Starting phenix.real_space_refine on Fri Jul 19 09:23:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzp_41765/07_2024/8tzp_41765.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzp_41765/07_2024/8tzp_41765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzp_41765/07_2024/8tzp_41765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzp_41765/07_2024/8tzp_41765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzp_41765/07_2024/8tzp_41765.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzp_41765/07_2024/8tzp_41765.cif" } resolution = 3.23 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= 0.002 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 75 5.16 5 C 4470 2.51 5 N 1170 2.21 5 O 1204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 71": "OD1" <-> "OD2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 325": "OD1" <-> "OD2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 244": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6920 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2342 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 289} Chain breaks: 1 Chain: "B" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4037 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 21, 'TRANS': 474} Chain: "C" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 484 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PAM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 4.52, per 1000 atoms: 0.65 Number of scatterers: 6920 At special positions: 0 Unit cell: (87.98, 92.96, 129.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 1 15.00 O 1204 8.00 N 1170 7.00 C 4470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 73 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 309 " distance=2.04 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 263 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 225 " - pdb=" SG CYS C 250 " 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 custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 6 sheets defined 52.7% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 removed outlier: 4.293A pdb=" N LYS A 40 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 55 through 77 removed outlier: 3.637A pdb=" N ILE A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 125 Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 154 through 170 removed outlier: 4.000A pdb=" N TYR A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 195 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.583A pdb=" N LEU A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 10 through 35 removed outlier: 3.835A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 121 through 125 removed outlier: 4.142A pdb=" N GLN B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 227 through 258 Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 264 through 282 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 295 through 322 removed outlier: 3.584A pdb=" N ILE B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 334 Processing helix chain 'B' and resid 335 through 357 Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'B' and resid 367 through 370 Processing helix chain 'B' and resid 371 through 414 removed outlier: 3.820A pdb=" N SER B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 456 Processing helix chain 'B' and resid 469 through 492 Processing helix chain 'C' and resid 210 through 219 removed outlier: 4.797A pdb=" N TYR C 215 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS C 217 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 236 Processing helix chain 'C' and resid 238 through 250 Processing helix chain 'C' and resid 258 through 270 removed outlier: 3.823A pdb=" N GLN C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER C 270 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 202 Processing sheet with id=AA2, first strand: chain 'A' and resid 252 through 254 removed outlier: 5.852A pdb=" N VAL A 236 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 294 removed outlier: 4.193A pdb=" N TYR A 346 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 46 removed outlier: 6.870A pdb=" N ASP B 117 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE B 219 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN B 115 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU B 221 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 113 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY B 223 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 111 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B 114 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.504A pdb=" N ALA B 152 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR B 140 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU B 150 " --> pdb=" O TYR B 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 462 removed outlier: 3.619A pdb=" N VAL B 465 " --> pdb=" O TRP B 462 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 1050 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: 