Starting phenix.real_space_refine on Mon Nov 17 15:37:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ip7_60764/11_2025/9ip7_60764.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ip7_60764/11_2025/9ip7_60764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ip7_60764/11_2025/9ip7_60764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ip7_60764/11_2025/9ip7_60764.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ip7_60764/11_2025/9ip7_60764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ip7_60764/11_2025/9ip7_60764.map" } resolution = 3.21 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 3634 2.51 5 N 1002 2.21 5 O 1118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5809 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3938 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 23, 'TRANS': 484} Chain breaks: 7 Chain: "D" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 13, 'TRANS': 216} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.32, per 1000 atoms: 0.23 Number of scatterers: 5809 At special positions: 0 Unit cell: (67.768, 110.32, 123.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1118 8.00 N 1002 7.00 C 3634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 34 " distance=2.02 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 531 " distance=2.04 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 223 " distance=2.03 Simple disulfide: pdb=" SG CYS D 289 " - pdb=" SG CYS D 363 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 701 " - " ASN A 337 " " NAG A 702 " - " ASN A 504 " " NAG B 1 " - " ASN A 328 " " NAG C 1 " - " ASN A 420 " Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 308.1 milliseconds 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 15 sheets defined 8.5% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 Processing helix chain 'A' and resid 318 through 322 removed outlier: 4.249A pdb=" N PHE A 321 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 removed outlier: 3.759A pdb=" N PHE A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.547A pdb=" N ASP A 369 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 407 through 410 Processing helix chain 'A' and resid 471 through 478 Processing helix chain 'D' and resid 295 through 299 removed outlier: 3.755A pdb=" N TYR D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 354 through 358 removed outlier: 4.012A pdb=" N THR D 358 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 247 Processing sheet with id=AA4, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 294 Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA7, first strand: chain 'A' and resid 346 through 347 removed outlier: 7.681A pdb=" N LEU A 381 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 524 through 526 Processing sheet with id=AA9, first strand: chain 'A' and resid 562 through 563 Processing sheet with id=AB1, first strand: chain 'D' and resid 134 through 136 Processing sheet with id=AB2, first strand: chain 'D' and resid 180 through 183 removed outlier: 6.524A pdb=" N TRP D 170 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 270 through 273 removed outlier: 3.505A pdb=" N SER D 292 " --> pdb=" O GLN D 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 277 through 279 removed outlier: 3.656A pdb=" N ALA D 359 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AB6, first strand: chain 'D' and resid 304 through 306 91 hydrogen bonds defined for protein. 189 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: 0.76 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 971 1.32 - 1.44: 1563 1.44 - 1.57: 3321 1.57 - 1.69: 0 1.69 - 1.82: 70 Bond restraints: 5925 Sorted by residual: bond pdb=" N GLY A 315 " pdb=" CA GLY A 315 " ideal model delta sigma weight residual 1.444 1.481 -0.037 9.60e-03 1.09e+04 1.45e+01 bond pdb=" N VAL A 284 " pdb=" CA VAL A 284 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.14e-02 7.69e+03 1.29e+01 bond pdb=" N ILE A 316 " pdb=" CA ILE A 316 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.10e-02 8.26e+03 1.24e+01 