Starting phenix.real_space_refine on Tue Feb 13 16:46:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqh_25385/02_2024/7sqh_25385.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqh_25385/02_2024/7sqh_25385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqh_25385/02_2024/7sqh_25385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqh_25385/02_2024/7sqh_25385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqh_25385/02_2024/7sqh_25385.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqh_25385/02_2024/7sqh_25385.pdb" } resolution = 2.5 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4500 2.51 5 N 1134 2.21 5 O 1287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 176": "OE1" <-> "OE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6954 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2255 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 269} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2255 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 269} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2255 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 269} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 4.36, per 1000 atoms: 0.63 Number of scatterers: 6954 At special positions: 0 Unit cell: (81.4625, 81.4625, 126.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1287 8.00 N 1134 7.00 C 4500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 401 " - " ASN A 148 " " NAG A 402 " - " ASN A 162 " " NAG A 403 " - " ASN A 190 " " NAG A 404 " - " ASN A 155 " " NAG B 401 " - " ASN B 148 " " NAG B 402 " - " ASN B 162 " " NAG B 403 " - " ASN B 190 " " NAG B 404 " - " ASN B 155 " " NAG C 401 " - " ASN C 148 " " NAG C 402 " - " ASN C 162 " " NAG C 403 " - " ASN C 190 " " NAG C 404 " - " ASN C 155 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.4 seconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1638 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 4 sheets defined 38.6% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 57 through 95 removed outlier: 3.793A pdb=" N LYS A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 179 removed outlier: 3.515A pdb=" N LYS A 179 " --> pdb=" O GLU A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 179' Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.649A pdb=" N PHE A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.305A pdb=" N SER A 277 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 278 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.638A pdb=" N ASN A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 302' Processing helix chain 'A' and resid 302 through 339 removed outlier: 3.906A pdb=" N THR A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 95 removed outlier: 3.793A pdb=" N LYS B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 179 removed outlier: 3.515A pdb=" N LYS B 179 " --> pdb=" O GLU B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 179' Processing helix chain 'B' and resid 206 through 212 removed outlier: 3.649A pdb=" N PHE B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 272 through 278 removed outlier: 4.305A pdb=" N SER B 277 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 278 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.639A pdb=" N ASN B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 298 through 302' Processing helix chain 'B' and resid 302 through 339 removed outlier: 3.906A pdb=" N THR B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 95 removed outlier: 3.793A pdb=" N LYS C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 removed outlier: 3.515A pdb=" N LYS C 179 " --> pdb=" O GLU C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 179' Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.649A pdb=" N PHE C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 272 through 278 removed outlier: 4.305A pdb=" N SER C 277 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA C 278 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.639A pdb=" N ASN C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 302' Processing helix chain 'C' and resid 302 through 339 removed outlier: 3.906A pdb=" N THR C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 100 through 107 current: chain 'A' and resid 181 through 189 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 