Starting phenix.real_space_refine on Thu Jul 2 13:12:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wgr_37515/07_2026/8wgr_37515_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wgr_37515/07_2026/8wgr_37515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wgr_37515/07_2026/8wgr_37515_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wgr_37515/07_2026/8wgr_37515_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wgr_37515/07_2026/8wgr_37515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wgr_37515/07_2026/8wgr_37515.map" } resolution = 2.75 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= 0.002 sd= 0.159 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 S 20 5.16 5 Cl 1 4.86 5 C 2981 2.51 5 N 683 2.21 5 O 773 1.98 5 H 4371 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8830 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8754 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 528} Chain breaks: 1 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 74 Ad-hoc single atom residues: {' CL': 1, ' K': 1} Unusual residues: {'DSM': 2} Classifications: {'undetermined': 2, 'water': 34} Link IDs: {None: 34} Chain breaks: 2 Time building chain proxies: 2.02, per 1000 atoms: 0.23 Number of scatterers: 8830 At special positions: 0 Unit cell: (70.3625, 70.3625, 99.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 Cl 1 17.00 S 20 16.00 O 773 8.00 N 683 7.00 C 2981 6.00 H 4371 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " 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 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 362.7 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 1 sheets defined 84.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.719A pdb=" N VAL A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.611A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.774A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.619A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.158A pdb=" N ILE A 230 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.664A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.796A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.630A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.746A pdb=" N LYS A 303 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.689A pdb=" N ALA A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 375 through 379 removed outlier: 4.000A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 392 - end of helix removed outlier: 3.617A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.581A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.800A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 497 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.521A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 592 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 599 through 604 removed outlier: 4.333A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 616 removed outlier: 3.879A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 295 hydrogen bonds defined for protein. 852 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: 2.07 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4364 1.03 - 1.23: 19 1.23 - 1.42: 2021 1.42 - 1.62: 2505 1.62 - 1.81: 31 Bond restraints: 8940 Sorted by residual: bond pdb=" C ALA A 73 " pdb=" O ALA A 73 " ideal model delta sigma weight residual 1.235 1.161 0.075 1.26e-02 6.30e+03 3.50e+01 bond pdb=" C VAL A 74 " pdb=" O VAL A 74 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.19e-02 7.06e+03 3.18e+01 bond pdb=" C ASN A 78 " pdb=" O ASN A 78 " ideal model delta sigma weight residual 1.236 1.176 0.061 1.18e-02 7.18e+03 2.63e+01 bond pdb=" C ASP A 75 " pdb=" O ASP A 75 " ideal model delta sigma weight residual 1.233 1.178 0.055 1.17e-02 7.31e+03 2.20e+01 bond pdb=" C ASP A 75 " pdb=" N LEU A 76 " ideal model delta sigma weight residual 1.335 1.277 0.058 1.34e-02 5.57e+03 1.88e+01 ... (remaining 8935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.06: 16083 7.06 - 14.12: 12 14.12 - 21.18: 0 21.18 - 28.24: 0 28.24 - 35.30: 3 Bond angle restraints: 16098 Sorted by residual: angle pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 73.70 35.30 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 110.00 76.58 33.42 3.00e+00 1.11e-01 1.24e+02 angle pdb=" CB TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 76.12 32.88 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CA ASP A 75 " pdb=" CB ASP A 75 " pdb=" CG ASP A 75 " ideal model delta sigma weight residual 112.60 119.52 -6.92 1.00e+00 1.00e+00 4.79e+01 angle pdb=" O GLY A 71 " pdb=" C GLY A 71 " pdb=" N PHE A 72 " ideal model delta sigma weight residual 122.24 115.98 6.26 1.06e+00 8.90e-01 3.49e+01 ... (remaining 16093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 3745 17.77 - 35.55: 337 35.55 - 53.32: 103 53.32 - 71.10: 41 71.10 - 88.87: 7 Dihedral angle restraints: 4233 sinusoidal: 2150 harmonic: 2083 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -132.22 9.62 0 2.50e+00 1.60e-01 1.48e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 132.02 -9.22 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 4230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 663 0.083 - 0.165: 25 0.165 - 0.248: 1 0.248 - 0.331: 0 0.331 - 0.413: 1 Chirality restraints: 