Starting phenix.real_space_refine on Tue Aug 4 14:32:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13bd_76936/08_2026/13bd_76936.cif Found real_map, /net/cci-nas-00/data/ceres_data/13bd_76936/08_2026/13bd_76936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/13bd_76936/08_2026/13bd_76936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13bd_76936/08_2026/13bd_76936.map" model { file = "/net/cci-nas-00/data/ceres_data/13bd_76936/08_2026/13bd_76936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13bd_76936/08_2026/13bd_76936.cif" } resolution = 2.65 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= 0.014 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 13 5.16 5 C 2478 2.51 5 N 617 2.21 5 O 717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3825 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1873 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 11, 'TRANS': 220} Chain breaks: 4 Chain: "A" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1840 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 14, 'TRANS': 214} 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.80, per 1000 atoms: 0.21 Number of scatterers: 3825 At special positions: 0 Unit cell: (88.192, 81.536, 89.024, 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 13 16.00 O 717 8.00 N 617 7.00 C 2478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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-ASN " NAG A1301 " - " ASN A 343 " " NAG B 1 " - " ASN C 165 " " NAG C1301 " - " ASN C 281 " " NAG C1302 " - " ASN C 233 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 122 " " NAG C1305 " - " ASN C 99 " Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 78.1 milliseconds 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 868 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 8 sheets defined 9.5% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.063A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.697A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.638A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.634A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.916A pdb=" N ASN C 61 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR C 268 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER C 205 " --> pdb=" O PRO C 224 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N HIS C 207 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N LEU C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL C 36 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.043A pdb=" N ASP C 286 " --> pdb=" O LYS C 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.821A pdb=" N GLY C 103 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 328 Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.366A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 132 hydrogen bonds defined for protein. 327 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: 0.50 Time building geometry restraints manager: 0.27 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: 1157 1.34 - 1.46: 1009 1.46 - 1.58: 1752 1.58 - 1.70: 0 1.70 - 1.82: 13 Bond restraints: 3931 Sorted by residual: bond pdb=" N ILE C 284 " pdb=" CA ILE C 284 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.17e-02 7.31e+03 9.45e+00 bond pdb=" N THR C 283 " pdb=" CA THR C 283 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.30e-02 5.92e+03 8.05e+00 bond pdb=" N ILE A 410 " pdb=" CA ILE A 410 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.15e+00 bond pdb=" CB GLU A 340 " pdb=" CG GLU A 340 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CB VAL C 126 " pdb=" CG2 VAL C 126 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 ... (remaining 3926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 5029 1.21 - 2.42: 249 2.42 - 3.63: 44 3.63 - 4.84: 19 4.84 - 6.05: 3 Bond angle restraints: 5344 Sorted by residual: angle pdb=" N SER A 366 " pdb=" CA SER A 366 " pdb=" C SER A 366 " ideal model delta sigma weight residual 114.31 109.55 4.76 1.29e+00 6.01e-01 1.36e+01 angle pdb=" N ASP A 446 " pdb=" CA ASP A 446 " pdb=" C ASP A 446 " ideal model delta sigma weight residual 114.16 109.63 4.53 1.48e+00 4.57e-01 9.36e+00 angle pdb=" N ASN C 125 " pdb=" CA ASN C 125 " pdb=" C ASN C 125 " ideal model delta sigma weight residual 108.52 112.92 -4.40 1.52e+00 4.33e-01 8.36e+00 angle pdb=" N THR A 523 " pdb=" CA THR A 523 " pdb=" C THR A 523 " ideal model delta sigma weight residual 114.31 