Starting phenix.real_space_refine on Mon Dec 30 14:15:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8byi_16326/12_2024/8byi_16326_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8byi_16326/12_2024/8byi_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_16326/12_2024/8byi_16326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8byi_16326/12_2024/8byi_16326.map" model { file = "/net/cci-nas-00/data/ceres_data/8byi_16326/12_2024/8byi_16326_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8byi_16326/12_2024/8byi_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-5532/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: 8.15, 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: 3.70 Conformation dependent library (CDL) restraints added in 1.8 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: 1.08 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: 3.18 Time building geometry restraints manager: 3.81 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: 0.00 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: 0.780 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.420 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- 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 13360 Z= 0.522 Angle : 0.725 12.228 18310 Z= 0.290 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 *********************** 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 : 1.702 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: 0.2772 time to fit residues: 175.3835 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 : 1.807 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 13360 Z= 0.248 Angle : 0.585 8.362 18310 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 *********************** 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 : 1.568 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: 0.8136 (tptp) cc_final: 0.7680 (tmmt) REVERT: A 180 ILE cc_start: 0.7969 (mm) cc_final: 0.7655 (mt) REVERT: B 16 ARG cc_start: 0.7301 (ttp-170) cc_final: 0.7032 (ttp80) REVERT: B 19 LYS cc_start: 0.8138 (tptp) cc_final: 0.7627 (tmmt) REVERT: B 184 GLU cc_start: 0.7446 (pt0) cc_final: 0.6638 (mt-10) REVERT: B 234 PHE cc_start: 0.7363 (t80) cc_final: 0.6996 (t80) REVERT: B 298 PHE cc_start: 0.7858 (m-80) cc_final: 0.7575 (m-80) REVERT: C 13 ASP cc_start: 0.7857 (p0) cc_final: 0.7407 (m-30) REVERT: C 16 ARG cc_start: 0.8271 (ttp-110) cc_final: 0.8008 (ttp-170) REVERT: C 19 LYS cc_start: 0.8285 (tptp) cc_final: 0.7730 (tmmt) REVERT: C 57 GLU cc_start: 0.7421 (tp30) cc_final: 0.7063 (tp30) REVERT: C 108 GLU cc_start: 0.7584 (pt0) cc_final: 0.7313 (pm20) REVERT: D 19 LYS cc_start: 0.8222 (tptp) cc_final: 0.7663 (tmmt) REVERT: D 178 TYR cc_start: 0.6317 (p90) cc_final: 0.5897 (p90) REVERT: D 227 MET cc_start: 0.8339 (ttp) cc_final: 0.6668 (tpt) REVERT: E 19 LYS cc_start: 0.8348 (tptp) cc_final: 0.7769 (tmmt) REVERT: E 56 LYS cc_start: 0.8278 (mtmt) cc_final: 0.8038 (mmtt) REVERT: E 165 SER cc_start: 0.7493 (t) cc_final: 0.7277 (m) REVERT: E 227 MET cc_start: 0.7983 (ttp) cc_final: 0.6746 (tpt) REVERT: E 271 MET cc_start: 0.7737 (tpt) cc_final: 0.7536 (tpp) REVERT: E 435 ILE cc_start: 0.6408 (mt) cc_final: 0.5381 (mt) outliers start: 1 outliers final: 1 residues processed: 352 average time/residue: 0.2593 time to fit residues: 133.7428 Evaluate side-chains 265 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 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 A 295 ASN B 186 GLN C 186 GLN C 295 ASN D 68 HIS D 186 GLN E 186 GLN E 295 