1.74 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1085 1.31 - 1.44: 1983 1.44 - 1.57: 3918 1.57 - 1.69: 3 1.69 - 1.82: 108 Bond restraints: 7097 Sorted by residual: bond pdb=" C31 POV B 601 " pdb=" O31 POV B 601 " ideal model delta sigma weight residual 1.327 1.418 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C21 POV B 601 " pdb=" O21 POV B 601 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb="C210 POV B 601 " pdb="C211 POV B 601 " ideal model delta sigma weight residual 1.497 1.558 -0.061 2.00e-02 2.50e+03 9.42e+00 bond pdb=" N POV B 601 " pdb=" C14 POV B 601 " ideal model delta sigma weight residual 1.490 1.436 0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" C28 POV B 601 " pdb=" C29 POV B 601 " ideal model delta sigma weight residual 1.497 1.548 -0.051 2.00e-02 2.50e+03 6.44e+00 ... (remaining 7092 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.50: 223 106.50 - 113.39: 3787 113.39 - 120.29: 2597 120.29 - 127.18: 2879 127.18 - 134.08: 99 Bond angle restraints: 9585 Sorted by residual: angle pdb=" CA PRO A 56 " pdb=" N PRO A 56 " pdb=" CD PRO A 56 " ideal model delta sigma weight residual 112.00 103.61 8.39 1.40e+00 5.10e-01 3.60e+01 angle pdb=" C THR A 297 " pdb=" N ALA A 298 " pdb=" CA ALA A 298 " ideal model delta sigma weight residual 120.09 125.66 -5.57 1.25e+00 6.40e-01 1.99e+01 angle pdb=" O13 POV B 601 " pdb=" P POV B 601 " pdb=" O14 POV B 601 " ideal model delta sigma weight residual 121.11 109.35 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O11 POV B 601 " pdb=" P POV B 601 " pdb=" O12 POV B 601 " ideal model delta sigma weight residual 97.67 109.26 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CA LYS B 208 " pdb=" CB LYS B 208 " pdb=" CG LYS B 208 " ideal model delta sigma weight residual 114.10 121.79 -7.69 2.00e+00 2.50e-01 1.48e+01 ... (remaining 9580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 3786 18.02 - 36.04: 355 36.04 - 54.05: 83 54.05 - 72.07: 21 72.07 - 90.09: 9 Dihedral angle restraints: 4254 sinusoidal: 1775 harmonic: 2479 Sorted by residual: dihedral pdb=" CB CYS C 217 " pdb=" SG CYS C 217 " pdb=" SG CYS C 229 " pdb=" CB CYS C 229 " ideal model delta sinusoidal sigma weight residual -86.00 -163.07 77.07 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS A 324 " pdb=" SG CYS A 324 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual 93.00 155.26 -62.26 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS A 38 " pdb=" SG CYS A 38 " pdb=" SG CYS A 52 " pdb=" CB CYS A 52 " ideal model delta sinusoidal sigma weight residual -86.00 -146.52 60.52 1 1.00e+01 1.00e-02 4.87e+01 ... (remaining 4251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 599 0.029 - 0.058: 283 0.058 - 0.087: 99 0.087 - 0.116: 38 0.116 - 0.146: 10 Chirality restraints: 1029 Sorted by residual: chirality pdb=" CA CYS C 250 " pdb=" N CYS C 250 " pdb=" C CYS C 250 " pdb=" CB CYS C 250 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CB THR A 343 " pdb=" CA THR A 343 " pdb=" OG1 THR A 343 " pdb=" CG2 THR A 343 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1026 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 55 " 0.100 5.00e-02 4.00e+02 1.46e-01 3.42e+01 pdb=" N PRO A 56 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO A 56 " 0.077 5.00e-02 4.00e+02 pdb=" CD PRO A 56 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 67 " 0.063 5.00e-02 4.00e+02 9.46e-02 1.43e+01 pdb=" N PRO B 68 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 68 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 68 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 208 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C LYS B 208 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS B 208 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE B 209 " -0.012 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 2 2.05 - 2.76: 1128 2.76 - 3.48: 9683 3.48 - 4.19: 15535 4.19 - 4.90: 28735 Nonbonded interactions: 55083 Sorted by model distance: nonbonded pdb=" OG SER A 206 " pdb=" O1 PAM A 601 " model vdw 1.341 2.440 nonbonded pdb=" OG SER A 206 " pdb=" C1 PAM A 601 " model vdw 1.375 3.270 nonbonded pdb=" O ASN A 181 " pdb=" ND2 ASN A 185 " model vdw 2.169 2.520 nonbonded pdb=" O LEU B 312 " pdb=" OH TYR B 392 " model vdw 2.273 2.440 nonbonded pdb=" O ARG C 231 " pdb=" OG SER C 235 " model vdw 2.314 2.440 ... (remaining 55078 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.040 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.004 0.099 7097 Z= 0.298 Angle : 0.732 11.763 9585 Z= 0.377 Chirality : 0.041 0.146 1029 Planarity : 0.006 0.146 1206 Dihedral : 15.231 90.091 2605 Min Nonbonded Distance : 1.341 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.27 % Allowed : 12.52 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.28), residues: 851 helix: 2.20 (0.25), residues: 387 sheet: 0.14 (0.53), residues: 92 loop : -0.60 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 481 HIS 0.005 0.001 HIS B 322 PHE 0.016 0.001 PHE B 432 TYR 