181 through 189 current: chain 'A' and resid 254 through 266 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 254 through 266 current: chain 'B' and resid 181 through 189 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 181 through 189 current: chain 'B' and resid 254 through 266 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 254 through 266 current: chain 'C' and resid 181 through 189 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 181 through 189 current: chain 'C' and resid 254 through 266 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 157 removed outlier: 4.120A pdb=" N ASP A 200 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 151 through 157 removed outlier: 4.121A pdb=" N ASP B 200 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 151 through 157 removed outlier: 4.120A pdb=" N ASP C 200 " --> pdb=" O TYR C 119 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1086 1.27 - 1.41: 1809 1.41 - 1.54: 4098 1.54 - 1.67: 60 1.67 - 1.81: 51 Bond restraints: 7104 Sorted by residual: bond pdb=" C GLN C 152 " pdb=" O GLN C 152 " ideal model delta sigma weight residual 1.234 1.138 0.096 1.26e-02 6.30e+03 5.86e+01 bond pdb=" C ARG C 180 " pdb=" O ARG C 180 " ideal model delta sigma weight residual 1.235 1.146 0.090 1.26e-02 6.30e+03 5.07e+01 bond pdb=" C GLN B 152 " pdb=" O GLN B 152 " ideal model delta sigma weight residual 1.234 1.153 0.081 1.22e-02 6.72e+03 4.37e+01 bond pdb=" C TYR B 132 " pdb=" O TYR B 132 " ideal model delta sigma weight residual 1.235 1.163 0.072 1.14e-02 7.69e+03 3.95e+01 bond pdb=" C GLN A 152 " pdb=" O GLN A 152 " ideal model delta sigma weight residual 1.234 1.156 0.078 1.26e-02 6.30e+03 3.83e+01 ... (remaining 7099 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.19: 224 107.19 - 113.97: 3999 113.97 - 120.76: 3045 120.76 - 127.54: 2287 127.54 - 134.32: 66 Bond angle restraints: 9621 Sorted by residual: angle pdb=" CA ARG B 180 " pdb=" C ARG B 180 " pdb=" O ARG B 180 " ideal model delta sigma weight residual 122.14 114.88 7.26 1.24e+00 6.50e-01 3.43e+01 angle pdb=" CA ARG A 180 " pdb=" C ARG A 180 " pdb=" O ARG A 180 " ideal model delta sigma weight residual 122.45 115.48 6.97 1.30e+00 5.92e-01 2.87e+01 angle pdb=" O HIS B 131 " pdb=" C HIS B 131 " pdb=" N TYR B 132 " ideal model delta sigma weight residual 123.15 116.72 6.43 1.30e+00 5.92e-01 2.44e+01 angle pdb=" O HIS A 131 " pdb=" C HIS A 131 " pdb=" N TYR A 132 " ideal model delta sigma weight residual 123.15 116.90 6.25 1.30e+00 5.92e-01 2.31e+01 angle pdb=" O HIS C 131 " pdb=" C HIS C 131 " pdb=" N TYR C 132 " ideal model delta sigma weight residual 123.15 117.42 5.73 1.30e+00 5.92e-01 1.95e+01 ... (remaining 9616 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 3950 21.16 - 42.32: 313 42.32 - 63.48: 104 63.48 - 84.65: 12 84.65 - 105.81: 28 Dihedral angle restraints: 4407 sinusoidal: 1893 harmonic: 2514 Sorted by residual: dihedral pdb=" C2 NAG C 404 " pdb=" C3 NAG C 404 " pdb=" C4 NAG C 404 " pdb=" O4 NAG C 404 " ideal model delta sinusoidal sigma weight residual 175.11 69.30 105.81 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG A 404 " pdb=" C3 NAG A 404 " pdb=" C4 NAG A 404 " pdb=" O4 NAG A 404 " ideal model delta sinusoidal sigma weight residual 175.11 69.33 105.78 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG B 404 " pdb=" C3 NAG B 404 " pdb=" C4 NAG B 404 " pdb=" O4 NAG B 404 " ideal model delta sinusoidal sigma weight residual 175.11 69.34 105.77 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 4404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 893 0.057 - 0.114: 166 0.114 - 0.170: 33 0.170 - 0.227: 2 0.227 - 0.284: 4 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CA ARG B 180 " pdb=" N ARG B 180 " pdb=" C ARG B 180 " pdb=" CB ARG B 180 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 148 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 148 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1095 not shown) Planarity restraints: 1212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 132 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C TYR B 132 " -0.063 2.00e-02 2.50e+03 pdb=" O TYR B 132 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU B 133 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 132 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C