bond pdb=" N ILE A 401 " pdb=" CA ILE A 401 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.14e-02 7.69e+03 1.22e+01 bond pdb=" N VAL A 97 " pdb=" CA VAL A 97 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.23e-02 6.61e+03 1.16e+01 ... (remaining 5920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 7138 1.82 - 3.63: 762 3.63 - 5.45: 101 5.45 - 7.26: 7 7.26 - 9.08: 2 Bond angle restraints: 8010 Sorted by residual: angle pdb=" N GLY A 281 " pdb=" CA GLY A 281 " pdb=" C GLY A 281 " ideal model delta sigma weight residual 115.27 108.60 6.67 1.41e+00 5.03e-01 2.24e+01 angle pdb=" N HIS A 334 " pdb=" CA HIS A 334 " pdb=" C HIS A 334 " ideal model delta sigma weight residual 112.38 106.87 5.51 1.22e+00 6.72e-01 2.04e+01 angle pdb=" CA GLY A 520 " pdb=" C GLY A 520 " pdb=" O GLY A 520 " ideal model delta sigma weight residual 122.14 117.67 4.47 1.05e+00 9.07e-01 1.81e+01 angle pdb=" CA GLY A 490 " pdb=" C GLY A 490 " pdb=" O GLY A 490 " ideal model delta sigma weight residual 121.76 118.07 3.69 8.70e-01 1.32e+00 1.80e+01 angle pdb=" CA ILE A 451 " pdb=" C ILE A 451 " pdb=" O ILE A 451 " ideal model delta sigma weight residual 121.58 117.54 4.04 1.00e+00 1.00e+00 1.64e+01 ... (remaining 8005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3133 17.80 - 35.60: 403 35.60 - 53.40: 105 53.40 - 71.19: 39 71.19 - 88.99: 9 Dihedral angle restraints: 3689 sinusoidal: 1583 harmonic: 2106 Sorted by residual: dihedral pdb=" CB CYS A 271 " pdb=" SG CYS A 271 " pdb=" SG CYS A 283 " pdb=" CB CYS A 283 " ideal model delta sinusoidal sigma weight residual 93.00 -178.01 -88.99 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS A 7 " pdb=" SG CYS A 7 " pdb=" SG CYS A 34 " pdb=" CB CYS A 34 " ideal model delta sinusoidal sigma weight residual 93.00 161.99 -68.99 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS A 515 " pdb=" SG CYS A 515 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual -86.00 -146.53 60.53 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 3686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 731 0.093 - 0.186: 153 0.186 - 0.280: 11 0.280 - 0.373: 0 0.373 - 0.466: 1 Chirality restraints: 896 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.05e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA ILE A 119 " pdb=" N ILE A 119 " pdb=" C ILE A 119 " pdb=" CB ILE A 119 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 893 not shown) Planarity restraints: 1033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.274 2.00e-02 2.50e+03 2.30e-01 6.61e+02 pdb=" C7 NAG C 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.390 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.192 2.00e-02 2.50e+03 1.60e-01 3.21e+02 pdb=" C7 NAG C 1 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.138 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.264 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 315 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C MET D 315 " -0.046 2.00e-02 2.50e+03 pdb=" O MET D 315 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY D 316 " 0.016 2.00e-02 2.50e+03 ... (remaining 1030 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 809 2.76 - 3.29: 5899 3.29 - 3.83: 9957 3.83 - 4.36: 12373 4.36 - 4.90: 19970 Nonbonded interactions: 49008 Sorted by model distance: nonbonded pdb=" O CYS A 287 " pdb=" OG SER A 291 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP A 232 " pdb=" N GLU A 233 " model vdw 2.237 3.120 nonbonded pdb=" N ARG A 231 " pdb=" O ALA A 265 " model vdw 2.275 3.120 nonbonded pdb=" O SER A 529 " pdb=" OG SER A 529 " model vdw 2.304 3.040 nonbonded pdb=" O CYS A 313 " pdb=" N SER A 342 " model vdw 2.318 3.120 ... (remaining 49003 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 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.770 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.680 Find NCS groups from input model: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 : 0.008 0.046 5949 Z= 0.611 Angle : 1.112 10.596 8064 Z= 0.761 Chirality : 0.070 0.466 896 Planarity : 0.011 0.230 1029 