Starting phenix.real_space_refine on Thu Jul 2 08:19:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zaa_39876/07_2026/8zaa_39876.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zaa_39876/07_2026/8zaa_39876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zaa_39876/07_2026/8zaa_39876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zaa_39876/07_2026/8zaa_39876.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zaa_39876/07_2026/8zaa_39876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zaa_39876/07_2026/8zaa_39876.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.050 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 2 5.49 5 S 33 5.16 5 C 4923 2.51 5 N 1374 2.21 5 O 1441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7773 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1846 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 213} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1789 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2058 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 237} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2065 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 238} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EIP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.55, per 1000 atoms: 0.20 Number of scatterers: 7773 At special positions: 0 Unit cell: (95.8797, 144.358, 132.508, 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 33 16.00 P 2 15.00 O 1441 8.00 N 1374 7.00 C 4923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 452.5 milliseconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1802 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 10 sheets defined 20.1% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'C' and resid 259 through 290 removed outlier: 3.694A pdb=" N ALA C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 270 " --> pdb=" O TRP C 266 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 277 " --> pdb=" O GLN C 273 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 304 Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.549A pdb=" N THR C 319 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 399 Processing helix chain 'D' and resid 267 through 292 removed outlier: 4.184A pdb=" N ARG D 276 " --> pdb=" O GLU D 272 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 288 " --> pdb=" O ARG D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 removed outlier: 4.164A pdb=" N TRP D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 252 Processing helix chain 'G' and resid 254 through 293 removed outlier: 3.603A pdb=" N GLU G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 431 No H-bonds generated for 'chain 'G' and resid 429 through 431' Processing helix chain 'E' and resid 241 through 292 removed outlier: 4.038A pdb=" N PHE E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU E 263 " --> pdb=" O ARG E 259 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA E 265 " --> pdb=" O THR E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 309 Processing sheet with id=AA1, first strand: chain 'C' and resid 324 through 326 removed outlier: 3.928A pdb=" N GLU C 369 " --> pdb=" O CYS C 482 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 442 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS C 454 " --> pdb=" O PHE C 444 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN C 446 " --> pdb=" O HIS C 452 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS C 452 " --> pdb=" O ASN C 446 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.722A pdb=" N TRP C 378 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 420 " --> pdb=" O THR C 414 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 309 through 310 removed outlier: 5.802A pdb=" N ASN D 446 " --> pdb=" O HIS D 452 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N HIS D 452 " --> pdb=" O ASN D 446 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 309 through 310 Processing sheet with id=AA5, first strand: chain 'D' and resid 324 through 326 Processing sheet with id=AA6, first strand: chain 'D' and resid 354 through 356 Processing sheet with id=AA7, first strand: chain 'G' and resid 313 through 315 removed outlier: 3.566A pdb=" N VAL G 322 " --> pdb=" O ILE G 469 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE G 469 " --> pdb=" O VAL G 322 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU G 297 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU E 297 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL E 433 " --> pdb=" O CYS E 447 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR E 445 " --> pdb=" O PHE E 435 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASN E 437 " --> pdb=" O HIS E 443 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N HIS E 443 