TYR A 132 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR A 132 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU A 133 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 132 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C TYR C 132 " -0.053 2.00e-02 2.50e+03 pdb=" O TYR C 132 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU C 133 " 0.018 2.00e-02 2.50e+03 ... (remaining 1209 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1410 2.79 - 3.31: 6126 3.31 - 3.84: 11152 3.84 - 4.37: 13265 4.37 - 4.90: 23067 Nonbonded interactions: 55020 Sorted by model distance: nonbonded pdb=" O ASP C 269 " pdb=" OD1 ASP C 269 " model vdw 2.257 3.040 nonbonded pdb=" O ASP B 269 " pdb=" OD1 ASP B 269 " model vdw 2.258 3.040 nonbonded pdb=" O ASP A 269 " pdb=" OD1 ASP A 269 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR C 119 " pdb=" OH TYR C 156 " model vdw 2.266 2.440 nonbonded pdb=" OH TYR B 119 " pdb=" OH TYR B 156 " model vdw 2.266 2.440 ... (remaining 55015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 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: 11.420 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 21.700 Find NCS groups from input model: 0.410 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: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.006 0.096 7104 Z= 0.361 Angle : 0.740 7.318 9621 Z= 0.465 Chirality : 0.050 0.284 1098 Planarity : 0.004 0.037 1200 Dihedral : 19.411 105.807 2769 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 20.75 % Favored : 79.25 % 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: 1.93 (0.29), residues: 843 helix: 3.21 (0.27), residues: 312 sheet: 0.58 (0.27), residues: 312 loop : -0.53 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 330 HIS 0.003 0.001 HIS B 130 PHE 0.014 0.001 PHE C 204 TYR 0.022 0.001 TYR A 132 ARG 0.003 0.000 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7058 (t80) cc_final: 0.6852 (t80) REVERT: A 122 GLN cc_start: 0.8847 (mm110) cc_final: 0.8488 (mm110) REVERT: A 153 ARG cc_start: 0.7453 (mtp85) cc_final: 0.7166 (mtp85) REVERT: A 180 ARG cc_start: 0.7846 (mtp180) cc_final: 0.7618 (mtp180) REVERT: A 253 ARG cc_start: 0.7686 (ptm-80) cc_final: 0.7002 (ptm-80) REVERT: A 297 ASP cc_start: 0.8455 (t0) cc_final: 0.8182 (t0) REVERT: A 325 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7692 (ttmt) REVERT: B 72 PHE cc_start: 0.6920 (m-10) cc_final: 0.6677 (m-80) REVERT: B 87 ARG cc_start: 0.7355 (tpm-80) cc_final: 0.7111 (tpp80) REVERT: B 91 ASP cc_start: 0.8205 (m-30) cc_final: 0.7920 (m-30) REVERT: B 247 THR cc_start: 0.9088 (m) cc_final: 0.8847 (t) REVERT: B 275 LYS cc_start: 0.8027 (mttm) cc_final: 0.7747 (ttmm) REVERT: B 296 GLN cc_start: 0.8308 (tt0) cc_final: 0.8092 (tp40) REVERT: C 72 PHE cc_start: 0.7282 (m-10) cc_final: 0.6994 (m-80) REVERT: C 266 ASN cc_start: 0.8740 (t0) cc_final: 0.8452 (t0) REVERT: C 275 LYS cc_start: 0.8050 (mttm) cc_final: 0.7809 (ttmm) REVERT: C 297 ASP cc_start: 0.8530 (t0) cc_final: 0.8229 (t0) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 1.7486 time to fit residues: 462.5975 Evaluate side-chains 184 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN A 152 GLN A 260 GLN A 266 ASN A 293 GLN ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 212 GLN C 143 GLN C 152 GLN C 279 GLN C 293 GLN C 296 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7104 Z= 0.276 Angle : 0.598 7.235 9621 Z= 0.295 Chirality : 0.048 0.344 1098 Planarity : 0.004 0.050 1200 Dihedral : 12.569 69.872 1164 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.63 % Allowed : 26.28 % Favored : 71.09 % 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: 2.09 (0.29), residues: 843 helix: 3.34 (0.27), residues: 312 sheet: 0.69 (0.28), residues: 312 loop : -0.50 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 230 HIS 0.003 0.002 HIS B 98 PHE 0.024 0.002 PHE C 92 TYR 0.010 0.001 TYR B 111 ARG 0.011 0.001 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7104 (t80) cc_final: 0.6897 (t80) REVERT: A 95 LYS cc_start: 0.8566 (mttt) cc_final: 0.8197 (mtmm) REVERT: A 153 ARG cc_start: 0.7421 (mtp85) cc_final: 0.7156 (mtp85) REVERT: A 180 ARG cc_start: 0.7716 (mtp180) cc_final: 0.7486 (mtp180) REVERT: A 224 GLU cc_start: 0.7022 (tp30) cc_final: 0.6793 (tp30) REVERT: A 275 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7759 (mtpp) REVERT: A 294 LYS cc_start: 0.8086 (tmmt) cc_final: 0.7643 (tmmt) REVERT: A 325 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7734 (ttmt) REVERT: B 72 PHE cc_start: 0.6953 (m-10) cc_final: 0.6721 (m-80) REVERT: B 77 LEU cc_start: 0.7932 (mm) cc_final: 0.7693 (mm) REVERT: B 91 ASP cc_start: 0.8261 (m-30) cc_final: 0.8024 (m-30) REVERT: B 208 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7691 (mp10) REVERT: B 224 GLU cc_start: 0.7250 (tp30) cc_final: 0.7027 (tp30) REVERT: C 72 PHE cc_start: 0.7299 (m-10) cc_final: 0.7001 (m-80) REVERT: C 95 LYS cc_start: 0.8548 (mttt) cc_final: 0.8298 (mtmm) REVERT: C 133 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6806 (tm-30) REVERT: C 147 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7572 (tpp) REVERT: C 180 ARG cc_start: 0.7547 (mtp180) cc_final: 0.7327 (mtp180) REVERT: C 266 ASN cc_start: 0.8774 (t0) cc_final: 0.8460 (t0) REVERT: C 297 ASP cc_start: 0.8701 (t0) cc_final: 0.8450 (t0) REVERT: C 326 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7902 (mm) REVERT: C 333 LYS cc_start: 0.8280 (tttt) cc_final: 0.7850 (ttpt) outliers start: 19 outliers final: 4 residues processed: 202 average time/residue: 1.6732 time to fit residues: 350.3832 Evaluate side-chains 196 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 189 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 326 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN C 279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7104 Z= 0.288 Angle : 0.575 6.987 9621 Z= 0.284 Chirality : 0.046 0.334 1098 Planarity : 0.003 0.034 1200 Dihedral : 8.616 58.137 1164 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.32 % Allowed : 27.94 % Favored : 68.74 % 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: 2.06 (0.29), residues: 843 helix: 3.20 (0.27), residues: 315 sheet: 0.77 (0.28), residues: 312 loop : -0.55 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 230 HIS 0.002 0.001 HIS C 130 PHE 0.024 0.001 PHE B 92 TYR 0.008 0.001 TYR A 201 ARG 0.009 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8005 (tptp) cc_final: 0.7691 (tmmt) REVERT: A 92 PHE cc_start: 0.7151 (t80) cc_final: 0.6912 (t80) REVERT: A 153 ARG cc_start: 0.7433 (mtp85) cc_final: 0.7141 (mtp85) REVERT: A 180 ARG cc_start: 0.7700 (mtp180) cc_final: 0.7452 (mtp180) REVERT: A 224 GLU cc_start: 0.7135 (tp30) cc_final: 0.6830 (tp30) REVERT: A 275 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7803 (mtpp) REVERT: A 294 LYS cc_start: 0.8076 (tmmt) cc_final: 0.7584 (tmmt) REVERT: A 325 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7751 (ttmt) REVERT: A 333 LYS cc_start: 0.8461 (tttt) cc_final: 0.7914 (ttpp) REVERT: B 72 PHE cc_start: 0.6933 (m-10) cc_final: 0.6714 (m-80) REVERT: B 77 LEU cc_start: 0.7987 (mm) cc_final: 0.7724 (mm) REVERT: B 87 ARG cc_start: 0.7505 (tpp-160) cc_final: 0.7287 (ttm-80) REVERT: B 91 ASP cc_start: 0.8329 (m-30) cc_final: 0.8109 (m-30) REVERT: B 156 TYR cc_start: 0.8214 (p90) cc_final: 0.7933 (p90) REVERT: B 325 LYS cc_start: 0.7940 (ttmt) cc_final: 0.7732 (ttmt) REVERT: B 333 LYS cc_start: 0.8441 (tttt) cc_final: 0.7858 (ttpp) REVERT: C 72 PHE cc_start: 0.7286 (m-10) cc_final: 0.7015 (m-80) REVERT: C 87 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7124 (tpm-80) REVERT: C 95 LYS cc_start: 0.8564 (mttt) cc_final: 0.8288 (mttm) REVERT: C 133 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6723 (tm-30) REVERT: C 180 ARG cc_start: 0.7546 (mtp180) cc_final: 0.7282 (mtp180) REVERT: C 297 ASP cc_start: 0.8691 (t0) cc_final: 0.8483 (t0) REVERT: C 326 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7944 (mm) REVERT: C 333 LYS cc_start: 0.8358 (tttt) cc_final: 0.7982 (ttpt) outliers start: 24 outliers final: 10 residues processed: 215 average time/residue: 1.6925 time to fit residues: 376.9376 Evaluate side-chains 209 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 21 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN C 143 GLN C 279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7104 Z= 0.221 Angle : 0.548 7.650 9621 Z= 0.272 Chirality : 0.045 0.309 1098 Planarity : 0.004 0.046 1200 Dihedral : 6.814 57.819 1164 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.18 % Allowed : 29.46 % Favored : 67.36 % 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: 2.15 (0.29), residues: 