Starting phenix.real_space_refine on Mon Mar 11 01:48:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/03_2024/8t2u_40988_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/03_2024/8t2u_40988.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/03_2024/8t2u_40988_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/03_2024/8t2u_40988_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/03_2024/8t2u_40988_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/03_2024/8t2u_40988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/03_2024/8t2u_40988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/03_2024/8t2u_40988_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/03_2024/8t2u_40988_updated.pdb" } resolution = 3.1 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= 0.016 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 28 5.16 5 C 4128 2.51 5 N 1099 2.21 5 O 1290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 168": "OE1" <-> "OE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 126": "OD1" <-> "OD2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6552 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3435 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 26, 'TRANS': 421} Chain: "B" Number of atoms: 2895 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 2886 Classifications: {'peptide': 368} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 349} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 368, 2886 Classifications: {'peptide': 368} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 349} Chain breaks: 1 bond proxies already assigned to first conformer: 2927 Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 57 Unusual residues: {'MPT': 1, 'NH2': 1} Classifications: {'peptide': 6, 'undetermined': 2} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="MPT C 1 " pdbres="HRG C 2 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'MPT:plan-1': 1, 'HRG:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 19 Unusual residues: {' CA': 2, ' MG': 1, 'NAG': 1} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN B 272 " occ=0.48 ... (16 atoms not shown) pdb=" NE2BGLN B 272 " occ=0.52 Time building chain proxies: 5.21, per 1000 atoms: 0.80 Number of scatterers: 6552 At special positions: 0 Unit cell: (81, 82.08, 127.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 28 16.00 Mg 1 11.99 O 1290 8.00 N 1099 7.00 C 4128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.06 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.02 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.05 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.04 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.04 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 additional links: simple=1, symmetry=0 Simple link: pdb=" SG MPT C 1 " - pdb=" SG CYS C 7 " Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " BMA D 3 " - " BMA D 4 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " BETA1-6 " BMA E 3 " - " BMA E 4 " NAG-ASN " NAG A1101 " - " ASN A 249 " " NAG B2004 " - " ASN B 99 " " NAG D 1 " - " ASN A 15 " " NAG E 1 " - " ASN B 320 " " NAG F 1 " - " ASN B 371 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.5 seconds 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 13 sheets defined 13.1% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'B' and resid 123 through 145 removed outlier: 5.625A pdb=" N TRP B 129 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS B 137 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 145 " --> pdb=" O MET B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 200 through 209 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 282 through 286 removed outlier: 4.434A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 301 Processing helix chain 'B' and resid 312 through 324 removed outlier: 3.576A pdb=" N VAL B 315 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN B 316 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 350 removed outlier: 3.941A pdb=" N LEU B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 12 Processing sheet with id= B, first strand: chain 'A' and resid 52 through 57 removed outlier: 3.734A pdb=" N SER A 22 " --> pdb=" O GLY A 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= D, first strand: chain 'A' and resid 96 through 100 removed outlier: 3.547A pdb=" N SER A 96 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 172 through 175 Processing sheet with id= F, first strand: chain 'A' and resid 238 through 242 Processing sheet with id= G, first strand: chain 'A' and resid 293 through 296 Processing sheet with id= H, first strand: chain 'A' and resid 314 through 317 Processing sheet with id= I, first strand: chain 'A' and resid 374 through 377 removed outlier: 