Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 01:14:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/08_2023/8t2u_40988_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/08_2023/8t2u_40988.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/08_2023/8t2u_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_40988/08_2023/8t2u_40988_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/08_2023/8t2u_40988_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/08_2023/8t2u_40988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/08_2023/8t2u_40988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/08_2023/8t2u_40988_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2u_40988/08_2023/8t2u_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-1.21rc1-5044/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 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 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 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 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 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: 5.20, per 1000 atoms: 0.79 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: 3.35 Conformation dependent library (CDL) restraints added in 1.6 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: 1.22 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: 1.82 Time building geometry restraints manager: 3.48 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: 3756 34.55 - 69.10: 127 69.10 - 103.66: 11 103.66 - 138.21: 0 138.21 - 172.76: 1 Dihedral angle restraints: 3895 sinusoidal: 1544 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 3892 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: 0.000 Extract box with map and model: 4.070 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 24.130 Find NCS groups from input model: 0.170 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.270 ------------------------------------------------------------------------------- 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 : 17.063 172.759 2378 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 % 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 *********************** 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 : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 10 residues processed: 94 average time/residue: 0.2138 time to fit residues: 26.0739 Evaluate side-chains 63 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0646 time to fit residues: 2.2496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 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 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: 0.7601 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 6692 Z= 0.278 Angle : 0.740 12.547 9091 Z= 0.367 Chirality : 0.049 0.307 1027 Planarity : 0.004 0.042 1176 Dihedral : 8.009 173.179 904 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.11 % Rotamer Outliers : 2.31 % 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: -1.87 (0.28), residues: 816 helix: -1.58 (0.46), residues: 102 sheet: -0.82 (0.33), residues: 243 loop : -1.38 (0.28), residues: 471 *********************** 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 71 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.874 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 68 average time/residue: 0.1618 time to fit residues: 16.3055 Evaluate side-chains 57 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0775 time to fit residues: 1.9182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 chunk 78 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7586 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 6692 Z= 0.233 Angle : 0.682 9.479 9091 Z= 0.336 Chirality : 0.047 0.281 1027 Planarity : 0.004 0.042 1176 Dihedral : 8.045 179.871 904 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.11 % Rotamer Outliers : 2.31 % 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: -1.79 (0.29), residues: 816 helix: -1.51 (0.47), residues: 100 sheet: -0.73 (0.33), residues: 249 loop : -1.36 (0.29), residues: 467 *********************** 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 71 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 69 average time/residue: 0.1506 time to fit residues: 15.4307 Evaluate side-chains 56 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.748 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1273 time to fit residues: 2.2056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 48 optimal weight: 0.3980 chunk 73 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7587 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 6692 Z= 0.223 Angle : 0.682 9.789 9091 Z= 0.333 Chirality : 0.047 0.260 1027 Planarity : 0.004 0.042 1176 Dihedral : 7.871 176.140 904 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.64 % Favored : 93.23 % Rotamer Outliers : 2.17 % 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: -1.79 (0.28), residues: 816 helix: -1.74 (0.46), residues: 100 sheet: -0.55 (0.34), residues: 228 loop : -1.40 (0.28), residues: 488 *********************** 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 69 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 68 average time/residue: 0.1604 time to fit residues: 15.8220 Evaluate side-chains 56 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.765 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.0709 time to fit residues: 1.8863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 6692 Z= 0.251 Angle : 0.692 11.437 9091 Z= 0.339 Chirality : 0.046 0.254 1027 Planarity : 0.004 0.046 1176 Dihedral : 7.812 174.146 904 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.50 % Favored : 92.37 % Rotamer Outliers : 1.59 % 