843 helix: 3.35 (0.27), residues: 312 sheet: 0.77 (0.28), residues: 312 loop : -0.47 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 230 HIS 0.002 0.000 HIS B 130 PHE 0.024 0.001 PHE B 92 TYR 0.009 0.001 TYR A 201 ARG 0.006 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 218 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8019 (tptp) cc_final: 0.7722 (tmmt) REVERT: A 153 ARG cc_start: 0.7429 (mtp85) cc_final: 0.7172 (mtp85) REVERT: A 180 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7449 (mtp180) REVERT: A 224 GLU cc_start: 0.7117 (tp30) cc_final: 0.6769 (tp30) REVERT: A 275 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7839 (mtpp) REVERT: A 294 LYS cc_start: 0.8123 (tmmt) cc_final: 0.7770 (tmmt) REVERT: A 325 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7753 (ttmt) REVERT: A 333 LYS cc_start: 0.8476 (tttt) cc_final: 0.7916 (ttpp) REVERT: B 72 PHE cc_start: 0.6913 (m-10) cc_final: 0.6700 (m-80) REVERT: B 77 LEU cc_start: 0.8014 (mm) cc_final: 0.7773 (mm) REVERT: B 87 ARG cc_start: 0.7498 (tpp-160) cc_final: 0.7289 (ttm-80) REVERT: B 91 ASP cc_start: 0.8313 (m-30) cc_final: 0.8094 (m-30) REVERT: B 325 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7709 (ttmt) REVERT: B 333 LYS cc_start: 0.8458 (tttt) cc_final: 0.7842 (ttpp) REVERT: C 72 PHE cc_start: 0.7292 (m-10) cc_final: 0.7024 (m-80) REVERT: C 87 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7123 (tpm-80) REVERT: C 95 LYS cc_start: 0.8560 (mttt) cc_final: 0.8295 (mttm) REVERT: C 147 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7995 (tpp) REVERT: C 180 ARG cc_start: 0.7541 (mtp180) cc_final: 0.7234 (mtp180) REVERT: C 326 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7935 (mm) REVERT: C 333 LYS cc_start: 0.8319 (tttt) cc_final: 0.7938 (ttpt) outliers start: 23 outliers final: 11 residues processed: 224 average time/residue: 1.7533 time to fit residues: 406.4117 Evaluate side-chains 211 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 197 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN B 212 GLN C 279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7104 Z= 0.314 Angle : 0.574 7.485 9621 Z= 0.287 Chirality : 0.046 0.337 1098 Planarity : 0.004 0.038 1200 Dihedral : 6.222 56.163 1164 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.01 % Allowed : 29.74 % Favored : 66.25 % 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: 2.05 (0.29), residues: 843 helix: 3.18 (0.27), residues: 312 sheet: 0.79 (0.29), residues: 312 loop : -0.52 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 230 HIS 0.002 0.000 HIS A 130 PHE 0.028 0.002 PHE B 92 TYR 0.009 0.001 TYR C 201 ARG 0.007 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 214 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7765 (tmmt) REVERT: A 153 ARG cc_start: 0.7443 (mtp85) cc_final: 0.7241 (mtp85) REVERT: A 180 ARG cc_start: 0.7660 (mtp180) cc_final: 0.7422 (mtp180) REVERT: A 224 GLU cc_start: 0.7241 (tp30) cc_final: 0.6806 (tp30) REVERT: A 275 LYS cc_start: 0.8102 (ttmm) cc_final: 0.7900 (mtpp) REVERT: A 294 LYS cc_start: 0.8074 (tmmt) cc_final: 0.7658 (tmmt) REVERT: A 329 LYS cc_start: 0.8348 (tttt) cc_final: 0.8104 (tttt) REVERT: A 333 LYS cc_start: 0.8520 (tttt) cc_final: 0.8013 (ttpp) REVERT: B 77 LEU cc_start: 0.8068 (mm) cc_final: 0.7863 (mm) REVERT: B 87 ARG cc_start: 0.7494 (tpp-160) cc_final: 0.7275 (ttm-80) REVERT: B 91 ASP cc_start: 0.8342 (m-30) cc_final: 0.8117 (m-30) REVERT: B 227 TYR cc_start: 0.8655 (m-80) cc_final: 0.8390 (m-80) REVERT: B 294 LYS cc_start: 0.8141 (tmmt) cc_final: 0.7914 (tmmt) REVERT: B 333 LYS cc_start: 0.8536 (tttt) cc_final: 0.7971 (ttpp) REVERT: C 72 PHE cc_start: 0.7292 (m-10) cc_final: 0.7000 (m-80) REVERT: C 87 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7115 (tpm-80) REVERT: C 95 LYS cc_start: 0.8576 (mttt) cc_final: 0.8335 (mttm) REVERT: C 180 ARG cc_start: 0.7535 (mtp180) cc_final: 0.7209 (mtp180) REVERT: C 188 ARG cc_start: 0.7830 (ttt90) cc_final: 0.7529 (ttt90) REVERT: C 326 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7979 (mm) REVERT: C 333 LYS cc_start: 0.8412 (tttt) cc_final: 0.7877 (ttpp) outliers start: 29 outliers final: 16 residues processed: 223 average time/residue: 1.6455 time to fit residues: 380.1425 Evaluate side-chains 223 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN B 