Dihedral : 17.204 87.035 2283 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 3.12 % Allowed : 31.67 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.24 (0.31), residues: 718 helix: -1.05 (1.10), residues: 22 sheet: -2.72 (0.45), residues: 106 loop : -1.37 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 228 TYR 0.017 0.002 TYR D 184 PHE 0.018 0.002 PHE D 371 TRP 0.018 0.003 TRP D 375 HIS 0.005 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00838 ( 5925) covalent geometry : angle 1.09654 ( 8010) SS BOND : bond 0.00396 ( 18) SS BOND : angle 0.98439 ( 36) hydrogen bonds : bond 0.24809 ( 91) hydrogen bonds : angle 11.76019 ( 189) link_BETA1-4 : bond 0.03266 ( 2) link_BETA1-4 : angle 4.59508 ( 6) link_NAG-ASN : bond 0.00844 ( 4) link_NAG-ASN : angle 3.85896 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.7976 (t80) cc_final: 0.7642 (t80) REVERT: A 152 MET cc_start: 0.7168 (pmm) cc_final: 0.6669 (pmm) REVERT: A 272 PRO cc_start: 0.7841 (OUTLIER) cc_final: 0.7631 (Cg_exo) REVERT: A 275 TYR cc_start: 0.4616 (m-10) cc_final: 0.4180 (m-10) REVERT: D 299 TYR cc_start: 0.7764 (m-80) cc_final: 0.7423 (m-80) outliers start: 20 outliers final: 6 residues processed: 114 average time/residue: 0.0982 time to fit residues: 14.0239 Evaluate side-chains 87 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 272 PRO Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 524 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.0370 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.227806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.173276 restraints weight = 7571.926| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 2.80 r_work: 0.4118 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5949 Z= 0.137 Angle : 0.648 9.364 8064 Z= 0.315 Chirality : 0.049 0.426 896 Planarity : 0.004 0.042 1029 Dihedral : 6.385 44.267 929 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 5.15 % Allowed : 29.95 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.90 (0.31), residues: 718 helix: 0.74 (1.25), residues: 16 sheet: -2.40 (0.46), residues: 110 loop : -1.17 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 154 TYR 0.020 0.002 TYR D 184 PHE 0.017 0.002 PHE D 371 TRP 0.012 0.002 TRP D 375 HIS 0.007 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5925) covalent geometry : angle 0.62653 ( 8010) SS BOND : bond 0.00359 ( 18) SS BOND : angle 1.77802 ( 36) hydrogen bonds : bond 0.03996 ( 91) hydrogen bonds : angle 8.06261 ( 189) link_BETA1-4 : bond 0.00166 ( 2) link_BETA1-4 : angle 1.83291 ( 6) link_NAG-ASN : bond 0.00586 ( 4) link_NAG-ASN : angle 3.01872 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.5663 (p90) cc_final: 0.5447 (p90) REVERT: A 67 ILE cc_start: 0.5123 (OUTLIER) cc_final: 0.4882 (tp) REVERT: A 126 PHE cc_start: 0.8114 (t80) cc_final: 0.7837 (t80) REVERT: A 128 ASN cc_start: 0.8501 (t0) cc_final: 0.8005 (t0) REVERT: A 275 TYR cc_start: 0.3649 (m-10) cc_final: 0.3441 (m-10) REVERT: A 294 MET cc_start: 0.5440 (tmm) cc_final: 0.4377 (tmm) REVERT: A 300 ARG cc_start: 0.5635 (tpp80) cc_final: 0.5412 (tpp80) REVERT: A 306 GLU cc_start: 0.5620 (OUTLIER) cc_final: 0.5287 (mm-30) REVERT: D 301 MET cc_start: 0.8082 (tpp) cc_final: 0.7879 (tpt) outliers start: 33 outliers final: 14 residues processed: 116 average time/residue: 0.0978 time to fit residues: 14.3693 Evaluate side-chains 93 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 355 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.0170 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.240920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.197745 restraints weight = 7454.412| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 3.64 r_work: 0.4218 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5949 Z= 0.146 Angle : 0.618 10.092 8064 Z= 0.304 Chirality : 0.048 0.353 896 Planarity : 0.004 0.043 1029 Dihedral : 6.132 42.620 919 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 4.52 % Allowed : 29.95 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.91 (0.31), residues: 718 