690 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB VAL A 74 " pdb=" CA VAL A 74 " pdb=" CG1 VAL A 74 " pdb=" CG2 VAL A 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 687 not shown) Planarity restraints: 1281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 78 " 0.029 2.00e-02 2.50e+03 3.78e-02 2.14e+01 pdb=" CG ASN A 78 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 78 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN A 78 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 78 " -0.057 2.00e-02 2.50e+03 pdb="HD22 ASN A 78 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ILE A 103 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 75 " -0.015 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" CG ASP A 75 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASP A 75 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP A 75 " -0.020 2.00e-02 2.50e+03 ... (remaining 1278 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.24: 839 2.24 - 2.96: 23151 2.96 - 3.69: 33227 3.69 - 4.41: 50817 4.41 - 5.14: 80780 Nonbonded interactions: 188814 Sorted by model distance: nonbonded pdb=" OE1 GLN A 612 " pdb=" H GLN A 612 " model vdw 1.509 2.450 nonbonded pdb=" OE1 GLU A 425 " pdb="HH22 ARG A 442 " model vdw 1.629 2.450 nonbonded pdb=" H HIS A 178 " pdb=" OD1 ASN A 181 " model vdw 1.631 2.450 nonbonded pdb=" O ILE A 561 " pdb=" HG SER A 564 " model vdw 1.676 2.450 nonbonded pdb=" O ALA A 476 " pdb=" HG SER A 480 " model vdw 1.681 2.450 ... (remaining 188809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.060 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.810 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: 0.010 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 0.075 4570 Z= 0.274 Angle : 0.709 9.254 6233 Z= 0.369 Chirality : 0.041 0.413 690 Planarity : 0.005 0.050 754 Dihedral : 17.038 88.869 1537 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.69 % Rotamer: Outliers : 2.38 % Allowed : 22.08 % Favored : 75.54 % 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: 1.68 (0.38), residues: 544 helix: 1.68 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -0.10 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 512 TYR 0.014 0.001 TYR A 271 PHE 0.027 0.001 PHE A 72 TRP 0.007 0.001 TRP A 553 HIS 0.003 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.27 ( 4569) covalent geometry : angle 0.70851 / 0.37 ( 6231) SS BOND : bond 0.00027 / 0.02 ( 1) SS BOND : angle 1.50410 / 0.57 ( 2) hydrogen bonds : bond 0.11994 / 8.03 ( 295) hydrogen bonds : angle 5.10887 / 3.58 ( 852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7184 (mm) cc_final: 0.6771 (mt) REVERT: A 113 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7837 (mt-10) REVERT: A 174 THR cc_start: 0.8224 (m) cc_final: 0.7984 (p) REVERT: A 301 ARG cc_start: 0.7514 (tpt90) cc_final: 0.7312 (tpt90) REVERT: A 376 ILE cc_start: 0.8183 (tt) cc_final: 0.7397 (mp) REVERT: A 458 LEU cc_start: 0.7707 (tt) cc_final: 0.7493 (tt) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.5926 time to fit residues: 57.5167 Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 493 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.134587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113563 restraints weight = 15278.876| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.79 r_work: 0.3352 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4570 Z= 0.160 Angle : 0.589 7.868 6233 Z= 0.298 Chirality : 0.041 0.428 690 Planarity : 0.005 0.037 754 Dihedral : 11.409 144.316 618 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.03 % Allowed : 20.13 % Favored : 76.84 % 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: 1.47 (0.38), residues: 544 helix: 1.49 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.20 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.017 0.001 TYR A 84 PHE 0.012 0.001 PHE A 94 TRP 0.007 0.001 TRP A 553 HIS 0.004 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 4569) covalent geometry : angle 0.58778 / 0.30 ( 6231) SS BOND : bond 0.00033 / 0.02 ( 1) SS BOND : angle 2.18901 / 0.80 ( 2) hydrogen bonds : bond 0.05200 / 3.43 ( 295) hydrogen bonds : angle 4.81633 / 3.37 ( 852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7185 (mm) cc_final: 0.6748 (mt) REVERT: A 376 ILE cc_start: 0.8288 (tt) cc_final: 0.7448 (mp) REVERT: A 439 LYS cc_start: 0.7774 (ttmt) cc_final: 0.7431 (ttmp) REVERT: A 458 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7318 (tt) outliers start: 14 outliers final: 5 residues processed: 67 average time/residue: 0.6056 time to fit residues: 43.8996 Evaluate side-chains 57 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114421 restraints weight = 15385.403| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.78 r_work: 0.3361 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4570 Z= 0.118 Angle : 0.538 9.057 6233 Z= 0.266 Chirality : 0.039 0.415 690 Planarity : 0.005 0.036 754 Dihedral : 10.954 139.539 611 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.95 % Allowed : 20.78 % Favored : 77.27 % 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: 1.59 (0.38), residues: 544 helix: 1.61 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.26 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 440 TYR 0.015 0.001 TYR A 84 PHE 