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13360 Z= 0.299 Angle : 0.590 5.424 18310 Z= 0.307 Chirality : 0.047 0.164 2190 Planarity : 0.005 0.042 2200 Dihedral : 6.167 56.587 2260 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: 0.21 (0.21), residues: 1580 helix: 1.62 (0.22), residues: 525 sheet: -0.29 (0.27), residues: 385 loop : -0.73 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 128 HIS 0.007 0.003 HIS B 68 PHE 0.019 0.002 PHE D 234 TYR 0.023 0.002 TYR E 284 ARG 0.004 0.001 ARG E 249 *********************** 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 327 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.575 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: 0.7624 (ttp-170) cc_final: 0.7196 (ttp80) REVERT: A 19 LYS cc_start: 0.8264 (tptp) cc_final: 0.7741 (tmmt) REVERT: A 52 ASP cc_start: 0.8105 (t0) cc_final: 0.7905 (t0) REVERT: A 57 GLU cc_start: 0.7596 (tp30) cc_final: 0.7370 (tp30) REVERT: A 153 THR cc_start: 0.8642 (p) cc_final: 0.8345 (t) REVERT: A 169 THR cc_start: 0.8639 (t) cc_final: 0.8397 (p) REVERT: B 16 ARG cc_start: 0.7343 (ttp-170) cc_final: 0.7015 (ttp80) REVERT: B 17 LEU cc_start: 0.7611 (tt) cc_final: 0.7410 (tt) REVERT: B 19 LYS cc_start: 0.8207 (tptp) cc_final: 0.7645 (tmmt) REVERT: B 184 GLU cc_start: 0.7685 (pt0) cc_final: 0.6993 (mt-10) REVERT: B 234 PHE cc_start: 0.7635 (t80) cc_final: 0.7071 (t80) REVERT: C 16 ARG cc_start: 0.8262 (ttp-110) cc_final: 0.7962 (ttp-170) REVERT: C 19 LYS cc_start: 0.8419 (tptp) cc_final: 0.7790 (tmmt) REVERT: C 56 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8380 (mmtp) REVERT: C 179 MET cc_start: 0.6279 (ttt) cc_final: 0.5952 (ttt) REVERT: D 19 LYS cc_start: 0.8288 (tptp) cc_final: 0.7693 (tmmt) REVERT: D 56 LYS cc_start: 0.8390 (mtmt) cc_final: 0.8154 (mmtt) REVERT: D 73 PHE cc_start: 0.7871 (p90) cc_final: 0.7662 (p90) REVERT: D 74 GLN cc_start: 0.7893 (mt0) cc_final: 0.7672 (mt0) REVERT: D 178 TYR cc_start: 0.6398 (p90) cc_final: 0.6000 (p90) REVERT: D 234 PHE cc_start: 0.7555 (t80) cc_final: 0.7298 (t80) REVERT: E 19 LYS cc_start: 0.8364 (tptp) cc_final: 0.7826 (tmmt) REVERT: E 57 GLU cc_start: 0.7832 (tp30) cc_final: 0.7508 (tp30) REVERT: E 93 ASP cc_start: 0.7614 (m-30) cc_final: 0.7385 (m-30) REVERT: E 169 THR cc_start: 0.8612 (t) cc_final: 0.8379 (p) REVERT: E 179 MET cc_start: 0.6420 (ttm) cc_final: 0.6140 (ttm) REVERT: E 184 GLU cc_start: 0.7535 (pt0) cc_final: 0.6915 (mt-10) REVERT: E 227 MET cc_start: 0.8054 (ttp) cc_final: 0.6686 (tpt) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2370 time to fit residues: 115.8674 Evaluate side-chains 262 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 146 optimal weight: 0.0020 chunk 154 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.5126 ------------------------------------------------------------------------------- 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 186 GLN D 295 ASN E 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13360 Z= 0.138 Angle : 0.506 5.818 18310 Z= 0.260 Chirality : 0.043 0.140 2190 Planarity : 0.004 0.048 2200 Dihedral : 5.306 48.594 2260 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.68 % 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: 0.29 (0.21), residues: 1580 helix: 1.73 (0.23), residues: 515 sheet: -0.03 (0.25), residues: 420 loop : -0.88 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 65 HIS 0.007 0.001 HIS E 442 PHE 0.014 0.001 PHE D 234 TYR 0.016 0.001 TYR C 443 ARG 0.004 0.000 ARG E 249 *********************** 