0.011 0.001 TYR B 308 ARG 0.003 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.782 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.1703 time to fit residues: 23.4147 Evaluate side-chains 88 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.0000 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7097 Z= 0.196 Angle : 0.532 6.786 9585 Z= 0.277 Chirality : 0.040 0.147 1029 Planarity : 0.005 0.090 1206 Dihedral : 8.197 86.682 968 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.10 % Allowed : 11.57 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.28), residues: 851 helix: 2.31 (0.25), residues: 394 sheet: 0.09 (0.51), residues: 109 loop : -0.62 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 481 HIS 0.005 0.001 HIS B 322 PHE 0.012 0.001 PHE B 432 TYR 0.011 0.001 TYR B 484 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: B 423 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8197 (mm) outliers start: 23 outliers final: 11 residues processed: 105 average time/residue: 0.1815 time to fit residues: 26.0901 Evaluate side-chains 102 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN B 100 HIS B 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7097 Z= 0.282 Angle : 0.554 7.205 9585 Z= 0.287 Chirality : 0.042 0.231 1029 Planarity : 0.005 0.071 1206 Dihedral : 7.797 89.575 968 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.23 % Allowed : 12.38 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.28), residues: 851 helix: 2.06 (0.25), residues: 403 sheet: -0.08 (0.50), residues: 109 loop : -0.69 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 481 HIS 0.003 0.001 HIS A 117 PHE 0.011 0.001 PHE B 432 TYR 0.017 0.002 TYR A 313 ARG 0.002 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.825 Fit side-chains REVERT: A 346 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6805 (m-10) REVERT: B 103 MET cc_start: 0.8404 (mtt) cc_final: 0.8183 (mtt) outliers start: 24 outliers final: 15 residues processed: 104 average time/residue: 0.1799 time to fit residues: 25.7793 Evaluate side-chains 101 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 488 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7097 Z= 0.217 Angle : 0.527 6.784 9585 Z= 0.273 Chirality : 0.041 0.175 1029 Planarity : 0.004 0.060 1206 Dihedral : 7.535 85.772 968 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.36 % Allowed : 11.98 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 851 helix: 2.15 (0.25), residues: 403 sheet: -0.06 (0.50), residues: 109 loop : -0.68 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 PHE 0.012 0.001 PHE B 432 TYR 0.017 0.001 TYR A 318 ARG 0.002 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 346 TYR cc_start: 0.7057 (OUTLIER) cc_final: 0.6771 (m-10) REVERT: B 423 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8231 (mm) REVERT: C 236 LYS cc_start: 0.7310 (tppt) cc_final: 0.7027 (mmtm) outliers start: 25 outliers final: 19 residues processed: 110 average time/residue: 0.1601 time to fit residues: 24.5186 Evaluate side-chains 113 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 488 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 20 optimal weight: 0.0030 chunk 27 optimal weight: 5.9990 overall best weight: 0.5888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7097 Z= 0.171 Angle : 0.493 6.702 9585 Z= 0.256 Chirality : 0.040 0.151 1029 Planarity : 0.004 0.053 1206 Dihedral : 7.273 84.260 968 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.36 % Allowed : 12.25 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.29), residues: 851 helix: 2.31 (0.25), residues: 404 sheet: -0.10 (0.51), residues: 109 loop : -0.62 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 PHE 0.016 0.001 PHE B 240 TYR 0.019 0.001 TYR A 318 ARG 0.003 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.643 Fit side-chains REVERT: A 346 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6871 (m-10) REVERT: B 377 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7148 (mp) REVERT: C 236 LYS cc_start: 0.7334 (tppt) cc_final: 0.7038 (mmtm) outliers start: 25 outliers final: 17 residues processed: 112 average time/residue: 0.1643 time to fit residues: 25.9045 Evaluate side-chains 110 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7097 Z= 0.185 Angle : 0.508 6.653 9585 Z= 0.261 Chirality : 0.040 0.200 1029 Planarity : 0.004 0.050 1206 Dihedral : 7.225 85.033 968 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.23 % Allowed : 13.06 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.29), residues: 851 helix: 2.50 (0.25), residues: 395 sheet: -0.15 (0.51), residues: 109 loop : -0.46 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 PHE 0.011 0.001 PHE A 166 TYR 0.021 0.001 TYR A 318 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 0.726 Fit side-chains REVERT: B 377 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7145 (mp) REVERT: C 236 LYS cc_start: 0.7349 (tppt) cc_final: 0.7048 (mmtm) outliers start: 24 outliers final: 17 residues processed: 