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 313 through 315 removed outlier: 4.422A pdb=" N LEU E 297 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU G 297 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL G 433 " --> pdb=" O THR G 446 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR G 446 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE G 435 " --> pdb=" O ILE G 444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 346 through 348 removed outlier: 3.715A pdb=" N TRP G 370 " --> pdb=" O MET G 398 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 346 through 348 removed outlier: 3.922A pdb=" N TRP E 370 " --> pdb=" O MET E 398 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 855 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: 1.12 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2590 1.34 - 1.46: 1587 1.46 - 1.58: 3742 1.58 - 1.69: 4 1.69 - 1.81: 44 Bond restraints: 7967 Sorted by residual: bond pdb=" O5 EIP D 501 " pdb=" P4 EIP D 501 " ideal model delta sigma weight residual 1.743 1.644 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" CB PRO C 310 " pdb=" CG PRO C 310 " ideal model delta sigma weight residual 1.492 1.659 -0.167 5.00e-02 4.00e+02 1.12e+01 bond pdb=" O5 EIP D 501 " pdb=" P8 EIP D 501 " ideal model delta sigma weight residual 1.607 1.646 -0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" CB ASN C 386 " pdb=" CG ASN C 386 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.20e+00 bond pdb=" CB PRO G 335 " pdb=" CG PRO G 335 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.92e+00 ... (remaining 7962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 10681 3.33 - 6.67: 94 6.67 - 10.00: 16 10.00 - 13.34: 1 13.34 - 16.67: 1 Bond angle restraints: 10793 Sorted by residual: angle pdb=" CA PRO C 310 " pdb=" N PRO C 310 " pdb=" CD PRO C 310 " ideal model delta sigma weight residual 112.00 95.33 16.67 1.40e+00 5.10e-01 1.42e+02 angle pdb=" N PRO C 310 " pdb=" CD PRO C 310 " pdb=" CG PRO C 310 " ideal model delta sigma weight residual 103.20 96.28 6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" CA GLN C 273 " pdb=" CB GLN C 273 " pdb=" CG GLN C 273 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CA GLN E 245 " pdb=" CB GLN E 245 " pdb=" CG GLN E 245 " ideal model delta sigma weight residual 114.10 122.04 -7.94 2.00e+00 2.50e-01 1.58e+01 angle pdb=" CB LYS E 382 " pdb=" CG LYS E 382 " pdb=" CD LYS E 382 " ideal model delta sigma weight residual 111.30 120.14 -8.84 2.30e+00 1.89e-01 1.48e+01 ... (remaining 10788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4037 17.95 - 35.91: 612 35.91 - 53.86: 141 53.86 - 71.81: 17 71.81 - 89.77: 11 Dihedral angle restraints: 4818 sinusoidal: 2042 harmonic: 2776 Sorted by residual: dihedral pdb=" CA ARG E 293 " pdb=" C ARG E 293 " pdb=" N ARG E 294 " pdb=" CA ARG E 294 " ideal model delta harmonic sigma weight residual -180.00 -138.38 -41.62 0 5.00e+00 4.00e-02 6.93e+01 dihedral pdb=" CA ARG E 294 " pdb=" C ARG E 294 " pdb=" N THR E 295 " pdb=" CA THR E 295 " ideal model delta harmonic sigma weight residual 180.00 148.20 31.80 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CA SER G 407 " pdb=" C SER G 407 " pdb=" N SER G 408 " pdb=" CA SER G 408 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 4815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 951 0.059 - 0.119: 178 0.119 - 0.178: 18 0.178 - 0.237: 0 0.237 - 0.297: 1 Chirality restraints: 1148 Sorted by residual: chirality pdb=" C12 EIP D 501 " pdb=" C11 EIP D 501 " pdb=" C13 EIP D 501 " pdb=" C14 EIP D 501 " both_signs ideal model delta sigma weight residual False -2.48 -2.77 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA LYS G 271 " pdb=" N LYS G 271 " pdb=" C LYS G 271 " pdb=" CB LYS G 271 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA VAL G 367 " pdb=" N VAL G 367 " pdb=" C VAL G 367 " pdb=" CB VAL G 367 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1145 not shown) Planarity restraints: 1405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 309 " -0.087 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO C 310 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO C 310 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 310 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 334 " 0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO G 335 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO G 335 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO G 335 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 386 " -0.016 2.00e-02 2.50e+03 3.06e-02 9.33e+00 pdb=" C ASN C 386 " 0.053 2.00e-02 2.50e+03 pdb=" O ASN C 386 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL C 387 " -0.017 2.00e-02 2.50e+03 ... (remaining 1402 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 