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 322 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 321 time to evaluate : 1.446 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: 0.7517 (ttp-170) cc_final: 0.7121 (ttp80) REVERT: A 19 LYS cc_start: 0.8189 (tptp) cc_final: 0.7662 (tmmt) REVERT: A 56 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8212 (mmmt) REVERT: A 153 THR cc_start: 0.8692 (p) cc_final: 0.8388 (t) REVERT: A 254 ILE cc_start: 0.8484 (mm) cc_final: 0.8278 (mm) REVERT: B 17 LEU cc_start: 0.7331 (tt) cc_final: 0.7040 (tt) REVERT: B 19 LYS cc_start: 0.8130 (tptp) cc_final: 0.7534 (tmmt) REVERT: B 56 LYS cc_start: 0.8465 (mtpt) cc_final: 0.8210 (mmtt) REVERT: B 153 THR cc_start: 0.8604 (p) cc_final: 0.8395 (t) REVERT: B 184 GLU cc_start: 0.7560 (pt0) cc_final: 0.6821 (mt-10) REVERT: B 234 PHE cc_start: 0.7635 (t80) cc_final: 0.6994 (t80) REVERT: C 19 LYS cc_start: 0.8371 (tptp) cc_final: 0.7653 (tmmt) REVERT: C 56 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8427 (mmtp) REVERT: C 298 PHE cc_start: 0.7720 (m-80) cc_final: 0.7224 (m-80) REVERT: D 19 LYS cc_start: 0.8146 (tptp) cc_final: 0.7496 (tmmt) REVERT: D 153 THR cc_start: 0.8668 (p) cc_final: 0.8415 (t) REVERT: D 179 MET cc_start: 0.6290 (ttt) cc_final: 0.6040 (ttm) REVERT: D 435 ILE cc_start: 0.6688 (mm) cc_final: 0.6154 (mm) REVERT: E 19 LYS cc_start: 0.8220 (tptp) cc_final: 0.7679 (tmmt) REVERT: E 57 GLU cc_start: 0.7629 (tp30) cc_final: 0.7429 (tp30) REVERT: E 179 MET cc_start: 0.6353 (ttm) cc_final: 0.6071 (ttm) REVERT: E 184 GLU cc_start: 0.7445 (pt0) cc_final: 0.6823 (mt-10) REVERT: E 227 MET cc_start: 0.7979 (ttp) cc_final: 0.6722 (tpt) outliers start: 1 outliers final: 1 residues processed: 321 average time/residue: 0.2380 time to fit residues: 113.8965 Evaluate side-chains 265 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 0.0370 chunk 115 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 overall best weight: 2.2066 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13360 Z= 0.239 Angle : 0.561 7.444 18310 Z= 0.288 Chirality : 0.044 0.140 2190 Planarity : 0.004 0.044 2200 Dihedral : 5.655 53.491 2260 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: 0.22 (0.21), residues: 1580 helix: 1.66 (0.23), residues: 515 sheet: -0.12 (0.28), residues: 320 loop : -0.79 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.007 0.002 HIS E 442 PHE 0.018 0.002 PHE B 73 TYR 0.020 0.001 TYR E 284 ARG 0.003 0.000 ARG D 135 *********************** 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 313 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.587 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: 0.7603 (ttp-170) cc_final: 0.7174 (ttp80) REVERT: A 19 LYS cc_start: 0.8211 (tptp) cc_final: 0.7682 (tmmt) REVERT: A 56 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8247 (mmtt) REVERT: A 153 THR cc_start: 0.8727 (p) cc_final: 0.8451 (t) REVERT: A 169 THR cc_start: 0.8616 (t) cc_final: 0.8341 (p) REVERT: B 19 LYS cc_start: 0.8182 (tptp) cc_final: 0.7635 (tmmt) REVERT: B 56 LYS cc_start: 0.8523 (mtpt) cc_final: 0.8239 (mmtt) REVERT: C 19 LYS cc_start: 0.8368 (tptp) cc_final: 0.7717 (tmmt) REVERT: C 56 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8460 (mmtp) REVERT: C 127 MET cc_start: 0.8269 (mtm) cc_final: 0.7870 (ttm) REVERT: C 153 THR cc_start: 0.8680 (p) cc_final: 0.8422 (t) REVERT: C 298 PHE cc_start: 0.7524 (m-80) cc_final: 0.7268 (m-80) REVERT: D 19 LYS cc_start: 0.8136 (tptp) cc_final: 0.7561 (tmmt) REVERT: D 56 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8389 (mmtt) REVERT: D 179 MET cc_start: 0.6327 (ttt) cc_final: 0.6018 (ttm) REVERT: D 435 ILE cc_start: 0.6710 (mm) cc_final: 0.6298 (mt) REVERT: E 19 LYS cc_start: 0.8263 (tptp) cc_final: 0.7706 (tmmt) REVERT: E 56 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8458 (mmtt) REVERT: E 179 MET cc_start: 0.6346 (ttm) cc_final: 0.6137 (ttm) REVERT: E 184 GLU cc_start: 0.7671 (pt0) cc_final: 0.7092 (mt-10) REVERT: E 227 MET cc_start: 0.8084 (ttp) cc_final: 0.6752 (tpt) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.2640 time to fit residues: 121.9653 Evaluate side-chains 252 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13360 Z= 0.334 Angle : 0.614 6.929 18310 Z= 0.319 Chirality : 0.046 0.150 2190 Planarity : 0.005 0.047 2200 Dihedral : 6.265 52.890 2260 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: -0.17 (0.21), residues: 1580 helix: 1.18 (0.22), residues: 520 sheet: -0.54 (0.28), residues: 340 loop : -0.79 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 128 HIS 0.007 0.003 HIS B 68 PHE 0.012 0.002 PHE D 73 TYR 0.021 0.002 TYR E 284 ARG 0.005 0.001 ARG B 135 *********************** 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 319 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7650 (ttp-170) cc_final: 0.7201 (ttp80) REVERT: A 19 LYS cc_start: 0.8277 (tptp) cc_final: 0.7786 (tmmt) REVERT: A 153 THR cc_start: 0.8813 (p) cc_final: 0.8558 (t) REVERT: A 169 THR cc_start: 0.8665 (t) cc_final: 0.8347 (p) REVERT: B 16 ARG cc_start: 0.7435 (ttp-170) cc_final: 0.7041 (ttp80) REVERT: B 19 LYS cc_start: 0.8245 (tptp) cc_final: 0.7710 (tmmt) REVERT: C 19 LYS cc_start: 0.8416 (tptp) cc_final: 0.7809 (tmmt) REVERT: C 128 TRP cc_start: 0.9105 (t60) cc_final: 0.8761 (t60) REVERT: C 184 GLU cc_start: 0.7831 (pt0) cc_final: 0.7261 (mt-10) REVERT: C 213 LYS cc_start: 0.7923 (ttpp) cc_final: 0.7644 (ttpp) REVERT: D 19 LYS cc_start: 0.8262 (tptp) cc_final: 0.7673 (tmmt) REVERT: D 56 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8398 (mmtt) REVERT: E 19 LYS cc_start: 0.8320 (tptp) cc_final: 0.7823 (tmmt) REVERT: E 179 MET cc_start: 0.6316 (ttm) cc_final: 0.6016 (ttm) REVERT: E 213 LYS cc_start: 0.7929 (ttpp) cc_final: 0.7714 (ttpp) REVERT: E 227 MET cc_start: 0.8410 (ttp) cc_final: 0.6950 (tpt) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2688 time to fit residues: 127.2328 Evaluate side-chains 261 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 113 optimal weight: 0.0010 chunk 87 optimal weight: 0.0010 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 154 optimal weight: 0.4980 chunk 96 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 overall best weight: 1.0996 ------------------------------------------------------------------------------- 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 D 186 GLN E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13360 Z= 0.175 Angle : 0.555 6.893 18310 Z= 0.281 Chirality : 0.044 0.224 2190 Planarity : 0.004 0.045 2200 Dihedral : 5.789 50.496 2260 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.07 % Allowed : 1.73 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1580 helix: 1.41 (0.23), residues: 515 sheet: -0.35 (0.27), residues: 350 loop : -0.87 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 65 HIS 0.006 0.002 HIS C 442 PHE 0.022 0.002 PHE C 73 TYR 0.019 0.001 TYR D 284 ARG 0.004 0.000 ARG E 249 *********************** 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 318 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7578 (ttp-170) cc_final: 