start: 0.8292 (tptp) cc_final: 0.7758 (tmmt) REVERT: E 227 MET cc_start: 0.8223 (ttp) cc_final: 0.6575 (tpp) REVERT: E 435 ILE cc_start: 0.6438 (mt) cc_final: 0.5903 (mt) outliers start: 1 outliers final: 1 residues processed: 313 average time/residue: 0.2557 time to fit residues: 121.7926 Evaluate side-chains 255 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 35 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 155 optimal weight: 0.0270 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 0.0270 chunk 118 optimal weight: 8.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.147209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.121540 restraints weight = 17096.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.122296 restraints weight = 13514.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.123435 restraints weight = 11866.899| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13370 Z= 0.118 Angle : 0.546 6.987 18335 Z= 0.280 Chirality : 0.044 0.189 2190 Planarity : 0.005 0.045 2200 Dihedral : 5.869 52.504 2260 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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 : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1580 helix: 1.42 (0.23), residues: 515 sheet: -0.68 (0.28), residues: 320 loop : -1.06 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 185 HIS 0.007 0.002 HIS B 442 PHE 0.019 0.002 PHE E 73 TYR 0.018 0.001 TYR E 284 ARG 0.003 0.000 ARG E 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 5) link_NAG-ASN : angle 0.76056 ( 15) hydrogen bonds : bond 0.03539 ( 420) hydrogen bonds : angle 4.09002 ( 1260) SS BOND : bond 0.00077 ( 5) SS BOND : angle 0.77589 ( 10) covalent geometry : bond 0.00271 (13360) covalent geometry : angle 0.54602 (18310) *********************** 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 311 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7370 (ttp-170) cc_final: 0.7092 (ttp80) REVERT: A 19 LYS cc_start: 0.8207 (tptp) cc_final: 0.7745 (tmmt) REVERT: A 435 ILE cc_start: 0.6603 (mm) cc_final: 0.5693 (mm) REVERT: B 19 LYS cc_start: 0.8192 (tptp) cc_final: 0.7686 (tmmt) REVERT: B 56 LYS cc_start: 0.8918 (mmtp) cc_final: 0.8716 (mmtt) REVERT: B 227 MET cc_start: 0.6706 (tpt) cc_final: 0.6280 (tpp) REVERT: C 19 LYS cc_start: 0.8340 (tptp) cc_final: 0.7726 (tmmt) REVERT: C 73 PHE cc_start: 0.7827 (p90) cc_final: 0.7573 (p90) REVERT: C 82 TYR cc_start: 0.8425 (m-80) cc_final: 0.8106 (m-80) REVERT: C 178 TYR cc_start: 0.6339 (p90) cc_final: 0.5987 (p90) REVERT: C 184 GLU cc_start: 0.7551 (pt0) cc_final: 0.7175 (mt-10) REVERT: C 213 LYS cc_start: 0.7937 (ttpp) cc_final: 0.7680 (ttpp) REVERT: C 227 MET cc_start: 0.8052 (ttm) cc_final: 0.6486 (tpt) REVERT: D 19 LYS cc_start: 0.8124 (tptp) cc_final: 0.7613 (tmmt) REVERT: D 271 MET cc_start: 0.7914 (tpp) cc_final: 0.7419 (tpp) REVERT: E 19 LYS cc_start: 0.8249 (tptp) cc_final: 0.7724 (tmmt) REVERT: E 56 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8569 (mmtt) REVERT: E 227 MET cc_start: 0.8189 (ttp) cc_final: 0.6590 (tpp) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.2884 time to fit residues: 133.8516 Evaluate side-chains 244 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 141 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 4 optimal weight: 0.2980 chunk 118 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN C 186 GLN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.146611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.120698 restraints weight = 17165.