3.962A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 357 through 360 removed outlier: 6.341A pdb=" N ALA B 89 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL B 63 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG B 91 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ALA B 61 " --> pdb=" O ARG B 91 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 96 through 105 Processing sheet with id= L, first strand: chain 'B' and resid 329 through 332 removed outlier: 6.857A pdb=" N HIS B 244 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE B 307 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 246 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA B 309 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE B 248 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP B 119 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA B 155 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N HIS B 192 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 371 through 373 203 hydrogen bonds defined for protein. 456 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: 1.92 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1098 1.30 - 1.44: 1832 1.44 - 1.58: 3720 1.58 - 1.72: 1 1.72 - 1.86: 41 Bond restraints: 6692 Sorted by residual: bond pdb=" C MET B 287 " pdb=" N ASP B 288 " ideal model delta sigma weight residual 1.331 1.243 0.088 1.26e-02 6.30e+03 4.87e+01 bond pdb=" C PRO A 362 " pdb=" O PRO A 362 " ideal model delta sigma weight residual 1.235 1.158 0.077 1.30e-02 5.92e+03 3.55e+01 bond pdb=" C GLN A 18 " pdb=" O GLN A 18 " ideal model delta sigma weight residual 1.233 1.166 0.067 1.29e-02 6.01e+03 2.69e+01 bond pdb=" C VAL A 239 " pdb=" O VAL A 239 " ideal model delta sigma weight residual 1.236 1.282 -0.046 9.90e-03 1.02e+04 2.19e+01 bond pdb=" CA ALA A 185 " pdb=" CB ALA A 185 " ideal model delta sigma weight residual 1.532 1.476 0.056 1.26e-02 6.30e+03 1.95e+01 ... (remaining 6687 not shown) Histogram of bond angle deviations from ideal: 95.33 - 103.24: 49 103.24 - 111.15: 2213 111.15 - 119.06: 3686 119.06 - 126.97: 3082 126.97 - 134.88: 61 Bond angle restraints: 9091 Sorted by residual: angle pdb=" N MET B 124 " pdb=" CA MET B 124 " pdb=" C MET B 124 " ideal model delta sigma weight residual 112.34 104.96 7.38 1.30e+00 5.92e-01 3.22e+01 angle pdb=" N LYS B 253 " pdb=" CA LYS B 253 " pdb=" C LYS B 253 " ideal model delta sigma weight residual 110.43 103.18 7.25 1.31e+00 5.83e-01 3.07e+01 angle pdb=" C GLN B 267 " pdb=" N PRO B 268 " pdb=" CA PRO B 268 " ideal model delta sigma weight residual 119.84 126.70 -6.86 1.25e+00 6.40e-01 3.01e+01 angle pdb=" CA GLY A 193 " pdb=" C GLY A 193 " pdb=" O GLY A 193 " ideal model delta sigma weight residual 122.22 118.73 3.49 6.50e-01 2.37e+00 2.88e+01 angle pdb=" C PHE A 417 " pdb=" CA PHE A 417 " pdb=" CB PHE A 417 " ideal model delta sigma weight residual 109.90 102.04 7.86 1.56e+00 4.11e-01 2.54e+01 ... (remaining 9086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 3942 34.55 - 69.10: 143 69.10 - 103.66: 41 103.66 - 138.21: 12 138.21 - 172.76: 1 Dihedral angle restraints: 4139 sinusoidal: 1788 harmonic: 2351 Sorted by residual: dihedral pdb=" CB CYS B 232 " pdb=" SG CYS B 232 " pdb=" SG CYS B 273 " pdb=" CB CYS B 273 " ideal model delta sinusoidal sigma weight residual 93.00 45.81 47.19 1 1.00e+01 1.00e-02 3.08e+01 dihedral pdb=" CA PHE B 370 " pdb=" C PHE B 370 " pdb=" N ASN B 371 " pdb=" CA ASN B 371 " ideal model delta harmonic sigma weight residual 180.00 155.44 24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CB HRG C 2 " pdb=" CG HRG C 2 " pdb=" CG' HRG C 2 " pdb=" CD HRG C 2 " ideal model delta sinusoidal sigma weight residual 261.95 89.19 172.76 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 890 0.118 - 0.236: 134 0.236 - 0.354: 2 0.354 - 0.472: 0 0.472 - 0.590: 1 Chirality restraints: 1027 Sorted by residual: chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.02e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.07e+01 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.71e+01 ... (remaining 1024 not shown) Planarity restraints: 1181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B2004 " 0.242 2.00e-02 2.50e+03 2.06e-01 5.30e+02 pdb=" C7 NAG B2004 " -0.116 2.00e-02 2.50e+03 pdb=" C8 NAG B2004 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG B2004 " -0.325 2.00e-02 2.50e+03 pdb=" O7 NAG B2004 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.176 2.00e-02 2.50e+03 1.50e-01 2.83e+02 pdb=" C7 NAG F 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.143 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.234 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.182 2.00e-02 2.50e+03 1.49e-01 2.76e+02 pdb=" C7 NAG F 1 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.139 