0.7127 (ttp80) REVERT: A 19 LYS cc_start: 0.8208 (tptp) cc_final: 0.7697 (tmmt) REVERT: A 52 ASP cc_start: 0.8272 (t0) cc_final: 0.8068 (t0) REVERT: A 153 THR cc_start: 0.8833 (p) cc_final: 0.8536 (t) REVERT: A 178 TYR cc_start: 0.6485 (p90) cc_final: 0.6238 (p90) REVERT: B 19 LYS cc_start: 0.8162 (tptp) cc_final: 0.7580 (tmmt) REVERT: B 184 GLU cc_start: 0.7815 (pt0) cc_final: 0.7076 (mt-10) REVERT: C 19 LYS cc_start: 0.8324 (tptp) cc_final: 0.7685 (tmmt) REVERT: C 82 TYR cc_start: 0.8449 (m-80) cc_final: 0.8107 (m-80) REVERT: C 184 GLU cc_start: 0.7636 (pt0) cc_final: 0.7090 (mt-10) REVERT: C 213 LYS cc_start: 0.7800 (ttpp) cc_final: 0.7556 (ttpp) REVERT: D 19 LYS cc_start: 0.8157 (tptp) cc_final: 0.7560 (tmmt) REVERT: D 184 GLU cc_start: 0.7749 (pt0) cc_final: 0.7163 (mt-10) REVERT: D 435 ILE cc_start: 0.6806 (mm) cc_final: 0.6362 (mm) REVERT: E 19 LYS cc_start: 0.8274 (tptp) cc_final: 0.7740 (tmmt) REVERT: E 179 MET cc_start: 0.6418 (ttm) cc_final: 0.6160 (ttm) REVERT: E 213 LYS cc_start: 0.7922 (ttpp) cc_final: 0.7697 (ttpp) outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.2370 time to fit residues: 111.7478 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 : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 98 optimal weight: 0.5980 chunk 105 optimal weight: 0.0670 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 63 ASN B 186 GLN C 186 GLN D 186 GLN E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13360 Z= 0.211 Angle : 0.573 10.653 18310 Z= 0.289 Chirality : 0.044 0.171 2190 Planarity : 0.005 0.046 2200 Dihedral : 5.902 54.407 2260 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: -0.16 (0.21), residues: 1580 helix: 1.26 (0.23), residues: 515 sheet: -0.45 (0.28), residues: 350 loop : -0.89 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 65 HIS 0.006 0.002 HIS B 442 PHE 0.018 0.002 PHE C 73 TYR 0.019 0.001 TYR B 284 ARG 0.003 0.000 ARG C 249 *********************** 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 297 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7610 (ttp-170) cc_final: 0.7146 (ttp80) REVERT: A 19 LYS cc_start: 0.8187 (tptp) cc_final: 0.7684 (tmmt) REVERT: A 52 ASP cc_start: 0.8272 (t0) cc_final: 0.8054 (t0) REVERT: A 153 THR cc_start: 0.8841 (p) cc_final: 0.8563 (t) REVERT: A 169 THR cc_start: 0.8607 (t) cc_final: 0.8327 (p) REVERT: A 178 TYR cc_start: 0.6477 (p90) cc_final: 0.6219 (p90) REVERT: A 435 ILE cc_start: 0.6569 (mm) cc_final: 0.5809 (mt) REVERT: B 17 LEU cc_start: 0.7518 (tt) cc_final: 0.7267 (tt) REVERT: B 19 LYS cc_start: 0.8180 (tptp) cc_final: 0.7642 (tmmt) REVERT: B 56 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8237 (mmtp) REVERT: B 150 GLN cc_start: 0.8737 (mp10) cc_final: 0.8529 (mp10) REVERT: B 184 GLU cc_start: 0.7922 (pt0) cc_final: 0.7213 (mt-10) REVERT: B 227 MET cc_start: 0.8293 (ttp) cc_final: 0.6638 (tpp) REVERT: C 19 LYS cc_start: 0.8368 (tptp) cc_final: 0.7726 (tmmt) REVERT: C 56 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8532 (mmtt) REVERT: C 73 PHE cc_start: 0.7832 (p90) cc_final: 0.7574 (p90) REVERT: C 127 MET cc_start: 0.8119 (mtt) cc_final: 0.7741 (mtm) REVERT: C 184 GLU cc_start: 0.7802 (pt0) cc_final: 0.7181 (mt-10) REVERT: C 213 LYS cc_start: 0.7862 (ttpp) cc_final: 0.7620 (ttpp) REVERT: D 19 LYS cc_start: 0.8144 (tptp) cc_final: 0.7561 (tmmt) REVERT: D 56 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8458 (mmtt) REVERT: D 435 ILE cc_start: 0.6797 (mm) cc_final: 0.5842 (mm) REVERT: E 19 LYS cc_start: 0.8265 (tptp) cc_final: 0.7732 (tmmt) REVERT: E 56 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8342 (mmtt) REVERT: E 213 LYS cc_start: 0.7935 (ttpp) cc_final: 0.7711 (ttpp) REVERT: E 227 MET cc_start: 0.8255 (ttp) cc_final: 0.6608 (tpp) REVERT: E 271 MET cc_start: 0.8085 (tpt) cc_final: 0.7795 (tpt) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2490 time to fit residues: 109.0210 Evaluate side-chains 243 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN C 186 GLN D 186 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13360 Z= 0.328 Angle : 0.646 7.386 18310 Z= 0.330 Chirality : 0.047 0.194 2190 Planarity : 0.005 0.045 2200 Dihedral : 6.447 64.423 2260 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: -0.41 (0.21), residues: 1580 helix: 1.11 (0.22), residues: 515 sheet: -0.87 (0.28), residues: 355 loop : -0.91 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 128 HIS 0.008 0.003 HIS B 68 PHE 0.020 0.002 PHE D 73 TYR 0.030 0.002 TYR A 284 ARG 0.005 0.001 ARG C 249 *********************** 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 291 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7281 (ttp80) REVERT: A 19 LYS cc_start: 0.8276 (tptp) cc_final: 0.7778 (tmmt) REVERT: A 153 THR cc_start: 0.8828 (p) cc_final: 0.8579 (t) REVERT: A 169 THR cc_start: 0.8761 (t) cc_final: 0.8493 (p) REVERT: A 178 TYR cc_start: 0.6593 (p90) cc_final: 0.6372 (p90) REVERT: B 19 LYS cc_start: 0.8246 (tptp) cc_final: 0.7713 (tmmt) REVERT: B 150 GLN cc_start: 0.8708 (mp10) cc_final: 0.8434 (mp10) REVERT: B 179 MET cc_start: 0.6509 (ttt) cc_final: 0.5464 (ptp) REVERT: B 184 GLU cc_start: 0.7905 (pt0) cc_final: 0.7300 (mt-10) REVERT: B 227 MET cc_start: 0.8382 (ttp) cc_final: 0.6648 (tpp) REVERT: C 13 ASP cc_start: 0.7820 (p0) cc_final: 0.7285 (m-30) REVERT: C 19 LYS cc_start: 0.8418 (tptp) cc_final: 0.7785 (tmmt) REVERT: C 56 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8586 (mmtt) REVERT: C 184 GLU cc_start: 0.7834 (pt0) cc_final: 0.7280 (mt-10) REVERT: C 213 LYS cc_start: 0.7897 (ttpp) cc_final: 0.7624 (ttpp) REVERT: D 19 LYS cc_start: 0.8237 (tptp) cc_final: 0.7654 (tmmt) REVERT: D 56 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8365 (mmtt) REVERT: D 179 MET cc_start: 0.6476 (ttt) cc_final: 0.6221 (ttm) REVERT: D 435 ILE cc_start: 0.6829 (mm) cc_final: 0.5786 (mm) REVERT: E 19 LYS cc_start: 0.8292 (tptp) cc_final: 0.7807 (tmmt) REVERT: E 169 THR cc_start: 0.8807 (t) cc_final: 0.8475 (p) REVERT: E 213 LYS cc_start: 0.7926 (ttpp) cc_final: 0.7710 (ttpp) REVERT: E 227 MET cc_start: 0.8447 (ttp) cc_final: 0.6699 (tpp) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2333 time to fit residues: 102.0113 Evaluate side-chains 238 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.0370 chunk 92 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 13 optimal weight: 0.0270 chunk 98 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 overall best weight: 0.9920 ------------------------------------------------------------------------------- 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 D 186 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13360 Z= 0.183 Angle : 0.589 11.640 18310 Z= 0.296 Chirality : 0.044 0.252 2190 Planarity : 0.005 0.047 2200 Dihedral : 6.149 63.358 2260 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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 : 1.54 % 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: -0.29 (0.21), residues: 1580 helix: 1.23 (0.23), residues: 515 sheet: -0.65 (0.27), residues: 350 loop : -0.95 