256 2.70 - 3.25: 7624 3.25 - 3.80: 12591 3.80 - 4.35: 15764 4.35 - 4.90: 26223 Nonbonded interactions: 62458 Sorted by model distance: nonbonded pdb=" O HIS D 297 " pdb=" ND1 HIS D 297 " model vdw 2.148 3.120 nonbonded pdb=" O LYS G 243 " pdb=" NZ LYS G 243 " model vdw 2.161 3.120 nonbonded pdb=" O PRO G 414 " pdb=" NZ LYS G 416 " model vdw 2.207 3.120 nonbonded pdb=" OD1 ASP G 307 " pdb=" ND2 ASN G 337 " model vdw 2.209 3.120 nonbonded pdb=" OE2 GLU G 272 " pdb=" NH2 ARG E 273 " model vdw 2.233 3.120 ... (remaining 62453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 266 through 471 or (resid 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 484)) selection = (chain 'D' and (resid 266 through 274 or (resid 275 and (name N or name CA or na \ me C or name O or name CB )) or resid 276 through 286 or (resid 287 and (name N \ or name CA or name C or name O or name CB )) or resid 288 through 299 or (resid \ 300 and (name N or name CA or name C or name O or name CB )) or resid 301 throug \ h 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 484)) } ncs_group { reference = (chain 'E' and resid 240 through 492) selection = chain 'G' } 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: 5.300 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.320 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 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 0.167 7967 Z= 0.185 Angle : 0.833 16.672 10793 Z= 0.446 Chirality : 0.046 0.297 1148 Planarity : 0.007 0.120 1405 Dihedral : 17.606 89.766 3016 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.97 % Favored : 94.60 % Rotamer: Outliers : 0.12 % Allowed : 32.74 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.27), residues: 945 helix: 1.00 (0.40), residues: 167 sheet: -0.08 (0.36), residues: 206 loop : -1.08 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 276 TYR 0.017 0.002 TYR E 445 PHE 0.009 0.001 PHE E 425 TRP 0.052 0.002 TRP C 266 HIS 0.006 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 ( 7967) covalent geometry : angle 0.83272 / 0.45 (10793) hydrogen bonds : bond 0.15274 / 10.27 ( 300) hydrogen bonds : angle 5.97859 / 4.29 ( 855) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.185 Fit side-chains REVERT: C 269 MET cc_start: 0.7950 (ppp) cc_final: 0.7255 (mmm) REVERT: C 362 ILE cc_start: 0.7057 (tp) cc_final: 0.6589 (mt) REVERT: C 388 GLN cc_start: 0.7167 (tt0) cc_final: 0.6824 (tt0) REVERT: C 449 ASP cc_start: 0.7934 (p0) cc_final: 0.7598 (t0) REVERT: D 374 ASP cc_start: 0.6483 (p0) cc_final: 0.6267 (t70) REVERT: G 266 LEU cc_start: 0.8697 (mt) cc_final: 0.8473 (pp) REVERT: G 363 GLU cc_start: 0.5776 (mt-10) cc_final: 0.5412 (mp0) REVERT: G 464 CYS cc_start: 0.5361 (t) cc_final: 0.4909 (t) REVERT: E 289 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7644 (tt0) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.0774 time to fit residues: 16.5810 Evaluate side-chains 99 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 271 GLN C 321 ASN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN E 298 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.154303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.112541 restraints weight = 10895.034| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.27 r_work: 0.3401 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7967 Z= 0.169 Angle : 0.691 13.554 10793 Z= 0.357 Chirality : 0.045 0.139 1148 Planarity : 0.005 0.058 1405 Dihedral : 5.965 46.196 1066 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.82 % Favored : 93.76 % Rotamer: Outliers : 3.77 % Allowed : 28.62 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.27), residues: 945 helix: 1.68 (0.39), residues: 156 sheet: -0.25 (0.36), residues: 209 loop : -1.00 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 470 TYR 0.025 0.002 TYR G 359 PHE 0.015 0.002 PHE E 425 TRP 0.021 0.002 TRP C 266 HIS 0.006 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 7967) covalent geometry : angle 0.69118 / 0.36 (10793) hydrogen bonds : bond 0.04925 / 3.23 ( 300) hydrogen bonds : angle 5.30233 / 3.76 ( 855) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: C 269 MET cc_start: 0.8120 (ppp) cc_final: 0.7431 (mmm) REVERT: C 374 ASP cc_start: 0.7822 (p0) cc_final: 0.7559 (p0) REVERT: C 388 GLN cc_start: 0.7184 (tt0) cc_final: 0.6762 (tt0) REVERT: C 449 ASP cc_start: 0.7910 (p0) cc_final: 0.7308 (t0) REVERT: D 374 ASP cc_start: 0.7142 (p0) cc_final: 0.6714 (t70) REVERT: D 436 ASP cc_start: 0.5928 (t0) cc_final: 0.5400 (t0) REVERT: G 398 MET cc_start: 0.7548 (ttp) cc_final: 0.7103 (mtp) REVERT: G 464 CYS cc_start: 0.5581 (t) cc_final: 0.5309 (t) REVERT: E 418 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8566 (p) outliers start: 32 outliers final: 16 residues processed: 135 average time/residue: 