110.67 3.64 1.29e+00 6.01e-01 7.95e+00 angle pdb=" CG ARG C 158 " pdb=" CD ARG C 158 " pdb=" NE ARG C 158 " ideal model delta sigma weight residual 112.00 118.05 -6.05 2.20e+00 2.07e-01 7.57e+00 ... (remaining 5339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2144 17.99 - 35.98: 208 35.98 - 53.97: 38 53.97 - 71.96: 7 71.96 - 89.95: 2 Dihedral angle restraints: 2399 sinusoidal: 1048 harmonic: 1351 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 127.40 -34.40 1 1.00e+01 1.00e-02 1.68e+01 dihedral pdb=" CA VAL A 539 " pdb=" C VAL A 539 " pdb=" N ASN A 540 " pdb=" CA ASN A 540 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA THR C 283 " pdb=" C THR C 283 " pdb=" N ILE C 284 " pdb=" CA ILE C 284 " ideal model delta harmonic sigma weight residual 180.00 162.77 17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 2396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 372 0.038 - 0.076: 158 0.076 - 0.113: 57 0.113 - 0.151: 13 0.151 - 0.189: 3 Chirality restraints: 603 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 233 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.02e-01 ... (remaining 600 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 282 " -0.010 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C GLY C 282 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY C 282 " -0.012 2.00e-02 2.50e+03 pdb=" N THR C 283 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 209 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO A 521 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.020 5.00e-02 4.00e+02 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 2176 3.03 - 3.49: 3153 3.49 - 3.96: 5836 3.96 - 4.43: 6909 4.43 - 4.90: 11583 Nonbonded interactions: 29657 Sorted by model distance: nonbonded pdb=" O THR A 470 " pdb=" OG1 THR A 470 " model vdw 2.557 3.040 nonbonded pdb=" N GLU A 340 " pdb=" OE1 GLU A 340 " model vdw 2.577 3.120 nonbonded pdb=" N ASP A 446 " pdb=" N GLY A 447 " model vdw 2.613 2.560 nonbonded pdb=" N ASP C 293 " pdb=" O ASP C 293 " model vdw 2.626 2.496 nonbonded pdb=" N ASN C 122 " pdb=" O ASN C 122 " model vdw 2.634 2.496 ... (remaining 29652 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.380 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.610 Find NCS groups from input model: 0.020 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:8.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 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 0.037 3944 Z= 0.179 Angle : 0.698 11.557 5378 Z= 0.391 Chirality : 0.049 0.189 603 Planarity : 0.005 0.042 673 Dihedral : 14.066 89.951 1516 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.97 % Allowed : 15.25 % Favored : 83.78 % 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: -0.96 (0.39), residues: 447 helix: -2.84 (0.57), residues: 45 sheet: 1.32 (0.44), residues: 148 loop : -1.51 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 158 TYR 0.016 0.001 TYR A 396 PHE 0.012 0.001 PHE C 133 TRP 0.010 0.001 TRP C 64 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 ( 3931) covalent geometry : angle 0.65616 / 0.38 ( 5344) SS BOND : bond 0.00264 / 0.16 ( 5) SS BOND : angle 0.73023 / 0.53 ( 10) hydrogen bonds : bond 0.11889 / 8.17 ( 132) hydrogen bonds : angle 6.75319 / 4.69 ( 327) link_BETA1-4 : bond 0.00136 / 0.09 ( 1) link_BETA1-4 : angle 1.11278 / 0.86 ( 3) link_NAG-ASN : bond 0.00431 / 0.23 ( 7) link_NAG-ASN : angle 3.86060 / 3.07 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.091 Fit side-chains REVERT: A 340 GLU cc_start: 0.8400 (mp0) cc_final: 0.8055 (mp0) REVERT: A 474 GLN cc_start: 0.7301 (pt0) cc_final: 0.6586 (pp30) REVERT: A 489 TYR cc_start: 0.8255 (m-80) cc_final: 0.7996 (m-80) REVERT: A 498 ARG cc_start: 0.8533 (tpp80) cc_final: 0.8265 (mmt-90) outliers start: 4 outliers final: 1 residues processed: 44 average time/residue: 0.5499 time to fit residues: 24.8393 Evaluate side-chains 41 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.097989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.074470 restraints weight = 6857.007| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.08 r_work: 0.2844 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.0642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3944 Z= 0.132 Angle : 0.582 11.177 5378 Z= 0.295 Chirality : 0.048 0.189 603 Planarity : 0.004 0.037 673 Dihedral : 6.393 59.611 673 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.94 % Allowed : 15.25 % Favored : 82.81 % 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: -0.82 (0.39), residues: 447 helix: -2.63 (0.59), residues: 45 sheet: 1.40 (0.43), residues: 147 loop : -1.42 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 440 TYR 0.011 0.001 TYR A 396 PHE 0.009 0.001 PHE C 133 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 3931) covalent geometry : angle 0.53805 / 0.29 ( 5344) SS BOND : bond 0.00240 / 0.15 ( 5) SS BOND : angle 0.66699 / 0.46 ( 10) hydrogen bonds : bond 0.03564 / 2.26 ( 132) hydrogen bonds : angle 5.98199 / 4.19 ( 327) link_BETA1-4 : bond 0.00067 / 0.04 ( 1) link_BETA1-4 : angle 1.11465 / 0.89 ( 3) link_NAG-ASN : bond 0.00428 / 0.22 ( 7) link_NAG-ASN : angle 3.57906 / 2.90 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.086 Fit side-chains REVERT: C 79 PHE cc_start: 0.4717 (OUTLIER) cc_final: 0.4143 (t80) REVERT: C 280 GLU cc_start: 0.8676 (pm20) cc_final: 0.8457 (pm20) REVERT: A 340 GLU cc_start: 0.8382 (mp0) cc_final: 0.7990 (mp0) REVERT: A 474 GLN cc_start: 0.7173 (pt0) cc_final: 0.6479 (pp30) REVERT: A 498 ARG cc_start: 0.8514 (tpp80) cc_final: 0.8136 (mmt-90) REVERT: A 501 TYR cc_start: 0.9037 (m-10) cc_final: 0.8768 (m-10) outliers start: 8 outliers final: 2 residues processed: 50 average time/residue: 0.4602 time to fit residues: 23.5982 Evaluate side-chains 44 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain A residue 346 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN A 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.073237 restraints weight = 6807.618| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.07 r_work: 0.2827 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3944 Z= 0.171 Angle : 0.588 11.362 5378 Z= 0.300 Chirality : 0.049 0.188 603 Planarity : 0.004 0.036 673 Dihedral : 5.756 50.864 669 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.63 % Allowed : 14.53 % Favored : 81.84 % 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: -0.79 (0.39), residues: 447 helix: -2.47 (0.62), residues: 45 sheet: 1.39 (0.43), residues: 147 loop : -1.40 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 440 TYR 0.012 0.001 TYR C 268 PHE 0.011 0.001 PHE A 377 TRP 0.009 0.001 TRP C 64 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 3931) covalent geometry : angle 0.54436 / 0.29 ( 5344) SS BOND : bond 0.00329 / 0.21 ( 5) SS BOND : angle 0.74903 / 0.51 ( 10) hydrogen bonds : bond 0.03924 / 2.53 ( 132) hydrogen bonds : angle 5.98752 / 4.21 ( 327) link_BETA1-4 : bond 0.00011 / 0.01 ( 1) link_BETA1-4 : angle 1.14959 / 0.90 ( 3) link_NAG-ASN : bond 0.00399 / 0.21 ( 7) link_NAG-ASN : angle 3.57855 / 2.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.146 Fit side-chains REVERT: C 79 PHE cc_start: 0.4760 (OUTLIER) cc_final: 0.4106 (t80) REVERT: C 169 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: C 170 TYR cc_start: 0.8185 (t80) cc_final: 0.7829 (t80) REVERT: C 303 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8872 (mptm) REVERT: A 474 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6524 (pp30) REVERT: A 498 ARG cc_start: 0.8512 (tpp80) cc_final: 0.8179 (mmt-90) REVERT: A 501 TYR cc_start: 0.9040 (m-10) cc_final: 0.8775 (m-10) outliers start: 15 outliers final: 3 residues processed: 54 average time/residue: 0.6054 time to fit residues: 33.5052 Evaluate side-chains 47 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 303 LYS Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.096948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.073084 restraints weight = 6843.170| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.12 r_work: 0.2816 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3944 Z= 0.174 Angle : 0.602 11.431 5378 Z= 0.306 Chirality : 0.049 0.187 603 Planarity : 0.004 0.035 673 Dihedral : 5.744 51.083 669 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.66 % Allowed : 15.74 % Favored : 81.60 % 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: -0.78 (0.39), residues: 447 helix: -2.47 (0.62), residues: 45 sheet: 1.42 (0.43), residues: 147 loop : -1.41 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 440 TYR 0.012 0.001 TYR A 489 PHE 0.010 0.001 PHE A 377 TRP 0.009 0.001 TRP C 64 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 ( 3931) covalent geometry : angle 0.55529 / 0.30 ( 5344) SS BOND : bond 0.00325 / 0.20 ( 5) SS BOND : angle 0.69119 / 0.46 ( 10) hydrogen bonds : bond 0.03831 / 2.46 ( 132) hydrogen bonds : angle 5.95976 / 4.19 ( 