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.230 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.025 2.00e-02 2.50e+03 ... (remaining 1178 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 101 2.43 - 3.04: 4315 3.04 - 3.66: 10628 3.66 - 4.28: 15654 4.28 - 4.90: 25358 Nonbonded interactions: 56056 Sorted by model distance: nonbonded pdb=" O ARG A 303 " pdb="CA CA A1105 " model vdw 1.807 2.510 nonbonded pdb=" OD1 ASN A 299 " pdb="CA CA A1105 " model vdw 1.856 2.510 nonbonded pdb=" OG SER B 121 " pdb="MG MG B2001 " model vdw 1.889 2.170 nonbonded pdb=" OG SER B 123 " pdb="MG MG B2001 " model vdw 2.107 2.170 nonbonded pdb="MG MG B2001 " pdb=" O HOH B3101 " model vdw 2.166 2.170 ... (remaining 56051 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 'D' selection = chain 'E' } 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=0.00 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: 0.980 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: 3.760 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.410 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 : 0.014 0.088 6692 Z= 0.914 Angle : 1.653 9.248 9091 Z= 1.131 Chirality : 0.081 0.590 1027 Planarity : 0.011 0.206 1176 Dihedral : 20.641 172.759 2622 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 30.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.12 % Favored : 91.64 % Rotamer: Outliers : 4.62 % Allowed : 20.81 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.18 (0.28), residues: 816 helix: -1.68 (0.46), residues: 102 sheet: -0.96 (0.33), residues: 228 loop : -1.65 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.007 TRP A 110 HIS 0.018 0.005 HIS B 255 PHE 0.074 0.010 PHE A 21 TYR 0.047 0.009 TYR A 288 ARG 0.012 0.002 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 66 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.8167 (ptm160) cc_final: 0.7317 (mmm160) REVERT: A 285 MET cc_start: 0.7220 (ttt) cc_final: 0.6885 (ttt) REVERT: A 369 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8786 (p0) REVERT: B 109 ASP cc_start: 0.8069 (m-30) cc_final: 0.7857 (p0) REVERT: B 123 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8173 (p) REVERT: B 261 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6856 (tpt-90) outliers start: 32 outliers final: 10 residues processed: 94 average time/residue: 0.2153 time to fit residues: 26.2133 Evaluate side-chains 67 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 336 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN B 204 ASN B 210 GLN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6692 Z= 0.278 Angle : 0.743 10.974 9091 Z= 0.365 Chirality : 0.050 0.325 1027 Planarity : 0.004 0.038 1176 Dihedral : 16.201 173.242 1171 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.64 % Favored : 93.23 % Rotamer: Outliers : 3.61 % Allowed : 21.24 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.84 (0.28), residues: 816 helix: -1.54 (0.47), residues: 101 sheet: -0.73 (0.33), residues: 241 loop : -1.41 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 113 HIS 0.005 0.001 HIS B 255 PHE 0.011 0.002 PHE A 191 TYR 0.028 0.002 TYR A 371 ARG 0.012 0.001 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 55 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.9198 (mtpp) cc_final: 0.8670 (pptt) REVERT: A 90 ARG cc_start: 0.8159 (ptm160) cc_final: 0.7350 (mmm160) REVERT: A 168 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8196 (mt-10) REVERT: A 285 MET cc_start: 0.6964 (ttt) cc_final: 0.6434 (ttt) REVERT: B 277 SER cc_start: 0.8851 (t) cc_final: 0.8644 (p) outliers start: 25 outliers final: 12 residues processed: 77 average time/residue: 0.1754 time to fit residues: 19.2443 Evaluate side-chains 64 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 351 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6692 Z= 0.251 Angle : 0.705 7.891 9091 Z= 0.345 Chirality : 0.049 0.316 1027 Planarity : 0.004 0.041 1176 Dihedral : 13.911 179.456 1157 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.89 % Favored : 92.99 % Rotamer: Outliers : 4.19 % Allowed : 21.24 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.78 (0.29), residues: 816 helix: -1.55 (0.47), residues: 100 sheet: -0.60 (0.34), residues: 232 loop : -1.41 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 113 HIS 0.004 0.001 HIS B 255 PHE 0.018 0.002 PHE B 248 TYR 0.027 0.002 TYR A 371 ARG 0.002 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 55 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.9197 (mtpp) cc_final: 0.8650 (pptt) REVERT: A 90 ARG cc_start: 0.8097 (ptm160) cc_final: 0.7344 (mmm160) REVERT: A 285 MET cc_start: 0.7189 (ttt) cc_final: 0.6729 (ttt) REVERT: B 109 ASP cc_start: 0.8194 (m-30) cc_final: 0.7923 (p0) outliers start: 29 