0.0914 time to fit residues: 16.6007 Evaluate side-chains 113 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 444 ILE Chi-restraints excluded: chain G residue 453 SER Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain E residue 298 HIS Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 456 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 4 optimal weight: 0.0270 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 321 ASN C 399 ASN ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN E 298 HIS E 390 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.153510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.111407 restraints weight = 10792.999| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.34 r_work: 0.3392 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7967 Z= 0.150 Angle : 0.644 12.568 10793 Z= 0.333 Chirality : 0.044 0.135 1148 Planarity : 0.005 0.053 1405 Dihedral : 5.528 45.874 1066 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.76 % Favored : 94.81 % Rotamer: Outliers : 4.48 % Allowed : 28.15 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.27), residues: 945 helix: 1.72 (0.38), residues: 161 sheet: -0.45 (0.36), residues: 206 loop : -0.96 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 470 TYR 0.021 0.002 TYR G 359 PHE 0.012 0.001 PHE E 425 TRP 0.014 0.001 TRP C 266 HIS 0.006 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 7967) covalent geometry : angle 0.64380 / 0.33 (10793) hydrogen bonds : bond 0.04499 / 2.96 ( 300) hydrogen bonds : angle 5.22225 / 3.71 ( 855) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: C 334 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.7010 (tp-100) REVERT: C 374 ASP cc_start: 0.7797 (p0) cc_final: 0.7447 (p0) REVERT: C 388 GLN cc_start: 0.7154 (tt0) cc_final: 0.6746 (tt0) REVERT: D 374 ASP cc_start: 0.7043 (p0) cc_final: 0.6654 (t70) REVERT: D 436 ASP cc_start: 0.6081 (t0) cc_final: 0.5373 (t70) REVERT: D 479 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7609 (mt) REVERT: G 324 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7314 (ttm170) REVERT: G 464 CYS cc_start: 0.5772 (t) cc_final: 0.5314 (t) REVERT: E 242 ASN cc_start: 0.6643 (OUTLIER) cc_final: 0.6435 (p0) outliers start: 38 outliers final: 19 residues processed: 131 average time/residue: 0.0771 time to fit residues: 13.8863 Evaluate side-chains 112 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 444 ILE Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain E residue 242 ASN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 298 HIS Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 476 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 0.0060 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 321 ASN ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS E 390 GLN E 491 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.153632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.112132 restraints weight = 11032.923| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.44 r_work: 0.3379 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7967 Z= 0.153 Angle : 0.639 12.381 10793 Z= 0.330 Chirality : 0.044 0.143 1148 Planarity : 0.005 0.052 1405 Dihedral : 5.410 45.467 1066 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.08 % Favored : 94.50 % Rotamer: Outliers : 5.42 % Allowed : 26.97 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.27), residues: 945 helix: 1.85 (0.38), residues: 161 sheet: -0.65 (0.36), residues: 197 loop : -1.01 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 291 TYR 0.021 0.002 TYR G 359 PHE 0.012 0.001 PHE E 425 TRP 0.021 0.001 TRP C 266 HIS 0.006 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 7967) covalent geometry : angle 0.63929 / 0.33 (10793) hydrogen bonds : bond 0.04321 / 2.83 ( 300) hydrogen bonds : angle 5.20990 / 3.71 ( 855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 388 GLN cc_start: 0.7148 (tt0) cc_final: 0.6768 (tt0) REVERT: D 374 ASP cc_start: 0.7214 (p0) cc_final: 0.6851 (t70) REVERT: D 479 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7658 (mt) REVERT: G 324 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7317 (ttm170) REVERT: G 464 CYS cc_start: 0.5664 (t) cc_final: 0.5119 (t) REVERT: E 242 ASN cc_start: 0.6673 (OUTLIER) cc_final: 0.6470 (p0) outliers start: 46 outliers final: 29 residues processed: 139 average time/residue: 0.0901 time to fit residues: 16.5699 Evaluate side-chains 123 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 444 ILE Chi-restraints excluded: chain G residue 453 SER Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain E residue 242 ASN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 298 HIS Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain E residue 359 TYR Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 