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.121184 restraints weight = 16394.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.121260 restraints weight = 13945.084| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13370 Z= 0.142 Angle : 0.584 9.577 18335 Z= 0.296 Chirality : 0.045 0.178 2190 Planarity : 0.005 0.048 2200 Dihedral : 5.989 58.632 2260 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1580 helix: 1.25 (0.23), residues: 515 sheet: -0.80 (0.28), residues: 320 loop : -1.04 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 185 HIS 0.007 0.002 HIS B 442 PHE 0.019 0.002 PHE A 73 TYR 0.020 0.001 TYR B 284 ARG 0.003 0.000 ARG C 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 5) link_NAG-ASN : angle 0.77301 ( 15) hydrogen bonds : bond 0.03795 ( 420) hydrogen bonds : angle 4.25708 ( 1260) SS BOND : bond 0.00135 ( 5) SS BOND : angle 0.94619 ( 10) covalent geometry : bond 0.00330 (13360) covalent geometry : angle 0.58390 (18310) *********************** 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 306 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 3.077 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: 0.7461 (ttp-170) cc_final: 0.7124 (ttp80) REVERT: A 19 LYS cc_start: 0.8225 (tptp) cc_final: 0.7749 (tmmt) REVERT: A 33 GLN cc_start: 0.6909 (tt0) cc_final: 0.6425 (mt0) REVERT: A 435 ILE cc_start: 0.6658 (mm) cc_final: 0.5637 (mm) REVERT: B 19 LYS cc_start: 0.8238 (tptp) cc_final: 0.7733 (tmmt) REVERT: B 56 LYS cc_start: 0.8968 (mmtp) cc_final: 0.8717 (mmtt) REVERT: B 227 MET cc_start: 0.6783 (tpt) cc_final: 0.6368 (tpp) REVERT: B 250 ILE cc_start: 0.7717 (pt) cc_final: 0.7363 (pt) REVERT: C 19 LYS cc_start: 0.8334 (tptp) cc_final: 0.7766 (tmmt) REVERT: C 73 PHE cc_start: 0.7930 (p90) cc_final: 0.7706 (p90) REVERT: C 178 TYR cc_start: 0.6473 (p90) cc_final: 0.6089 (p90) REVERT: C 213 LYS cc_start: 0.7930 (ttpp) cc_final: 0.7702 (ttpp) REVERT: D 19 LYS cc_start: 0.8152 (tptp) cc_final: 0.7611 (tmmt) REVERT: D 271 MET cc_start: 0.7727 (tpp) cc_final: 0.7375 (tpp) REVERT: D 435 ILE cc_start: 0.7030 (mm) cc_final: 0.6223 (mm) REVERT: E 19 LYS cc_start: 0.8241 (tptp) cc_final: 0.7728 (tmmt) REVERT: E 56 LYS cc_start: 0.8821 (mmtm) cc_final: 0.8563 (mmtt) REVERT: E 169 THR cc_start: 0.8755 (t) cc_final: 0.8444 (p) REVERT: E 227 MET cc_start: 0.8307 (ttp) cc_final: 0.6833 (tpp) REVERT: E 271 MET cc_start: 0.8013 (tpp) cc_final: 0.7187 (tpp) REVERT: E 435 ILE cc_start: 0.6413 (mt) cc_final: 0.5534 (mt) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.3149 time to fit residues: 145.5926 Evaluate side-chains 248 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 18 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 122 optimal weight: 0.0970 chunk 40 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN B 186 GLN C 186 GLN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.147107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.120621 restraints weight = 17164.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.121417 restraints weight = 14737.