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 159 HIS 0.007 0.002 HIS A 442 PHE 0.018 0.002 PHE E 73 TYR 0.019 0.001 TYR B 252 ARG 0.005 0.000 ARG B 16 ********************** 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 293 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7633 (ttp-170) cc_final: 0.7190 (ttp80) REVERT: A 19 LYS cc_start: 0.8179 (tptp) cc_final: 0.7677 (tmmt) REVERT: A 153 THR cc_start: 0.8841 (p) cc_final: 0.8575 (t) REVERT: A 178 TYR cc_start: 0.6454 (p90) cc_final: 0.6226 (p90) REVERT: A 184 GLU cc_start: 0.7983 (pt0) cc_final: 0.7548 (mt-10) REVERT: A 271 MET cc_start: 0.8351 (tpt) cc_final: 0.8018 (tpt) REVERT: A 435 ILE cc_start: 0.6542 (mm) cc_final: 0.5782 (mm) REVERT: B 17 LEU cc_start: 0.7325 (tt) cc_final: 0.7122 (tt) REVERT: B 19 LYS cc_start: 0.8201 (tptp) cc_final: 0.7694 (tmmt) REVERT: B 150 GLN cc_start: 0.8667 (mp10) cc_final: 0.8448 (mp10) REVERT: B 179 MET cc_start: 0.6696 (ttt) cc_final: 0.5591 (ptp) REVERT: B 184 GLU cc_start: 0.7866 (pt0) cc_final: 0.7212 (mt-10) REVERT: B 227 MET cc_start: 0.8251 (ttp) cc_final: 0.6594 (tpp) REVERT: B 248 GLU cc_start: 0.8093 (tp30) cc_final: 0.7593 (mt-10) REVERT: B 250 ILE cc_start: 0.7555 (pt) cc_final: 0.7333 (pt) REVERT: C 19 LYS cc_start: 0.8335 (tptp) cc_final: 0.7686 (tmmt) REVERT: C 56 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8564 (mmtt) REVERT: C 82 TYR cc_start: 0.8366 (m-80) cc_final: 0.8101 (m-80) REVERT: C 184 GLU cc_start: 0.7771 (pt0) cc_final: 0.7138 (mt-10) REVERT: C 213 LYS cc_start: 0.7894 (ttpp) cc_final: 0.7620 (ttpp) REVERT: D 19 LYS cc_start: 0.8183 (tptp) cc_final: 0.7580 (tmmt) REVERT: D 56 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8414 (mmtt) REVERT: D 179 MET cc_start: 0.6567 (ttt) cc_final: 0.6309 (ttm) REVERT: D 268 SER cc_start: 0.8095 (t) cc_final: 0.7758 (t) REVERT: D 435 ILE cc_start: 0.6780 (mm) cc_final: 0.5774 (mm) REVERT: E 19 LYS cc_start: 0.8234 (tptp) cc_final: 0.7699 (tmmt) REVERT: E 213 LYS cc_start: 0.7950 (ttpp) cc_final: 0.7750 (ttpp) REVERT: E 227 MET cc_start: 0.8372 (ttp) cc_final: 0.6617 (tpp) REVERT: E 271 MET cc_start: 0.8190 (tpt) cc_final: 0.7970 (tpt) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2360 time to fit residues: 103.8514 Evaluate side-chains 243 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 chunk 16 optimal weight: 0.0670 chunk 23 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 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 = 0.3608 r_free = 0.3608 target = 0.148931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.121470 restraints weight = 17184.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.121734 restraints weight = 14775.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.122374 restraints weight = 12394.122| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13360 Z= 0.160 Angle : 0.569 7.369 18310 Z= 0.287 Chirality : 0.043 0.172 2190 Planarity : 0.005 0.046 2200 Dihedral : 6.002 60.053 2260 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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 : 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: -0.33 (0.21), residues: 1580 helix: 1.28 (0.23), residues: 515 sheet: -0.73 (0.26), residues: 390 loop : -1.02 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 185 HIS 0.007 0.001 HIS A 442 PHE 0.020 0.002 PHE B 73 TYR 0.019 0.001 TYR A 284 ARG 0.004 0.000 ARG C 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2867.94 seconds wall clock time: 54 minutes 5.10 seconds (3245.10 seconds total)