327) link_BETA1-4 : bond 0.00017 / 0.01 ( 1) link_BETA1-4 : angle 1.16862 / 0.92 ( 3) link_NAG-ASN : bond 0.00381 / 0.19 ( 7) link_NAG-ASN : angle 3.72929 / 2.98 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.158 Fit side-chains REVERT: C 79 PHE cc_start: 0.4820 (OUTLIER) cc_final: 0.4135 (t80) REVERT: C 169 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: A 474 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6538 (pp30) REVERT: A 498 ARG cc_start: 0.8525 (tpp80) cc_final: 0.8204 (mmt-90) outliers start: 11 outliers final: 5 residues processed: 50 average time/residue: 0.5939 time to fit residues: 30.5464 Evaluate side-chains 46 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.075283 restraints weight = 6716.524| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.09 r_work: 0.2873 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3944 Z= 0.113 Angle : 0.565 10.962 5378 Z= 0.285 Chirality : 0.047 0.192 603 Planarity : 0.004 0.032 673 Dihedral : 5.426 52.311 669 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.91 % Allowed : 15.25 % Favored : 81.84 % 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: -0.79 (0.39), residues: 447 helix: -2.42 (0.62), residues: 45 sheet: 1.37 (0.43), residues: 147 loop : -1.39 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 440 TYR 0.008 0.001 TYR C 278 PHE 0.008 0.001 PHE A 541 TRP 0.008 0.001 TRP C 64 HIS 0.001 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 3931) covalent geometry : angle 0.52174 / 0.28 ( 5344) SS BOND : bond 0.00203 / 0.13 ( 5) SS BOND : angle 0.50808 / 0.32 ( 10) hydrogen bonds : bond 0.03306 / 2.12 ( 132) hydrogen bonds : angle 5.78951 / 4.08 ( 327) link_BETA1-4 : bond 0.00151 / 0.10 ( 1) link_BETA1-4 : angle 1.11367 / 0.90 ( 3) link_NAG-ASN : bond 0.00427 / 0.22 ( 7) link_NAG-ASN : angle 3.47112 / 2.83 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.141 Fit side-chains REVERT: C 169 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8239 (tm-30) REVERT: A 340 GLU cc_start: 0.8355 (mp0) cc_final: 0.7978 (mp0) REVERT: A 474 GLN cc_start: 0.7261 (pt0) cc_final: 0.6569 (pp30) REVERT: A 498 ARG cc_start: 0.8462 (tpp80) cc_final: 0.8082 (mmt-90) REVERT: A 501 TYR cc_start: 0.8994 (m-10) cc_final: 0.8693 (m-10) outliers start: 12 outliers final: 4 residues processed: 52 average time/residue: 0.6045 time to fit residues: 32.3000 Evaluate side-chains 47 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.096646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.072930 restraints weight = 6927.962| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.09 r_work: 0.2826 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3944 Z= 0.209 Angle : 0.630 11.846 5378 Z= 0.319 Chirality : 0.050 0.194 603 Planarity : 0.004 0.034 673 Dihedral : 5.721 52.699 669 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.91 % Allowed : 15.50 % Favored : 81.60 % 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: -0.83 (0.39), residues: 447 helix: -2.44 (0.62), residues: 45 sheet: 1.43 (0.43), residues: 145 loop : -1.46 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 440 TYR 0.012 0.001 TYR C 278 PHE 0.012 0.001 PHE A 377 TRP 0.010 0.001 TRP C 64 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 ( 3931) covalent geometry : angle 0.58132 / 0.31 ( 5344) SS BOND : bond 0.00393 / 0.25 ( 5) SS BOND : angle 0.77239 / 0.52 ( 10) hydrogen bonds : bond 0.04042 / 2.62 ( 132) hydrogen bonds : angle 5.96503 / 4.20 ( 327) link_BETA1-4 : bond 0.00072 / 0.05 ( 1) link_BETA1-4 : angle 1.19641 / 0.94 ( 3) link_NAG-ASN : bond 0.00444 / 0.23 ( 7) link_NAG-ASN : angle 3.87940 / 3.04 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.148 Fit side-chains REVERT: C 169 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: C 170 TYR cc_start: 0.8286 (t80) cc_final: 0.7904 (t80) REVERT: A 474 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6641 (pp30) REVERT: A 498 ARG cc_start: 0.8588 (tpp80) cc_final: 0.8218 (mmt-90) outliers start: 12 outliers final: 5 residues processed: 49 average time/residue: 0.7200 time to fit residues: 36.2107 Evaluate side-chains 45 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.097954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.074825 restraints weight = 7004.132| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.05 r_work: 0.2870 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3944 Z= 0.152 Angle : 0.599 11.727 5378 Z= 0.304 Chirality : 