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.122916 restraints weight = 12772.110| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4831 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= 0.148 Angle : 0.593 7.801 18335 Z= 0.300 Chirality : 0.045 0.177 2190 Planarity : 0.005 0.044 2200 Dihedral : 6.112 64.052 2260 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1580 helix: 1.19 (0.23), residues: 515 sheet: -0.80 (0.27), residues: 350 loop : -0.85 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.007 0.002 HIS B 442 PHE 0.019 0.002 PHE E 73 TYR 0.020 0.001 TYR A 284 ARG 0.004 0.000 ARG A 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 5) link_NAG-ASN : angle 0.77600 ( 15) hydrogen bonds : bond 0.03793 ( 420) hydrogen bonds : angle 4.25310 ( 1260) SS BOND : bond 0.00159 ( 5) SS BOND : angle 0.99644 ( 10) covalent geometry : bond 0.00344 (13360) covalent geometry : angle 0.59300 (18310) *********************** 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 297 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7413 (ttp-170) cc_final: 0.7144 (ttp80) REVERT: A 19 LYS cc_start: 0.8245 (tptp) cc_final: 0.7795 (tmmt) REVERT: A 33 GLN cc_start: 0.6803 (tt0) cc_final: 0.6403 (mt0) REVERT: A 271 MET cc_start: 0.8394 (tpt) cc_final: 0.8147 (tpt) REVERT: A 435 ILE cc_start: 0.6520 (mm) cc_final: 0.5436 (mm) REVERT: B 17 LEU cc_start: 0.7248 (tt) cc_final: 0.7023 (tt) REVERT: B 19 LYS cc_start: 0.8242 (tptp) cc_final: 0.7765 (tmmt) REVERT: B 179 MET cc_start: 0.6579 (ttt) cc_final: 0.5506 (ptp) REVERT: B 184 GLU cc_start: 0.7596 (pt0) cc_final: 0.7241 (mt-10) REVERT: B 227 MET cc_start: 0.6725 (tpt) cc_final: 0.6321 (tpp) REVERT: C 19 LYS cc_start: 0.8336 (tptp) cc_final: 0.7778 (tmmt) REVERT: C 73 PHE cc_start: 0.7964 (p90) cc_final: 0.7758 (p90) REVERT: C 178 TYR cc_start: 0.6435 (p90) cc_final: 0.6021 (p90) REVERT: C 179 MET cc_start: 0.6300 (ttt) cc_final: 0.6013 (ttt) REVERT: C 213 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7583 (ttpp) REVERT: C 250 ILE cc_start: 0.7747 (pt) cc_final: 0.7514 (pt) REVERT: D 19 LYS cc_start: 0.8161 (tptp) cc_final: 0.7637 (tmmt) REVERT: D 271 MET cc_start: 0.7731 (tpp) cc_final: 0.7108 (tpp) REVERT: D 435 ILE cc_start: 0.6943 (mm) cc_final: 0.5884 (mm) REVERT: E 19 LYS cc_start: 0.8290 (tptp) cc_final: 0.7749 (tmmt) REVERT: E 56 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8287 (mptt) REVERT: E 169 THR cc_start: 0.8799 (t) cc_final: 0.8491 (p) REVERT: E 227 MET cc_start: 0.8339 (ttp) cc_final: 0.6858 (tpp) REVERT: E 254 ILE cc_start: 0.8465 (mm) cc_final: 0.8259 (mm) REVERT: E 271 MET cc_start: 0.8003 (tpp) cc_final: 0.7372 (tpp) REVERT: E 435 ILE cc_start: 0.6480 (mt) cc_final: 0.5569 (mt) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2534 time to fit residues: 114.1620 Evaluate side-chains 247 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 101 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN B 186 GLN C 186 GLN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.146182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.118065 restraints weight = 17376.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.118069 restraints weight = 17153.