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: -1.77 (0.29), residues: 816 helix: -1.61 (0.48), residues: 100 sheet: -0.51 (0.34), residues: 226 loop : -1.42 (0.28), residues: 490 *********************** 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 64 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.1550 time to fit residues: 14.7530 Evaluate side-chains 57 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.762 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.0747 time to fit residues: 1.9070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 64 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 6692 Z= 0.288 Angle : 0.702 9.638 9091 Z= 0.344 Chirality : 0.047 0.240 1027 Planarity : 0.004 0.049 1176 Dihedral : 7.903 175.511 904 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.63 % Favored : 92.25 % Rotamer Outliers : 1.88 % 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: -1.86 (0.28), residues: 816 helix: -1.84 (0.46), residues: 106 sheet: -0.57 (0.33), residues: 239 loop : -1.44 (0.28), residues: 471 *********************** 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 67 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 65 average time/residue: 0.1514 time to fit residues: 14.5150 Evaluate side-chains 56 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.812 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.0670 time to fit residues: 1.7772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 6692 Z= 0.289 Angle : 0.704 9.727 9091 Z= 0.344 Chirality : 0.047 0.250 1027 Planarity : 0.004 0.049 1176 Dihedral : 7.903 174.236 904 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.00 % Favored : 91.88 % Rotamer Outliers : 1.01 % 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: -1.88 (0.28), residues: 816 helix: -1.88 (0.46), residues: 106 sheet: -0.60 (0.32), residues: 240 loop : -1.44 (0.28), residues: 470 *********************** 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 59 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.1555 time to fit residues: 13.5544 Evaluate side-chains 56 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.767 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.0706 time to fit residues: 1.6328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2444 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= 0.251 Angle : 0.689 10.027 9091 Z= 0.336 Chirality : 0.046 0.239 1027 Planarity : 0.004 0.047 1176 Dihedral : 7.749 170.473 904 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.12 % Favored : 91.76 % Rotamer Outliers : 0.87 % 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: -1.69 (0.29), residues: 816 helix: -1.67 (0.48), residues: 100 sheet: -0.48 (0.33), residues: 239 loop : -1.33 (0.28), residues: 477 *********************** 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 57 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 0.2052 time to fit residues: 16.1781 Evaluate side-chains 50 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.700 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0648 time to fit residues: 1.1908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.6980 chunk 73 optimal weight: 0.0470 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 0.0980 chunk 64 optimal weight: 6.9990 chunk 67 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 6692 Z= 0.228 Angle : 0.687 9.846 9091 Z= 0.333 Chirality : 0.046 0.241 1027 Planarity : 0.004 0.045 1176 Dihedral : 7.557 165.747 904 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.50 % Favored : 92.37 % Rotamer Outliers : 0.29 % 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: -1.54 (0.29), residues: 816 helix: -1.55 (0.49), residues: 98 sheet: -0.38 (0.33), residues: 242 loop : -1.24 (0.29), residues: 476 *********************** 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 54 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 0.2050 time to fit residues: 16.1918 Evaluate side-chains 52 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 1.948 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1342 time to fit residues: 3.3078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 6692 Z= 0.239 Angle : 0.680 10.390 9091 Z= 0.332 Chirality : 0.046 0.228 1027 Planarity : 0.004 0.043 1176 Dihedral : 7.527 164.747 904 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.63 % Favored : 92.25 % Rotamer Outliers : 0.43 % 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: -1.52 (0.29), residues: 816 helix: -1.52 (0.49), residues: 98 sheet: -0.33 (0.33), residues: 233 loop : -1.24 (0.28), residues: 485 ********************** 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 55 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.1760 time to fit residues: 14.4323 Evaluate side-chains 54 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.792 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1259 time to fit residues: 2.0406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.100443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.076861 restraints weight = 35598.571| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 6.40 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 6692 Z= 0.295 Angle : 0.699 10.792 9091 Z= 0.345 Chirality : 0.046 0.233 1027 Planarity : 0.004 0.047 1176 Dihedral : 7.565 163.433 904 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.63 % Favored : 92.25 % Rotamer Outliers : 0.29 % 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 (0.29), residues: 816 helix: -1.55 (0.48), residues: 104 sheet: -0.38 (0.33), residues: 230 loop : -1.28 (0.29), residues: 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1771.10 seconds wall clock time: 33 minutes 17.11 seconds (1997.11 seconds total)