helix: 0.76 (1.24), residues: 17 sheet: -2.34 (0.45), residues: 120 loop : -1.16 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 196 TYR 0.013 0.001 TYR D 347 PHE 0.016 0.002 PHE D 371 TRP 0.012 0.002 TRP D 375 HIS 0.004 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5925) covalent geometry : angle 0.60331 ( 8010) SS BOND : bond 0.00395 ( 18) SS BOND : angle 1.16536 ( 36) hydrogen bonds : bond 0.03076 ( 91) hydrogen bonds : angle 7.17714 ( 189) link_BETA1-4 : bond 0.00226 ( 2) link_BETA1-4 : angle 2.01295 ( 6) link_NAG-ASN : bond 0.00469 ( 4) link_NAG-ASN : angle 2.70169 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.5179 (t) cc_final: 0.4959 (t) REVERT: A 67 ILE cc_start: 0.5414 (OUTLIER) cc_final: 0.4991 (tp) REVERT: A 126 PHE cc_start: 0.8098 (t80) cc_final: 0.7613 (t80) REVERT: A 211 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7026 (mp10) REVERT: A 294 MET cc_start: 0.5452 (tmm) cc_final: 0.4526 (tmm) REVERT: A 300 ARG cc_start: 0.5671 (tpp80) cc_final: 0.5469 (tpp80) REVERT: A 306 GLU cc_start: 0.5747 (OUTLIER) cc_final: 0.5291 (mm-30) REVERT: A 485 LEU cc_start: 0.6931 (tp) cc_final: 0.6596 (pp) outliers start: 29 outliers final: 16 residues processed: 109 average time/residue: 0.0926 time to fit residues: 12.9027 Evaluate side-chains 96 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 355 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.232285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.190311 restraints weight = 7397.256| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 3.48 r_work: 0.4169 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5949 Z= 0.204 Angle : 0.642 9.118 8064 Z= 0.314 Chirality : 0.048 0.313 896 Planarity : 0.004 0.041 1029 Dihedral : 6.007 44.075 917 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 5.46 % Allowed : 30.73 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.90 (0.31), residues: 718 helix: 1.04 (1.26), residues: 17 sheet: -2.54 (0.50), residues: 98 loop : -1.19 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.021 0.002 TYR D 184 PHE 0.016 0.002 PHE D 224 TRP 0.014 0.002 TRP D 300 HIS 0.007 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 5925) covalent geometry : angle 0.62917 ( 8010) SS BOND : bond 0.00474 ( 18) SS BOND : angle 1.20930 ( 36) hydrogen bonds : bond 0.02939 ( 91) hydrogen bonds : angle 6.90468 ( 189) link_BETA1-4 : bond 0.00326 ( 2) link_BETA1-4 : angle 1.87878 ( 6) link_NAG-ASN : bond 0.00293 ( 4) link_NAG-ASN : angle 2.61212 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8100 (t80) cc_final: 0.7520 (t80) REVERT: A 287 CYS cc_start: 0.5131 (OUTLIER) cc_final: 0.4403 (t) REVERT: A 294 MET cc_start: 0.5486 (tmm) cc_final: 0.4835 (tmm) REVERT: A 306 GLU cc_start: 0.5726 (OUTLIER) cc_final: 0.5292 (mm-30) REVERT: A 485 LEU cc_start: 0.7151 (tp) cc_final: 0.6770 (pp) outliers start: 35 outliers final: 20 residues processed: 106 average time/residue: 0.0958 time to fit residues: 12.9607 Evaluate side-chains 95 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 355 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.237393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.190435 restraints weight = 7603.675| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 2.77 r_work: 0.4229 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5949 Z= 0.187 Angle : 0.647 12.394 8064 Z= 0.312 Chirality : 0.048 0.306 896 Planarity : 0.004 0.043 1029 Dihedral : 5.999 44.123 917 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 5.15 % Allowed : 31.67 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.96 (0.31), residues: 718 helix: 1.30 (1.28), residues: 17 sheet: -2.47 (0.48), residues: 108 loop : -1.24 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 196 TYR 0.020 0.002 TYR D 184 PHE 0.015 0.002 PHE D 224 TRP 0.015 0.002 TRP D 300 HIS 0.007 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 5925) covalent geometry : angle 0.63495 ( 8010) SS BOND : bond 0.00339 ( 18) SS BOND : angle 1.12131 ( 36) hydrogen bonds : bond 0.02766 ( 91) hydrogen bonds : angle 