476 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 44 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 334 GLN ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS E 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.152095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.109953 restraints weight = 11133.586| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.51 r_work: 0.3354 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7967 Z= 0.183 Angle : 0.660 12.308 10793 Z= 0.340 Chirality : 0.045 0.134 1148 Planarity : 0.005 0.050 1405 Dihedral : 5.492 45.593 1066 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.61 % Favored : 93.97 % Rotamer: Outliers : 5.42 % Allowed : 27.09 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.27), residues: 945 helix: 1.84 (0.38), residues: 160 sheet: -0.63 (0.36), residues: 191 loop : -1.06 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 291 TYR 0.027 0.002 TYR G 359 PHE 0.017 0.002 PHE E 425 TRP 0.018 0.002 TRP C 266 HIS 0.006 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 7967) covalent geometry : angle 0.65979 / 0.34 (10793) hydrogen bonds : bond 0.04451 / 2.91 ( 300) hydrogen bonds : angle 5.34352 / 3.79 ( 855) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 374 ASP cc_start: 0.7304 (p0) cc_final: 0.6849 (t70) REVERT: D 479 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7765 (mt) REVERT: G 324 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7340 (ttm170) REVERT: G 464 CYS cc_start: 0.5814 (t) cc_final: 0.5253 (t) outliers start: 46 outliers final: 34 residues processed: 139 average time/residue: 0.0879 time to fit residues: 16.3374 Evaluate side-chains 127 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 444 ILE Chi-restraints excluded: chain G residue 453 SER Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 298 HIS Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain E residue 359 TYR Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 476 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS E 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.151839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.110064 restraints weight = 10860.815| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.24 r_work: 0.3369 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7967 Z= 0.170 Angle : 0.652 12.089 10793 Z= 0.336 Chirality : 0.045 0.135 1148 Planarity : 0.005 0.048 1405 Dihedral : 5.480 45.253 1066 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.50 % Favored : 94.07 % Rotamer: Outliers : 5.42 % Allowed : 27.21 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.27), residues: 945 helix: 1.80 (0.38), residues: 161 sheet: -0.57 (0.36), residues: 196 loop : -1.09 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 291 TYR 0.024 0.002 TYR G 359 PHE 0.015 0.002 PHE E 425 TRP 0.016 0.002 TRP C 266 HIS 0.005 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 7967) covalent geometry : angle 0.65213 / 0.34 (10793) hydrogen bonds : bond 0.04345 / 2.84 ( 300) hydrogen bonds : angle 5.33633 / 3.79 ( 855) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 99 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 388 GLN cc_start: 0.6760 (tt0) cc_final: 0.6427 (tt0) REVERT: C 404 MET cc_start: 0.7572 (tpp) cc_final: 0.7356 (tpp) REVERT: D 374 ASP cc_start: 0.7239 (p0) cc_final: 0.6815 (t70) REVERT: D 479 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7783 (mt) REVERT: G 324 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7358 (ttm170) REVERT: G 432 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7238 (m-30) outliers start: 46 outliers final: 35 residues processed: 131 average time/residue: 0.0824 time to fit residues: 14.7921 Evaluate side-chains 134 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 444 ILE Chi-restraints excluded: chain G residue 453 SER Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 298 HIS Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain E residue 359 TYR Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 476 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 27 optimal weight: 0.7980 chunk 79 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 399 HIS ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS E 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.152562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.110785 restraints weight = 10892.385| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.46 r_work: 0.3371 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7967 Z= 0.148 Angle : 0.638 12.160 10793 Z= 0.329 Chirality : 0.044 0.135 1148 Planarity : 0.005 0.048 1405 Dihedral : 5.417 44.934 1066 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.87 % Favored : 94.71 % Rotamer: Outliers : 5.06 % Allowed : 27.44 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.27), residues: 945 helix: 1.80 (0.37), residues: 161 sheet: -0.56 (0.36), residues: 202 loop : -1.05 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 291 TYR 0.019 0.002 TYR G 359 PHE 0.013 0.001 PHE G 425 TRP 0.015 0.001 TRP C 266 HIS 0.004 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 7967) covalent geometry : angle 0.63754 / 0.33 (10793) hydrogen bonds : bond 0.04147 / 2.72 ( 300) hydrogen bonds : angle 5.24724 / 3.73 ( 855) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 388 GLN cc_start: 0.6806 (tt0) cc_final: 0.6465 (tt0) REVERT: C 404 MET cc_start: 0.7678 (tpp) cc_final: 0.7468 (tpp) REVERT: D 374 ASP cc_start: 0.7288 (p0) cc_final: 0.6864 (t70) REVERT: G 324 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7418 (ttm170) REVERT: G 432 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: G 472 CYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6621 (t) REVERT: E 344 GLN cc_start: 0.6920 (pt0) cc_final: 0.6259 (pt0) REVERT: E 346 CYS cc_start: 0.4624 (m) cc_final: 0.4262 (m) outliers start: 43 outliers final: 31 residues processed: 131 average time/residue: 0.0811 time to fit residues: 14.5143 Evaluate side-chains 126 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 444 ILE Chi-restraints excluded: chain G residue 453 SER Chi-restraints excluded: chain G residue 472 CYS Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 298 HIS Chi-restraints excluded: chain E residue 359 TYR Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 476 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 85 optimal weight: 0.0370 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 399 HIS ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS E 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.153208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.111434 restraints weight = 10959.363| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.29 r_work: 0.3393 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7967 Z= 0.141 Angle : 0.637 11.938 10793 Z= 0.326 Chirality : 0.044 0.135 1148 Planarity : 0.005 0.048 1405 Dihedral : 5.364 44.613 1066 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.76 % Favored : 94.81 % Rotamer: Outliers : 4.95 % Allowed : 27.44 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.27), residues: 945 helix: 1.82 (0.38), residues: 161 sheet: -0.54 (0.36), residues: 202 loop : -1.02 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 291 TYR 0.019 0.002 TYR G 359 PHE 0.013 0.001 PHE G 425 TRP 0.010 0.001 TRP G 360 HIS 0.004 0.001 HIS E 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7967) covalent geometry : angle 0.63653 / 0.33 (10793) hydrogen bonds : bond 0.04047 / 2.65 ( 300) hydrogen bonds : angle 5.20339 / 3.70 ( 855) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 374 ASP cc_start: 0.7666 (p0) cc_final: 0.7166 (p0) REVERT: C 388 GLN cc_start: 0.6849 (tt0) cc_final: 0.6501 (tt0) REVERT: C 404 MET cc_start: 0.7622 (tpp) cc_final: 0.7386 (tpp) REVERT: D 296 ARG cc_start: 0.6587 (mtt180) cc_final: 0.5736 (mpp80) REVERT: D 374 ASP cc_start: 0.7283 (p0) cc_final: 0.6859 (t70) REVERT: G 324 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7418 (ttm170) REVERT: G 432 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7286 (m-30) REVERT: G 472 CYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6547 (t) outliers start: 42 outliers final: 34 residues processed: 129 average time/residue: 0.0816 time to fit residues: 14.5802 Evaluate side-chains 126 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain G residue 324 ARG Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 453 SER Chi-restraints excluded: chain G residue 472 CYS Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 298 HIS Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain E residue 359 TYR Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 476 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 0.0270 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 399 HIS ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS E 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.154055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.112441 restraints weight = 10913.508| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.45 r_work: 0.3398 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7967 Z= 0.129 Angle : 0.633 11.735 10793 Z= 0.326 Chirality : 0.044 0.135 1148 Planarity : 0.005 0.048 1405 Dihedral : 5.301 45.206 1066 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.34 % Favored : 95.24 % Rotamer: Outliers : 4.48 % Allowed : 28.15 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.27), residues: 945 helix: 1.54 (0.38), residues: 167 sheet: -0.50 (0.36), residues: 202 loop : -1.00 