outliers final: 19 residues processed: 81 average time/residue: 0.1587 time to fit residues: 18.3148 Evaluate side-chains 68 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 49 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 351 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 48 optimal weight: 0.0770 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.0570 chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 overall best weight: 0.4414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6692 Z= 0.204 Angle : 0.680 7.790 9091 Z= 0.332 Chirality : 0.048 0.313 1027 Planarity : 0.004 0.041 1176 Dihedral : 12.644 173.518 1155 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.01 % Favored : 92.87 % Rotamer: Outliers : 3.18 % Allowed : 22.11 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.73 (0.28), residues: 816 helix: -1.58 (0.47), residues: 100 sheet: -0.52 (0.34), residues: 228 loop : -1.37 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 113 HIS 0.003 0.001 HIS A 112 PHE 0.021 0.001 PHE B 248 TYR 0.031 0.002 TYR A 371 ARG 0.001 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.9166 (mtpp) cc_final: 0.8624 (pptt) REVERT: A 90 ARG cc_start: 0.8163 (ptm160) cc_final: 0.7384 (mmm160) REVERT: A 285 MET cc_start: 0.7184 (ttt) cc_final: 0.6747 (ttt) REVERT: A 363 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7116 (tt) outliers start: 22 outliers final: 12 residues processed: 77 average time/residue: 0.1709 time to fit residues: 18.4559 Evaluate side-chains 63 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 0.0870 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6692 Z= 0.218 Angle : 0.670 8.179 9091 Z= 0.328 Chirality : 0.047 0.300 1027 Planarity : 0.004 0.042 1176 Dihedral : 12.295 171.133 1153 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.38 % Favored : 92.50 % Rotamer: Outliers : 3.03 % Allowed : 23.84 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.65 (0.29), residues: 816 helix: -1.47 (0.47), residues: 100 sheet: -0.39 (0.34), residues: 226 loop : -1.37 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 113 HIS 0.002 0.001 HIS B 255 PHE 0.019 0.001 PHE B 248 TYR 0.027 0.002 TYR A 371 ARG 0.002 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 52 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.9179 (mtpp) cc_final: 0.8634 (pptt) REVERT: A 90 ARG cc_start: 0.8181 (ptm160) cc_final: 0.7464 (mmm160) REVERT: A 285 MET cc_start: 0.7238 (ttt) cc_final: 0.6814 (ttt) outliers start: 21 outliers final: 15 residues processed: 71 average time/residue: 0.1754 time to fit residues: 17.5847 Evaluate side-chains 67 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6692 Z= 0.253 Angle : 0.686 10.446 9091 Z= 0.334 Chirality : 0.047 0.286 1027 Planarity : 0.004 0.045 1176 Dihedral : 11.973 172.495 1153 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.13 % Favored : 92.74 % Rotamer: Outliers : 4.05 % Allowed : 23.12 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.63 (0.29), residues: 816 helix: -1.62 (0.46), residues: 100 sheet: -0.29 (0.35), residues: 218 loop : -1.35 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 113 HIS 0.002 0.001 HIS A 26 PHE 0.018 0.002 PHE B 248 TYR 0.024 0.002 TYR A 371 ARG 0.002 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 57 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.9193 (mtpp) cc_final: 0.8652 (pptt) REVERT: A 90 ARG cc_start: 0.8271 (ptm160) cc_final: 0.7504 (mmm160) REVERT: A 285 MET cc_start: 0.7280 (ttt) cc_final: 0.6890 (ttt) REVERT: A 363 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7094 (tt) REVERT: B 387 MET cc_start: 0.8007 (mmm) cc_final: 0.7477 (tpp) outliers start: 28 outliers final: 19 residues processed: 82 average time/residue: 0.1559 time to fit residues: 18.2798 Evaluate side-chains 73 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 53 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6692 Z= 0.241 Angle : 0.693 9.281 9091 Z= 0.336 Chirality : 0.048 0.287 1027 Planarity : 0.004 0.045 1176 Dihedral : 11.758 170.237 1153 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.26 % Favored : 92.62 % Rotamer: Outliers : 3.32 % Allowed : 24.13 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.59 (0.28), residues: 816 helix: -1.57 (0.47), residues: 100 sheet: -0.38 (0.34), residues: 223 loop : -1.28 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 113 HIS 0.002 0.001 HIS A 278 PHE 0.021 0.002 PHE B 414 TYR 0.019 0.002 TYR A 371 ARG 0.001 0.000 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 54 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.9195 (mtpp) cc_final: 0.8651 (pptt) REVERT: A 90 ARG cc_start: 0.8298 (ptm160) cc_final: 0.7529 (mmm160) REVERT: A 285 MET cc_start: 0.7288 (ttt) cc_final: 0.6923 (ttt) REVERT: B 387 