6.68357 ( 189) link_BETA1-4 : bond 0.00285 ( 2) link_BETA1-4 : angle 1.87423 ( 6) link_NAG-ASN : bond 0.00377 ( 4) link_NAG-ASN : angle 2.60178 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.4492 (OUTLIER) cc_final: 0.4270 (mm) REVERT: A 294 MET cc_start: 0.5535 (tmm) cc_final: 0.4983 (tmm) REVERT: A 306 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.5346 (mm-30) REVERT: D 358 THR cc_start: 0.7592 (OUTLIER) cc_final: 0.7181 (t) outliers start: 33 outliers final: 20 residues processed: 103 average time/residue: 0.0861 time to fit residues: 11.4548 Evaluate side-chains 98 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 358 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 25 optimal weight: 0.0000 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 HIS ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.236682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.183707 restraints weight = 7546.230| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 2.60 r_work: 0.4222 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5949 Z= 0.181 Angle : 0.644 9.479 8064 Z= 0.312 Chirality : 0.048 0.292 896 Planarity : 0.005 0.041 1029 Dihedral : 5.997 44.106 917 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 6.24 % Allowed : 30.73 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.98 (0.31), residues: 718 helix: 1.40 (1.28), residues: 17 sheet: -2.64 (0.48), residues: 98 loop : -1.26 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 228 TYR 0.020 0.002 TYR D 184 PHE 0.016 0.002 PHE D 224 TRP 0.038 0.002 TRP A 140 HIS 0.005 0.001 HIS D 302 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 5925) covalent geometry : angle 0.63256 ( 8010) SS BOND : bond 0.00332 ( 18) SS BOND : angle 1.06377 ( 36) hydrogen bonds : bond 0.02701 ( 91) hydrogen bonds : angle 6.56743 ( 189) link_BETA1-4 : bond 0.00265 ( 2) link_BETA1-4 : angle 1.79019 ( 6) link_NAG-ASN : bond 0.00384 ( 4) link_NAG-ASN : angle 2.52724 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 75 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.4519 (OUTLIER) cc_final: 0.4290 (mm) REVERT: A 69 LEU cc_start: 0.3850 (OUTLIER) cc_final: 0.3539 (pp) REVERT: A 126 PHE cc_start: 0.8140 (t80) cc_final: 0.7556 (t80) REVERT: A 287 CYS cc_start: 0.5196 (OUTLIER) cc_final: 0.4416 (t) REVERT: A 294 MET cc_start: 0.5558 (tmm) cc_final: 0.4706 (tmm) REVERT: A 300 ARG cc_start: 0.5805 (tpp80) cc_final: 0.5566 (tpp80) REVERT: A 306 GLU cc_start: 0.5703 (OUTLIER) cc_final: 0.5334 (mm-30) REVERT: A 485 LEU cc_start: 0.7066 (tp) cc_final: 0.6688 (pp) REVERT: D 301 MET cc_start: 0.7979 (tpt) cc_final: 0.7724 (tpt) outliers start: 40 outliers final: 24 residues processed: 111 average time/residue: 0.0833 time to fit residues: 12.0074 Evaluate side-chains 103 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 355 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN D 180 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.237110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.189743 restraints weight = 7539.313| |-----------------------------------------------------------------------------| r_work (start): 0.4512 rms_B_bonded: 2.86 r_work: 0.4230 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5949 Z= 0.151 Angle : 0.624 9.084 8064 Z= 0.301 Chirality : 0.047 0.288 896 Planarity : 0.004 0.041 1029 Dihedral : 5.876 43.127 917 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 5.46 % Allowed : 31.51 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.95 (0.31), residues: 718 helix: 1.50 (1.29), residues: 17 sheet: -2.66 (0.48), residues: 98 loop : -1.23 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 228 TYR 0.022 0.002 TYR D 184 PHE 0.016 0.002 PHE D 224 TRP 0.023 0.002 TRP A 140 HIS 0.004 0.001 HIS D 302 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 5925) covalent geometry : angle 0.61338 ( 8010) SS BOND : bond 0.00278 ( 18) SS BOND : angle 0.94683 ( 36) hydrogen bonds : bond 0.02591 ( 91) hydrogen bonds : angle 6.37830 ( 189) link_BETA1-4 : bond 0.00193 ( 2) link_BETA1-4 : angle 1.89760 ( 6) link_NAG-ASN : bond 0.00455 ( 4) link_NAG-ASN : angle 2.46490 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.4510 (OUTLIER) cc_final: 0.4278 (mm) REVERT: A 69 LEU cc_start: 0.3831 (OUTLIER) cc_final: 0.3571 (pp) REVERT: A 126 PHE cc_start: 0.8166 (t80) cc_final: 0.7871 (t80) REVERT: A 287 CYS cc_start: 0.5179 (OUTLIER) cc_final: 0.4366 (t) REVERT: A 294 MET cc_start: 0.5534 (tmm) cc_final: 0.4921 (tmm) REVERT: A 306 GLU cc_start: 0.5694 (OUTLIER) cc_final: 0.5326 (mm-30) REVERT: A 485 LEU cc_start: 0.7148 (tp) cc_final: 0.6844 (pp) outliers start: 35 outliers final: 24 residues processed: 108 average time/residue: 0.0788 time to fit residues: 11.1294 Evaluate side-chains 102 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 318 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.2980 chunk 55 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.238135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.196295 restraints weight = 7491.820| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 3.73 r_work: 0.4178 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5949 Z= 0.125 Angle : 0.612 8.903 8064 Z= 0.297 Chirality : 0.047 0.290 896 Planarity : 0.004 0.045 1029 Dihedral : 5.761 42.147 917 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 4.52 % Allowed : 32.29 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.95 (0.31), residues: 718 helix: 1.42 (1.28), residues: 17 sheet: -2.69 (0.48), residues: 98 loop : -1.22 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 196 TYR 0.017 0.002 TYR D 184 PHE 0.016 0.001 PHE D 224 TRP 0.018 0.001 TRP A 140 HIS 0.004 0.001 HIS D 302 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5925) covalent geometry : angle 0.60068 ( 8010) SS BOND : bond 0.00274 ( 18) SS BOND : angle 1.05306 ( 36) hydrogen bonds : bond 0.02658 ( 91) hydrogen bonds : angle 6.38935 ( 189) link_BETA1-4 : bond 0.00220 ( 2) link_BETA1-4 : angle 1.89836 ( 6) link_NAG-ASN : bond 0.00524 ( 4) link_NAG-ASN : angle 2.43278 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.4552 (OUTLIER) cc_final: 0.4330 (mm) REVERT: A 69 LEU cc_start: 0.4101 (OUTLIER) cc_final: 0.3791 (pp) REVERT: A 126 PHE cc_start: 0.8149 (t80) cc_final: 0.7802 (t80) REVERT: A 287 CYS cc_start: 0.5195 (OUTLIER) cc_final: 0.4386 (t) REVERT: A 294 MET cc_start: 0.5617 (tmm) cc_final: 0.4995 (tmm) REVERT: A 306 GLU cc_start: 0.5820 (OUTLIER) cc_final: 0.5325 (mm-30) REVERT: A 485 LEU cc_start: 0.7108 (tp) cc_final: 0.6809 (pp) outliers start: 29 outliers final: 22 residues processed: 101 average time/residue: 0.0821 time to fit residues: 10.8515 Evaluate side-chains 96 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 318 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 15 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 37 optimal weight: 0.0470 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.240233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.198197 restraints weight = 7612.045| |-----------------------------------------------------------------------------| r_work (start): 0.4585 rms_B_bonded: 3.56 r_work: 0.4207 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5949 Z= 0.107 Angle : 0.597 9.224 8064 Z= 0.290 Chirality : 0.047 0.294 896 Planarity : 0.005 0.072 1029 Dihedral : 5.564 40.641 917 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 4.68 % Allowed : 31.83 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.93 (0.31), residues: 718 helix: 1.84 (1.28), residues: 18 sheet: -2.66 (0.45), residues: 108 loop : -1.19 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 228 TYR 0.016 0.001 TYR D 299 PHE 0.018 0.001 PHE D 224 TRP 0.016 0.001 TRP A 140 HIS 0.003 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5925) covalent geometry : angle 0.58669 ( 8010) SS BOND : bond 0.00204 ( 18) SS BOND : angle 0.91493 ( 36) hydrogen bonds : bond 0.02527 ( 91) hydrogen bonds : angle 6.16867 ( 189) link_BETA1-4 : bond 0.00221 ( 2) link_BETA1-4 : angle 1.87496 ( 6) link_NAG-ASN : bond 0.00535 ( 4) link_NAG-ASN : angle 2.39224 