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.118588 restraints weight = 14759.713| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13370 Z= 0.137 Angle : 0.586 10.868 18335 Z= 0.296 Chirality : 0.045 0.172 2190 Planarity : 0.005 0.048 2200 Dihedral : 6.152 66.423 2260 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1580 helix: 1.23 (0.23), residues: 510 sheet: -0.84 (0.26), residues: 350 loop : -0.88 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 65 HIS 0.007 0.002 HIS B 442 PHE 0.028 0.002 PHE A 289 TYR 0.019 0.001 TYR D 284 ARG 0.003 0.000 ARG C 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00080 ( 5) link_NAG-ASN : angle 0.78008 ( 15) hydrogen bonds : bond 0.03751 ( 420) hydrogen bonds : angle 4.21293 ( 1260) SS BOND : bond 0.00163 ( 5) SS BOND : angle 0.92324 ( 10) covalent geometry : bond 0.00319 (13360) covalent geometry : angle 0.58523 (18310) ********************** 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 291 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7471 (ttp-170) cc_final: 0.7133 (ttp80) REVERT: A 19 LYS cc_start: 0.8219 (tptp) cc_final: 0.7768 (tmmt) REVERT: A 435 ILE cc_start: 0.6600 (mm) cc_final: 0.5901 (mm) REVERT: B 17 LEU cc_start: 0.7222 (tt) cc_final: 0.6978 (tt) REVERT: B 19 LYS cc_start: 0.8264 (tptp) cc_final: 0.7770 (tmmt) REVERT: B 179 MET cc_start: 0.6537 (ttt) cc_final: 0.5464 (ptp) REVERT: B 184 GLU cc_start: 0.7667 (pt0) cc_final: 0.7182 (mt-10) REVERT: B 227 MET cc_start: 0.6813 (tpt) cc_final: 0.6390 (tpp) REVERT: C 19 LYS cc_start: 0.8303 (tptp) cc_final: 0.7726 (tmmt) REVERT: C 56 LYS cc_start: 0.8850 (tppt) cc_final: 0.8576 (mmtt) REVERT: C 178 TYR cc_start: 0.6537 (p90) cc_final: 0.6106 (p90) REVERT: C 213 LYS cc_start: 0.7919 (ttpp) cc_final: 0.7564 (ttpp) REVERT: D 19 LYS cc_start: 0.8153 (tptp) cc_final: 0.7612 (tmmt) REVERT: D 271 MET cc_start: 0.7765 (tpp) cc_final: 0.7373 (tpp) REVERT: D 435 ILE cc_start: 0.6986 (mm) cc_final: 0.5849 (mm) REVERT: E 19 LYS cc_start: 0.8301 (tptp) cc_final: 0.7757 (tmmt) REVERT: E 56 LYS cc_start: 0.8813 (mmtm) cc_final: 0.8428 (mptt) REVERT: E 169 THR cc_start: 0.8767 (t) cc_final: 0.8449 (p) REVERT: E 435 ILE cc_start: 0.6444 (mt) cc_final: 0.6061 (tp) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2196 time to fit residues: 96.5403 Evaluate side-chains 247 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 96 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 0.1980 chunk 15 optimal weight: 8.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN B 186 GLN C 186 GLN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.144505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.115943 restraints weight = 17568.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.116418 restraints weight = 20047.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.117045 restraints weight = 17580.607| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5029 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= 0.174 Angle : 0.615 7.020 18335 Z= 0.315 Chirality : 0.046 0.180 2190 Planarity : 0.005 0.044 2200 Dihedral : 6.459 73.403 2260 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.21), residues: 1580 helix: 1.14 (0.23), residues: 515 sheet: -1.07 (0.27), residues: 355 loop : -0.93 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.006 0.003 HIS A 442 PHE 0.021 0.002 PHE A 289 TYR 0.022 0.002 TYR E 284 ARG 0.003 0.000 ARG E 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00032 ( 5) link_NAG-ASN : angle 0.79004 ( 15) hydrogen bonds : bond 0.03978 ( 420) hydrogen bonds : angle 4.28585 ( 1260) SS BOND : bond 0.00200 ( 5) SS BOND : angle 1.06546 ( 10) covalent geometry : bond 0.00409 (13360) covalent geometry : angle 0.61465 (18310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4333.86 seconds wall clock time: 79 minutes 23.36 seconds (4763.36 seconds total)