MET cc_start: 0.8039 (mmm) cc_final: 0.7495 (tpp) outliers start: 23 outliers final: 18 residues processed: 74 average time/residue: 0.1725 time to fit residues: 18.1908 Evaluate side-chains 73 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 55 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6692 Z= 0.248 Angle : 0.687 9.298 9091 Z= 0.335 Chirality : 0.047 0.281 1027 Planarity : 0.004 0.046 1176 Dihedral : 11.539 168.619 1151 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.26 % Favored : 92.62 % Rotamer: Outliers : 3.90 % Allowed : 23.41 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.49 (0.29), residues: 816 helix: -1.56 (0.47), residues: 100 sheet: -0.21 (0.34), residues: 221 loop : -1.25 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 113 HIS 0.002 0.001 HIS A 26 PHE 0.011 0.001 PHE B 370 TYR 0.019 0.002 TYR A 380 ARG 0.002 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 54 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.9194 (mtpp) cc_final: 0.8670 (pptt) REVERT: A 90 ARG cc_start: 0.8349 (ptm160) cc_final: 0.7549 (mmm160) REVERT: A 285 MET cc_start: 0.7258 (ttt) cc_final: 0.6907 (ttt) REVERT: B 387 MET cc_start: 0.8080 (mmm) cc_final: 0.7588 (tpp) outliers start: 27 outliers final: 20 residues processed: 77 average time/residue: 0.1697 time to fit residues: 18.2621 Evaluate side-chains 70 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 50 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.0030 chunk 73 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6692 Z= 0.210 Angle : 0.673 9.516 9091 Z= 0.328 Chirality : 0.047 0.277 1027 Planarity : 0.004 0.041 1176 Dihedral : 11.279 163.828 1151 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.26 % Favored : 92.62 % Rotamer: Outliers : 2.89 % Allowed : 24.42 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.40 (0.29), residues: 816 helix: -1.51 (0.48), residues: 100 sheet: -0.13 (0.34), residues: 222 loop : -1.19 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 113 HIS 0.002 0.001 HIS A 278 PHE 0.018 0.001 PHE B 248 TYR 0.018 0.002 TYR A 380 ARG 0.003 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.9175 (mtpp) cc_final: 0.8646 (pptt) REVERT: A 90 ARG cc_start: 0.8313 (ptm160) cc_final: 0.7532 (mmm160) REVERT: A 168 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8167 (mt-10) REVERT: A 285 MET cc_start: 0.7242 (ttt) cc_final: 0.6912 (ttt) REVERT: B 249 THR cc_start: 0.6037 (OUTLIER) cc_final: 0.5820 (t) REVERT: B 387 MET cc_start: 0.8006 (mmm) cc_final: 0.7525 (tpp) outliers start: 20 outliers final: 17 residues processed: 67 average time/residue: 0.1656 time to fit residues: 15.7587 Evaluate side-chains 69 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6692 Z= 0.245 Angle : 0.678 9.647 9091 Z= 0.333 Chirality : 0.047 0.269 1027 Planarity : 0.004 0.044 1176 Dihedral : 11.071 162.573 1149 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.01 % Favored : 92.87 % Rotamer: Outliers : 2.75 % Allowed : 24.86 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.47 (0.29), residues: 816 helix: -1.59 (0.48), residues: 101 sheet: -0.14 (0.35), residues: 208 loop : -1.23 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 113 HIS 0.002 0.001 HIS A 26 PHE 0.019 0.002 PHE B 248 TYR 0.020 0.002 TYR A 380 ARG 0.002 0.000 ARG A 327 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.9184 (mtpp) cc_final: 0.8650 (pptt) REVERT: A 90 ARG cc_start: 0.8385 (ptm160) cc_final: 0.7576 (mmm160) REVERT: A 285 MET cc_start: 0.7378 (ttt) cc_final: 0.7068 (ttt) REVERT: B 249 THR cc_start: 0.6174 (OUTLIER) cc_final: 0.5856 (t) REVERT: B 387 MET cc_start: 0.8037 (mmm) cc_final: 0.7630 (tpp) outliers start: 19 outliers final: 16 residues processed: 69 average time/residue: 0.1879 time to fit residues: 18.6694 Evaluate side-chains 69 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.101856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.078487 restraints weight = 33765.207| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 6.28 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6692 Z= 0.232 Angle : 0.676 10.243 9091 Z= 0.331 Chirality : 0.047 0.273 1027 Planarity : 0.004 0.043 1176 Dihedral : 10.904 158.133 1149 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.13 % Favored : 92.74 % Rotamer: Outliers : 3.18 % Allowed : 24.28 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.47 (0.29), residues: 816 helix: -1.59 (0.48), residues: 101 sheet: -0.10 (0.36), residues: 209 loop : -1.26 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 113 HIS 0.002 0.001 HIS A 278 PHE 0.012 0.001 PHE B 370 TYR 0.019 0.002 TYR A 380 ARG 0.002 0.000 ARG B 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1858.51 seconds wall clock time: 34 minutes 46.86 seconds (2086.86 seconds total)