212 GLN B 293 GLN C 143 GLN C 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7104 Z= 0.269 Angle : 0.561 8.785 9621 Z= 0.280 Chirality : 0.045 0.327 1098 Planarity : 0.004 0.041 1200 Dihedral : 5.919 54.054 1164 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.01 % Allowed : 29.88 % Favored : 66.11 % 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: 2.05 (0.29), residues: 843 helix: 3.20 (0.27), residues: 312 sheet: 0.77 (0.28), residues: 312 loop : -0.50 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 230 HIS 0.003 0.001 HIS B 98 PHE 0.025 0.002 PHE B 92 TYR 0.008 0.001 TYR C 201 ARG 0.009 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 215 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7775 (tmmt) REVERT: A 170 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8552 (mm) REVERT: A 180 ARG cc_start: 0.7627 (mtp180) cc_final: 0.7395 (mtp180) REVERT: A 224 GLU cc_start: 0.7241 (tp30) cc_final: 0.6847 (tp30) REVERT: A 275 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7915 (mtpp) REVERT: A 294 LYS cc_start: 0.8087 (tmmt) cc_final: 0.7640 (tmmt) REVERT: A 296 GLN cc_start: 0.8821 (tt0) cc_final: 0.8615 (tt0) REVERT: A 329 LYS cc_start: 0.8346 (tttt) cc_final: 0.8098 (tttt) REVERT: A 333 LYS cc_start: 0.8546 (tttt) cc_final: 0.8051 (ttpp) REVERT: B 72 PHE cc_start: 0.6845 (m-80) cc_final: 0.6558 (m-80) REVERT: B 87 ARG cc_start: 0.7501 (tpp-160) cc_final: 0.7292 (ttm-80) REVERT: B 91 ASP cc_start: 0.8327 (m-30) cc_final: 0.8120 (m-30) REVERT: B 227 TYR cc_start: 0.8626 (m-80) cc_final: 0.8415 (m-80) REVERT: B 248 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8512 (ttpp) REVERT: B 333 LYS cc_start: 0.8533 (tttt) cc_final: 0.8006 (ttpp) REVERT: C 72 PHE cc_start: 0.7287 (m-10) cc_final: 0.7008 (m-80) REVERT: C 87 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7107 (tpm-80) REVERT: C 95 LYS cc_start: 0.8590 (mttt) cc_final: 0.8337 (mttm) REVERT: C 180 ARG cc_start: 0.7543 (mtp180) cc_final: 0.7212 (mtp180) REVERT: C 188 ARG cc_start: 0.7817 (ttt90) cc_final: 0.7413 (ttt90) REVERT: C 326 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7977 (mm) REVERT: C 333 LYS cc_start: 0.8425 (tttt) cc_final: 0.7970 (ttpp) outliers start: 29 outliers final: 14 residues processed: 226 average time/residue: 1.6819 time to fit residues: 393.4229 Evaluate side-chains 216 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 197 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 143 GLN B 212 GLN B 293 GLN C 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7104 Z= 0.284 Angle : 0.588 9.323 9621 Z= 0.290 Chirality : 0.046 0.332 1098 Planarity : 0.004 0.041 1200 Dihedral : 5.508 49.447 1164 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.73 % Allowed : 30.29 % Favored : 65.98 % 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: 1.97 (0.29), residues: 843 helix: 3.11 (0.27), residues: 312 sheet: 0.74 (0.29), residues: 312 loop : -0.53 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 230 HIS 0.001 0.000 HIS B 130 PHE 0.027 0.002 PHE B 92 TYR 0.008 0.001 TYR B 201 ARG 0.008 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 0.796 Fit side-chains REVERT: A 63 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7881 (tmmt) REVERT: A 170 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8551 (mm) REVERT: A 180 ARG cc_start: 0.7621 (mtp180) cc_final: 0.7362 (mtp180) REVERT: A 224 GLU cc_start: 0.7260 (tp30) cc_final: 0.6899 (tp30) REVERT: A 275 LYS cc_start: 0.8133 (ttmm) cc_final: 0.7923 (mtpp) REVERT: A 294 LYS cc_start: 0.8096 (tmmt) cc_final: 0.7634 (tmmt) REVERT: A 329 LYS cc_start: 0.8344 (tttt) cc_final: 0.8094 (tttt) REVERT: A 331 MET cc_start: 0.6657 (tmm) cc_final: 0.6365 (tmm) REVERT: A 333 LYS cc_start: 0.8589 (tttt) cc_final: 0.8075 (ttpp) REVERT: B 72 PHE cc_start: 0.6903 (m-80) cc_final: 0.6572 (m-80) REVERT: B 87 ARG cc_start: 0.7493 (tpp-160) cc_final: 0.7284 (ttm-80) REVERT: B 91 ASP cc_start: 0.8327 (m-30) cc_final: 0.8119 (m-30) REVERT: B 188 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7920 (ppp80) REVERT: B 227 TYR cc_start: 0.8628 (m-80) cc_final: 0.8387 (m-80) REVERT: B 294 LYS cc_start: 0.8170 (tmmt) cc_final: 0.7933 (tmmt) REVERT: B 333 LYS cc_start: 0.8554 (tttt) cc_final: 0.8021 (ttpp) REVERT: C 72 PHE cc_start: 0.7273 (m-10) cc_final: 0.6987 (m-80) REVERT: C 87 