0.048 0.192 603 Planarity : 0.004 0.033 673 Dihedral : 5.553 52.874 669 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.66 % Allowed : 16.22 % Favored : 81.11 % 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: -0.83 (0.39), residues: 447 helix: -2.40 (0.62), residues: 45 sheet: 1.41 (0.43), residues: 145 loop : -1.46 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 440 TYR 0.016 0.001 TYR A 489 PHE 0.010 0.001 PHE C 65 TRP 0.010 0.001 TRP C 64 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 3931) covalent geometry : angle 0.55370 / 0.29 ( 5344) SS BOND : bond 0.00277 / 0.17 ( 5) SS BOND : angle 0.60727 / 0.40 ( 10) hydrogen bonds : bond 0.03628 / 2.34 ( 132) hydrogen bonds : angle 5.88263 / 4.14 ( 327) link_BETA1-4 : bond 0.00009 / 0.01 ( 1) link_BETA1-4 : angle 1.16050 / 0.92 ( 3) link_NAG-ASN : bond 0.00468 / 0.24 ( 7) link_NAG-ASN : angle 3.68586 / 2.96 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.099 Fit side-chains REVERT: C 169 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: C 303 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8842 (mptm) REVERT: A 474 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6696 (pp30) REVERT: A 498 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8166 (mmt-90) REVERT: A 501 TYR cc_start: 0.8978 (m-10) cc_final: 0.8727 (m-80) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.6928 time to fit residues: 35.5809 Evaluate side-chains 50 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 303 LYS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 498 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 16 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** 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 = 0.3348 r_free = 0.3348 target = 0.096719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.073448 restraints weight = 7043.096| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.07 r_work: 0.2843 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3944 Z= 0.223 Angle : 0.634 12.136 5378 Z= 0.325 Chirality : 0.050 0.204 603 Planarity : 0.005 0.035 673 Dihedral : 5.678 51.732 669 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.91 % Allowed : 15.50 % Favored : 81.60 % 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: -0.88 (0.39), residues: 447 helix: -2.45 (0.61), residues: 45 sheet: 1.41 (0.44), residues: 145 loop : -1.51 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 440 TYR 0.014 0.002 TYR A 501 PHE 0.013 0.002 PHE A 377 TRP 0.010 0.001 TRP C 64 HIS 0.002 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.22 ( 3931) covalent geometry : angle 0.58924 / 0.32 ( 5344) SS BOND : bond 0.00407 / 0.26 ( 5) SS BOND : angle 0.76673 / 0.50 ( 10) hydrogen bonds : bond 0.04136 / 2.68 ( 132) hydrogen bonds : angle 6.03170 / 4.25 ( 327) link_BETA1-4 : bond 0.00057 / 0.04 ( 1) link_BETA1-4 : angle 1.26036 / 0.98 ( 3) link_NAG-ASN : bond 0.00458 / 0.25 ( 7) link_NAG-ASN : angle 3.76196 / 3.01 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.145 Fit side-chains REVERT: C 169 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: C 170 TYR cc_start: 0.8323 (t80) cc_final: 0.7932 (t80) REVERT: C 303 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8848 (mptm) REVERT: A 474 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6741 (pp30) REVERT: A 498 ARG cc_start: 0.8593 (tpp80) cc_final: 0.8197 (mmt-90) outliers start: 12 outliers final: 5 residues processed: 51 average time/residue: 0.5785 time to fit residues: 30.3558 Evaluate side-chains 44 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 303 LYS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** 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 = 0.3371 r_free = 0.3371 target = 0.098293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075210 restraints weight = 7011.804| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.05 r_work: 0.2873 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3944 Z= 0.137 Angle : 0.606 11.803 5378 Z= 0.307 Chirality : 0.048 0.191 603 Planarity : 0.004 0.033 673 Dihedral : 5.481 52.863 669 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.94 % Allowed : 17.19 % Favored : 80.87 % 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: -0.85 (0.39), residues: 447 helix: -2.41 (0.62), residues: 45 sheet: 1.37 (0.43), residues: 145 loop : -1.45 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 440 TYR 0.018 0.001 TYR A 501 PHE 0.009 0.001 PHE C 186 TRP 