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 291 TYR 0.015 0.002 TYR G 359 PHE 0.017 0.001 PHE E 314 TRP 0.010 0.001 TRP G 394 HIS 0.004 0.001 HIS E 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 7967) covalent geometry : angle 0.63299 / 0.33 (10793) hydrogen bonds : bond 0.03961 / 2.63 ( 300) hydrogen bonds : angle 5.11147 / 3.64 ( 855) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 269 MET cc_start: 0.8111 (ppp) cc_final: 0.7265 (mmt) REVERT: C 374 ASP cc_start: 0.7664 (p0) cc_final: 0.7164 (p0) REVERT: C 388 GLN cc_start: 0.6855 (tt0) cc_final: 0.6503 (tt0) REVERT: C 404 MET cc_start: 0.7547 (tpp) cc_final: 0.7306 (tpp) REVERT: D 296 ARG cc_start: 0.6590 (mtt180) cc_final: 0.5734 (mpp80) REVERT: G 287 GLN cc_start: 0.7720 (mm110) cc_final: 0.7518 (mm110) REVERT: G 432 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: G 472 CYS cc_start: 0.6733 (OUTLIER) cc_final: 0.6517 (t) outliers start: 38 outliers final: 31 residues processed: 125 average time/residue: 0.0909 time to fit residues: 15.4327 Evaluate side-chains 122 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 453 SER Chi-restraints excluded: chain G residue 472 CYS Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 298 HIS Chi-restraints excluded: chain E residue 359 TYR Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 476 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 399 HIS ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.153070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.117280 restraints weight = 10859.480| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.94 r_work: 0.3390 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7967 Z= 0.155 Angle : 0.646 12.173 10793 Z= 0.331 Chirality : 0.044 0.133 1148 Planarity : 0.005 0.048 1405 Dihedral : 5.387 45.463 1066 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.97 % Favored : 94.60 % Rotamer: Outliers : 4.24 % Allowed : 27.80 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.27), residues: 945 helix: 1.70 (0.38), residues: 162 sheet: -0.48 (0.36), residues: 202 loop : -1.00 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 291 TYR 0.022 0.002 TYR G 359 PHE 0.015 0.002 PHE E 314 TRP 0.010 0.001 TRP G 360 HIS 0.005 0.001 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 7967) covalent geometry : angle 0.64586 / 0.33 (10793) hydrogen bonds : bond 0.04076 / 2.67 ( 300) hydrogen bonds : angle 5.14860 / 3.66 ( 855) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: C 269 MET cc_start: 0.8155 (ppp) cc_final: 0.7337 (mmt) REVERT: C 374 ASP cc_start: 0.7563 (p0) cc_final: 0.7098 (p0) REVERT: C 388 GLN cc_start: 0.6850 (tt0) cc_final: 0.6530 (tt0) REVERT: C 404 MET cc_start: 0.7699 (tpp) cc_final: 0.7481 (tpp) REVERT: G 432 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7207 (m-30) REVERT: E 259 ARG cc_start: 0.8426 (mmm160) cc_final: 0.8043 (mmm160) outliers start: 36 outliers final: 31 residues processed: 119 average time/residue: 0.0860 time to fit residues: 13.9063 Evaluate side-chains 119 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 ILE Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 453 SER Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 298 HIS Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain E residue 359 TYR Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 476 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 79 optimal weight: 0.0170 chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 0.0170 chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 0.0470 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 399 HIS ** G 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.156609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.114974 restraints weight = 10745.991| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.32 r_work: 0.3445 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7967 Z= 0.114 Angle : 0.634 12.061 10793 Z= 0.325 Chirality : 0.044 0.167 1148 Planarity : 0.005 0.048 1405 Dihedral : 5.171 44.536 1066 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.60 % Favored : 95.98 % Rotamer: Outliers : 3.53 % Allowed : 28.03 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.27), residues: 945 helix: 1.47 (0.39), residues: 168 sheet: -0.55 (0.35), residues: 218 loop : -0.90 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 291 TYR 0.010 0.001 TYR E 359 PHE 0.015 0.001 PHE E 314 TRP 0.013 0.001 TRP G 394 HIS 0.004 0.001 HIS G 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 7967) covalent geometry : angle 0.63382 / 0.32 (10793) hydrogen bonds : bond 0.03668 / 2.44 ( 300) hydrogen bonds : angle 4.94647 / 3.53 ( 855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2510.72 seconds wall clock time: 43 minutes 39.08 seconds (2619.08 seconds total)