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7135 (tpm-80) REVERT: C 95 LYS cc_start: 0.8612 (mttt) cc_final: 0.8354 (mttm) REVERT: C 180 ARG cc_start: 0.7541 (mtp180) cc_final: 0.7212 (mtp180) REVERT: C 188 ARG cc_start: 0.7834 (ttt90) cc_final: 0.7404 (ttt90) REVERT: C 326 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7956 (mm) REVERT: C 333 LYS cc_start: 0.8414 (tttt) cc_final: 0.7940 (ttpp) outliers start: 27 outliers final: 15 residues processed: 217 average time/residue: 1.6500 time to fit residues: 370.7187 Evaluate side-chains 217 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 197 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 15 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN B 143 GLN B 212 GLN B 293 GLN C 143 GLN C 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7104 Z= 0.227 Angle : 0.616 11.238 9621 Z= 0.296 Chirality : 0.052 0.878 1098 Planarity : 0.003 0.041 1200 Dihedral : 5.836 46.693 1164 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.63 % Allowed : 30.98 % Favored : 66.39 % 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: 2.02 (0.29), residues: 843 helix: 3.18 (0.27), residues: 312 sheet: 0.90 (0.28), residues: 312 loop : -0.80 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 304 HIS 0.001 0.000 HIS B 130 PHE 0.028 0.001 PHE C 92 TYR 0.007 0.001 TYR C 201 ARG 0.010 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 210 time to evaluate : 0.745 Fit side-chains REVERT: A 63 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7917 (tmmt) REVERT: A 153 ARG cc_start: 0.7455 (mtp85) cc_final: 0.7219 (mtp85) REVERT: A 180 ARG cc_start: 0.7609 (mtp180) cc_final: 0.7377 (mtp180) REVERT: A 224 GLU cc_start: 0.7245 (tp30) cc_final: 0.6910 (tp30) REVERT: A 294 LYS cc_start: 0.8142 (tmmt) cc_final: 0.7656 (tmmt) REVERT: A 329 LYS cc_start: 0.8316 (tttt) cc_final: 0.8067 (tttt) REVERT: A 331 MET cc_start: 0.6672 (tmm) cc_final: 0.6384 (tmm) REVERT: A 333 LYS cc_start: 0.8551 (tttt) cc_final: 0.8083 (ttpp) REVERT: B 72 PHE cc_start: 0.6843 (m-80) cc_final: 0.6566 (m-80) REVERT: B 77 LEU cc_start: 0.7963 (mp) cc_final: 0.7753 (mm) REVERT: B 87 ARG cc_start: 0.7491 (tpp-160) cc_final: 0.7283 (ttm-80) REVERT: B 91 ASP cc_start: 0.8311 (m-30) cc_final: 0.8104 (m-30) REVERT: B 333 LYS cc_start: 0.8557 (tttt) cc_final: 0.8024 (ttpp) REVERT: C 72 PHE cc_start: 0.7272 (m-10) cc_final: 0.7009 (m-80) REVERT: C 87 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7130 (tpm-80) REVERT: C 95 LYS cc_start: 0.8597 (mttt) cc_final: 0.8338 (mttm) REVERT: C 180 ARG cc_start: 0.7546 (mtp180) cc_final: 0.7234 (mtp180) REVERT: C 326 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8006 (mm) REVERT: C 333 LYS cc_start: 0.8430 (tttt) cc_final: 0.7975 (ttpp) outliers start: 19 outliers final: 12 residues processed: 214 average time/residue: 1.7102 time to fit residues: 378.6985 Evaluate side-chains 211 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 0.0370 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.0570 chunk 48 optimal weight: 0.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 296 GLN B 143 GLN B 212 GLN B 293 GLN C 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7104 Z= 0.199 Angle : 0.573 9.158 9621 Z= 0.281 Chirality : 0.045 0.319 1098 Planarity : 0.003 0.042 1200 Dihedral : 4.692 33.964 1164 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.77 % Allowed : 31.26 % Favored : 65.98 % 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: 2.05 (0.29), residues: 843 helix: 3.24 (0.27), residues: 312 sheet: 0.90 (0.28), residues: 312 loop : -0.79 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 304 HIS 0.001 0.000 HIS B 98 PHE 0.027 0.001 PHE B 92 TYR 0.007 0.001 TYR B 201 ARG 0.010 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7915 (tmmt) REVERT: A 153 ARG cc_start: 0.7457 (mtp85) cc_final: 0.7211 (mtp85) REVERT: A 180 ARG cc_start: 0.7605 (mtp180) cc_final: 0.7371 (ttp-170) REVERT: A 224 GLU cc_start: 0.7244 (tp30) cc_final: 0.6872 (tp30) REVERT: A 294 LYS cc_start: 0.8144 (tmmt) cc_final: 0.7643 (tmmt) REVERT: A 329 LYS cc_start: 0.8314 (tttt) cc_final: 0.8071 (tttt) REVERT: A 331 MET cc_start: 0.6689 (tmm) cc_final: 0.6419 (tmm) REVERT: A 333 LYS cc_start: 0.8541 (tttt) cc_final: 0.8079 (ttpp) REVERT: B 72 PHE cc_start: 0.6847 (m-80) cc_final: 0.6506 (m-80) REVERT: B 91 ASP