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.4357 (OUTLIER) cc_final: 0.3987 (mm) REVERT: A 69 LEU cc_start: 0.3883 (OUTLIER) cc_final: 0.3531 (pp) REVERT: A 126 PHE cc_start: 0.8125 (t80) cc_final: 0.7713 (t80) REVERT: A 287 CYS cc_start: 0.5101 (OUTLIER) cc_final: 0.4337 (t) REVERT: A 294 MET cc_start: 0.5539 (tmm) cc_final: 0.5101 (tmm) REVERT: A 306 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5265 (mm-30) REVERT: A 485 LEU cc_start: 0.7128 (tp) cc_final: 0.6830 (pp) outliers start: 30 outliers final: 21 residues processed: 103 average time/residue: 0.0903 time to fit residues: 12.0200 Evaluate side-chains 98 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 357 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 71 optimal weight: 0.0170 chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 54 optimal weight: 0.0670 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.4916 r_free = 0.4916 target = 0.237076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.189800 restraints weight = 7679.017| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 2.83 r_work: 0.4244 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5949 Z= 0.162 Angle : 0.632 9.086 8064 Z= 0.308 Chirality : 0.048 0.291 896 Planarity : 0.005 0.063 1029 Dihedral : 5.809 42.956 917 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 4.06 % Allowed : 32.76 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.99 (0.31), residues: 718 helix: 2.02 (1.28), residues: 18 sheet: -2.62 (0.44), residues: 118 loop : -1.23 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 196 TYR 0.018 0.002 TYR D 362 PHE 0.016 0.001 PHE D 224 TRP 0.017 0.002 TRP A 140 HIS 0.006 0.001 HIS D 302 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 5925) covalent geometry : angle 0.62101 ( 8010) SS BOND : bond 0.00313 ( 18) SS BOND : angle 1.03673 ( 36) hydrogen bonds : bond 0.02605 ( 91) hydrogen bonds : angle 6.19008 ( 189) link_BETA1-4 : bond 0.00162 ( 2) link_BETA1-4 : angle 1.87904 ( 6) link_NAG-ASN : bond 0.00350 ( 4) link_NAG-ASN : angle 2.38439 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.4448 (OUTLIER) cc_final: 0.4201 (mm) REVERT: A 126 PHE cc_start: 0.8105 (t80) cc_final: 0.7693 (t80) REVERT: A 176 TRP cc_start: 0.7580 (OUTLIER) cc_final: 0.6088 (t60) REVERT: A 287 CYS cc_start: 0.5176 (OUTLIER) cc_final: 0.4400 (t) REVERT: A 294 MET cc_start: 0.5565 (tmm) cc_final: 0.4917 (tmm) REVERT: A 306 GLU cc_start: 0.5684 (OUTLIER) cc_final: 0.5339 (mm-30) REVERT: A 485 LEU cc_start: 0.7220 (tp) cc_final: 0.6877 (pp) outliers start: 26 outliers final: 18 residues processed: 97 average time/residue: 0.0914 time to fit residues: 11.3289 Evaluate side-chains 91 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 357 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4899 r_free = 0.4899 target = 0.235183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.182390 restraints weight = 7501.827| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 2.60 r_work: 0.4235 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5949 Z= 0.190 Angle : 0.659 9.557 8064 Z= 0.322 Chirality : 0.049 0.284 896 Planarity : 0.005 0.057 1029 Dihedral : 5.988 43.491 917 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 4.21 % Allowed : 32.61 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.10 (0.31), residues: 718 helix: 2.25 (1.33), residues: 18 sheet: -2.84 (0.41), residues: 129 loop : -1.23 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 228 TYR 0.023 0.002 TYR D 362 PHE 0.018 0.002 PHE D 224 TRP 0.017 0.002 TRP A 140 HIS 0.006 0.001 HIS D 302 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 5925) covalent geometry : angle 0.64789 ( 8010) SS BOND : bond 0.00370 ( 18) SS BOND : angle 1.12568 ( 36) hydrogen bonds : bond 0.02603 ( 91) hydrogen bonds : angle 6.21345 ( 189) link_BETA1-4 : bond 0.00242 ( 2) link_BETA1-4 : angle 1.85877 ( 6) link_NAG-ASN : bond 0.00327 ( 4) link_NAG-ASN : angle 2.39894 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1869.51 seconds wall clock time: 32 minutes 45.70 seconds (1965.70 seconds total)