107 average time/residue: 0.1874 time to fit residues: 27.5846 Evaluate side-chains 107 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7097 Z= 0.232 Angle : 0.537 7.011 9585 Z= 0.275 Chirality : 0.041 0.173 1029 Planarity : 0.004 0.047 1206 Dihedral : 7.290 85.769 968 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.96 % Allowed : 14.00 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.29), residues: 851 helix: 2.39 (0.25), residues: 395 sheet: -0.58 (0.49), residues: 117 loop : -0.42 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 481 HIS 0.003 0.001 HIS A 117 PHE 0.013 0.001 PHE A 166 TYR 0.027 0.002 TYR A 346 ARG 0.003 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.720 Fit side-chains REVERT: B 249 MET cc_start: 0.8974 (tpp) cc_final: 0.8386 (mmt) REVERT: B 377 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7078 (mp) REVERT: C 236 LYS cc_start: 0.7306 (tppt) cc_final: 0.6990 (mmtm) outliers start: 22 outliers final: 18 residues processed: 103 average time/residue: 0.1643 time to fit residues: 23.5678 Evaluate side-chains 105 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7097 Z= 0.199 Angle : 0.526 6.797 9585 Z= 0.270 Chirality : 0.041 0.156 1029 Planarity : 0.004 0.046 1206 Dihedral : 7.229 85.048 968 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.69 % Allowed : 14.67 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.29), residues: 851 helix: 2.46 (0.24), residues: 395 sheet: -0.57 (0.49), residues: 117 loop : -0.37 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 PHE 0.011 0.001 PHE B 432 TYR 0.023 0.002 TYR A 318 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.726 Fit side-chains REVERT: B 249 MET cc_start: 0.8924 (tpp) cc_final: 0.8696 (mmm) REVERT: B 377 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7116 (mp) REVERT: C 236 LYS cc_start: 0.7314 (tppt) cc_final: 0.6996 (mmtm) outliers start: 20 outliers final: 18 residues processed: 100 average time/residue: 0.1727 time to fit residues: 23.9292 Evaluate side-chains 105 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7097 Z= 0.196 Angle : 0.527 6.798 9585 Z= 0.270 Chirality : 0.041 0.151 1029 Planarity : 0.004 0.046 1206 Dihedral : 7.198 85.229 968 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.69 % Allowed : 14.80 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.29), residues: 851 helix: 2.36 (0.24), residues: 402 sheet: -0.54 (0.49), residues: 117 loop : -0.47 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 PHE 0.011 0.001 PHE B 432 TYR 0.023 0.002 TYR A 318 ARG 0.004 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.794 Fit side-chains REVERT: A 290 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7597 (pp30) REVERT: B 377 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7105 (mp) REVERT: C 236 LYS cc_start: 0.7321 (tppt) cc_final: 0.6986 (mmtm) outliers start: 20 outliers final: 17 residues processed: 99 average time/residue: 0.1763 time to fit residues: 24.5542 Evaluate side-chains 104 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 84 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7097 Z= 0.184 Angle : 0.520 6.584 9585 Z= 0.268 Chirality : 0.041 0.149 1029 Planarity : 0.004 0.046 1206 Dihedral : 7.157 85.258 968 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.69 % Allowed : 15.07 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.29), residues: 851 helix: 2.40 (0.24), residues: 402 sheet: -0.53 (0.49), residues: 117 loop : -0.44 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 PHE 0.017 0.001 PHE B 291 TYR 0.023 0.002 TYR A 318 ARG 0.003 0.000 ARG A 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.704 Fit side-chains REVERT: A 290 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7617 (pp30) REVERT: B 377 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7063 (mp) REVERT: C 236 LYS cc_start: 0.7370 (tppt) cc_final: 0.7019 (mmtm) outliers start: 20 outliers final: 17 residues processed: 98 average time/residue: 0.1745 time to fit residues: 23.5938 Evaluate side-chains 104 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 9 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.179863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137823 restraints weight = 8242.180| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.16 r_work: 0.3496 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7097 Z= 0.261 Angle : 0.561 7.129 9585 Z= 0.287 Chirality : 0.042 0.238 1029 Planarity : 0.004 0.046 1206 Dihedral : 7.298 86.810 968 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.83 % Allowed : 15.21 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.29), residues: 851 helix: 2.37 (0.24), residues: 393 sheet: -0.55 (0.49), residues: 118 loop : -0.42 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 481 HIS 0.003 0.001 HIS A 117 PHE 0.016 0.001 PHE B 291 TYR 0.022 0.002 TYR A 313 ARG 0.004 0.000 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1784.24 seconds wall clock time: 32 minutes 35.98 seconds (1955.98 seconds total)