0.012 0.001 TRP C 64 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 3931) covalent geometry : angle 0.56197 / 0.30 ( 5344) SS BOND : bond 0.00330 / 0.22 ( 5) SS BOND : angle 1.22404 / 0.88 ( 10) hydrogen bonds : bond 0.03534 / 2.28 ( 132) hydrogen bonds : angle 5.87602 / 4.14 ( 327) link_BETA1-4 : bond 0.00117 / 0.08 ( 1) link_BETA1-4 : angle 1.19425 / 0.95 ( 3) link_NAG-ASN : bond 0.00482 / 0.25 ( 7) link_NAG-ASN : angle 3.59417 / 2.93 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.146 Fit side-chains REVERT: C 169 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: A 474 GLN cc_start: 0.7363 (pt0) cc_final: 0.6724 (pp30) REVERT: A 498 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8078 (mmt-90) REVERT: A 501 TYR cc_start: 0.8920 (m-80) cc_final: 0.8653 (m-80) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.7072 time to fit residues: 34.8474 Evaluate side-chains 46 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 498 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** 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 = 0.3371 r_free = 0.3371 target = 0.098308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.075207 restraints weight = 7015.363| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.06 r_work: 0.2873 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3944 Z= 0.143 Angle : 0.597 11.578 5378 Z= 0.303 Chirality : 0.048 0.195 603 Planarity : 0.004 0.033 673 Dihedral : 5.353 52.727 669 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.42 % Allowed : 16.22 % Favored : 81.36 % 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: -0.79 (0.39), residues: 447 helix: -2.12 (0.70), residues: 38 sheet: 1.36 (0.43), residues: 145 loop : -1.47 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 440 TYR 0.018 0.001 TYR A 501 PHE 0.010 0.001 PHE C 65 TRP 0.011 0.001 TRP C 64 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 3931) covalent geometry : angle 0.55408 / 0.29 ( 5344) SS BOND : bond 0.00277 / 0.18 ( 5) SS BOND : angle 1.18238 / 0.86 ( 10) hydrogen bonds : bond 0.03540 / 2.28 ( 132) hydrogen bonds : angle 5.84604 / 4.13 ( 327) link_BETA1-4 : bond 0.00091 / 0.06 ( 1) link_BETA1-4 : angle 1.18690 / 0.94 ( 3) link_NAG-ASN : bond 0.00477 / 0.25 ( 7) link_NAG-ASN : angle 3.49648 / 2.86 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 894 Ramachandran restraints generated. 447 Oldfield, 0 Emsley, 447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.145 Fit side-chains REVERT: C 169 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8281 (tm-30) REVERT: A 474 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6701 (pp30) REVERT: A 498 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8055 (mmt-90) REVERT: A 501 TYR cc_start: 0.8927 (m-80) cc_final: 0.8615 (m-80) outliers start: 10 outliers final: 6 residues processed: 47 average time/residue: 0.5154 time to fit residues: 24.9630 Evaluate side-chains 49 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 498 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** 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 = 0.3345 r_free = 0.3345 target = 0.096611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.073369 restraints weight = 7024.136| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.06 r_work: 0.2841 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3944 Z= 0.224 Angle : 0.648 12.131 5378 Z= 0.332 Chirality : 0.051 0.206 603 Planarity : 0.005 0.036 673 Dihedral : 5.554 51.557 669 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.66 % Allowed : 15.98 % Favored : 81.36 % 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: -0.86 (0.39), residues: 447 helix: -2.41 (0.62), residues: 45 sheet: 1.38 (0.44), residues: 145 loop : -1.48 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 440 TYR 0.022 0.002 TYR A 501 PHE 0.012 0.002 PHE A 377 TRP 0.011 0.001 TRP C 64 HIS 0.002 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.22 ( 3931) covalent geometry : angle 0.60400 / 0.32 ( 5344) SS BOND : bond 0.00429 / 0.27 ( 5) SS BOND : angle 1.43919 / 1.07 ( 10) hydrogen bonds : bond 0.04120 / 2.66 ( 132) hydrogen bonds : angle 6.01952 / 4.24 ( 327) link_BETA1-4 : bond 0.00049 / 0.03 ( 1) link_BETA1-4 : angle 1.27370 / 0.99 ( 3) link_NAG-ASN : bond 0.00467 / 0.25 ( 7) link_NAG-ASN : angle 3.65285 / 2.96 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1416.19 seconds wall clock time: 24 minutes 53.63 seconds (1493.63 seconds total)