cc_start: 0.8306 (m-30) cc_final: 0.8098 (m-30) REVERT: B 188 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7857 (ppp80) REVERT: B 294 LYS cc_start: 0.8212 (tmmt) cc_final: 0.8004 (tmmt) REVERT: B 333 LYS cc_start: 0.8572 (tttt) cc_final: 0.8036 (ttpp) REVERT: C 72 PHE cc_start: 0.7243 (m-10) cc_final: 0.6978 (m-80) REVERT: C 87 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7135 (tpm-80) REVERT: C 95 LYS cc_start: 0.8607 (mttt) cc_final: 0.8343 (mttm) REVERT: C 180 ARG cc_start: 0.7521 (mtp180) cc_final: 0.7216 (mtp180) REVERT: C 326 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8017 (mm) REVERT: C 333 LYS cc_start: 0.8421 (tttt) cc_final: 0.7970 (ttpp) outliers start: 20 outliers final: 14 residues processed: 211 average time/residue: 1.8009 time to fit residues: 394.5352 Evaluate side-chains 216 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 77 optimal weight: 0.4980 chunk 66 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 260 GLN B 143 GLN B 212 GLN B 293 GLN C 143 GLN C 279 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7104 Z= 0.214 Angle : 0.581 11.603 9621 Z= 0.286 Chirality : 0.045 0.323 1098 Planarity : 0.004 0.044 1200 Dihedral : 4.462 26.245 1164 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.90 % Allowed : 31.12 % Favored : 65.98 % 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: 2.05 (0.29), residues: 843 helix: 3.22 (0.27), residues: 312 sheet: 0.91 (0.28), residues: 312 loop : -0.79 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 304 HIS 0.001 0.000 HIS C 130 PHE 0.027 0.001 PHE B 92 TYR 0.007 0.001 TYR B 201 ARG 0.011 0.001 ARG C 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 211 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7915 (tmmt) REVERT: A 153 ARG cc_start: 0.7465 (mtp85) cc_final: 0.7224 (mtp85) REVERT: A 170 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8568 (mm) REVERT: A 180 ARG cc_start: 0.7600 (mtp180) cc_final: 0.7369 (ttp-170) REVERT: A 224 GLU cc_start: 0.7258 (tp30) cc_final: 0.6886 (tp30) REVERT: A 294 LYS cc_start: 0.8126 (tmmt) cc_final: 0.7553 (tmmt) REVERT: A 329 LYS cc_start: 0.8317 (tttt) cc_final: 0.8075 (tttt) REVERT: A 331 MET cc_start: 0.6703 (tmm) cc_final: 0.6435 (tmm) REVERT: A 333 LYS cc_start: 0.8545 (tttt) cc_final: 0.8088 (ttpp) REVERT: B 72 PHE cc_start: 0.6824 (m-80) cc_final: 0.6551 (m-80) REVERT: B 91 ASP cc_start: 0.8319 (m-30) cc_final: 0.8100 (m-30) REVERT: B 188 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7850 (ppp80) REVERT: B 294 LYS cc_start: 0.8236 (tmmt) cc_final: 0.8016 (tmmt) REVERT: B 333 LYS cc_start: 0.8581 (tttt) cc_final: 0.8042 (ttpp) REVERT: C 72 PHE cc_start: 0.7272 (m-10) cc_final: 0.7031 (m-80) REVERT: C 87 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7143 (tpm-80) REVERT: C 95 LYS cc_start: 0.8612 (mttt) cc_final: 0.8347 (mttm) REVERT: C 180 ARG cc_start: 0.7522 (mtp180) cc_final: 0.7219 (mtp180) REVERT: C 326 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8010 (mm) REVERT: C 333 LYS cc_start: 0.8430 (tttt) cc_final: 0.7969 (ttpp) outliers start: 21 outliers final: 14 residues processed: 218 average time/residue: 1.7771 time to fit residues: 400.7221 Evaluate side-chains 215 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 196 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 0.0570 chunk 12 optimal weight: 0.0570 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN B 143 GLN B 212 GLN B 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.084841 restraints weight = 12338.122| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.67 r_work: 0.3155 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 7104 Z= 0.221 Angle : 0.638 14.630 9621 Z= 0.332 Chirality : 0.047 0.349 1098 Planarity : 0.005 0.087 1200 Dihedral : 4.422 23.514 1164 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.77 % Allowed : 31.40 % Favored : 65.84 % 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: 2.04 (0.29), residues: 843 helix: 3.24 (0.26), residues: 312 sheet: 0.86 (0.28), residues: 312 loop : -0.79 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 304 HIS 0.004 0.001 HIS C 130 PHE 0.028 0.001 PHE B 92 TYR 0.007 0.001 TYR C 201 ARG 0.011 0.001 ARG C 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5456.68 seconds wall clock time: 96 minutes 11.66 seconds (5771.66 seconds total)