0.010 0.001 PHE A 316 TRP 0.006 0.001 TRP A 553 HIS 0.004 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 4569) covalent geometry : angle 0.53715 / 0.27 ( 6231) SS BOND : bond 0.00035 / 0.02 ( 1) SS BOND : angle 1.65953 / 0.62 ( 2) hydrogen bonds : bond 0.04417 / 2.89 ( 295) hydrogen bonds : angle 4.59247 / 3.23 ( 852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7202 (mm) cc_final: 0.6790 (mt) REVERT: A 376 ILE cc_start: 0.8272 (tt) cc_final: 0.7448 (mp) REVERT: A 439 LYS cc_start: 0.7713 (ttmt) cc_final: 0.7348 (ttmp) outliers start: 9 outliers final: 3 residues processed: 59 average time/residue: 0.5810 time to fit residues: 36.9997 Evaluate side-chains 53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 277 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.0470 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110584 restraints weight = 15451.546| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.77 r_work: 0.3320 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4570 Z= 0.158 Angle : 0.576 8.866 6233 Z= 0.290 Chirality : 0.041 0.434 690 Planarity : 0.005 0.039 754 Dihedral : 10.969 137.432 611 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.81 % Allowed : 19.05 % Favored : 78.14 % 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: 1.44 (0.37), residues: 544 helix: 1.52 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.37 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 440 TYR 0.019 0.001 TYR A 84 PHE 0.016 0.001 PHE A 316 TRP 0.007 0.001 TRP A 80 HIS 0.004 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 4569) covalent geometry : angle 0.57525 / 0.29 ( 6231) SS BOND : bond 0.00046 / 0.03 ( 1) SS BOND : angle 2.18738 / 0.80 ( 2) hydrogen bonds : bond 0.05128 / 3.37 ( 295) hydrogen bonds : angle 4.77670 / 3.36 ( 852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7181 (mm) cc_final: 0.6753 (mt) REVERT: A 301 ARG cc_start: 0.7400 (tpt90) cc_final: 0.6555 (ttt180) REVERT: A 376 ILE cc_start: 0.8281 (tt) cc_final: 0.7400 (mp) REVERT: A 436 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7051 (mm110) REVERT: A 439 LYS cc_start: 0.7705 (ttmt) cc_final: 0.6904 (ttpp) REVERT: A 440 ARG cc_start: 0.7763 (ttp-110) cc_final: 0.6882 (mtt90) REVERT: A 528 PHE cc_start: 0.7987 (m-80) cc_final: 0.7726 (m-80) outliers start: 13 outliers final: 3 residues processed: 65 average time/residue: 0.6439 time to fit residues: 45.0789 Evaluate side-chains 53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 436 GLN Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.111523 restraints weight = 14901.759| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.74 r_work: 0.3326 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4570 Z= 0.138 Angle : 0.554 8.939 6233 Z= 0.276 Chirality : 0.040 0.424 690 Planarity : 0.005 0.038 754 Dihedral : 10.978 138.196 611 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.73 % Allowed : 20.13 % Favored : 78.14 % 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: 1.49 (0.37), residues: 544 helix: 1.56 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -0.36 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 301 TYR 0.017 0.001 TYR A 84 PHE 0.013 0.001 PHE A 316 TRP 0.007 0.001 TRP A 80 HIS 0.003 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 4569) covalent geometry : angle 0.55283 / 0.28 ( 6231) SS BOND : bond 0.00159 / 0.10 ( 1) SS BOND : angle 1.85602 / 0.65 ( 2) hydrogen bonds : bond 0.04769 / 3.12 ( 295) hydrogen bonds : angle 4.70308 / 3.31 ( 852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6771 (mt) REVERT: A 301 ARG cc_start: 0.7354 (tpt90) cc_final: 0.6532 (ttt180) REVERT: A 376 ILE cc_start: 0.8338 (tt) cc_final: 0.7467 (mp) REVERT: A 436 GLN cc_start: 0.7683 (pt0) cc_final: 0.6901 (mm110) REVERT: A 439 LYS cc_start: 0.7694 (ttmt) cc_final: 0.6892 (ttpp) REVERT: A 528 PHE cc_start: 0.7934 (m-80) cc_final: 0.7636 (m-80) REVERT: A 581 GLN cc_start: 0.7883 (tt0) cc_final: 0.7639 (mt0) outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 0.6598 time to fit residues: 40.2018 Evaluate side-chains 54 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 450 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110546 restraints weight = 15031.252| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.75 r_work: 0.3317 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4570 Z= 0.152 Angle : 0.568 8.863 6233 Z= 0.284 Chirality : 0.041 0.432 690 Planarity : 0.005 0.040 754 Dihedral : 10.956 137.253 611 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.60 % Allowed : 18.83 % Favored : 78.57 % 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: 1.41 (0.37), residues: 544 helix: 1.51 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.42 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 440 TYR 0.018 0.001 TYR A 84 PHE 0.016 0.001 PHE A 316 TRP 0.007 0.001 TRP A 80 HIS 0.003 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 4569) covalent geometry : angle 0.56690 / 0.28 ( 6231) SS BOND : bond 0.00184 / 0.12 ( 1) SS BOND : angle 2.36844 / 0.82 ( 2) hydrogen bonds : bond 0.05002 / 3.28 ( 295) hydrogen bonds : angle 4.74964 / 3.34 ( 852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6760 (mt) REVERT: A 303 LYS cc_start: 0.8155 (ptmt) cc_final: 0.7291 (ptmm) REVERT: A 436 GLN cc_start: 0.7752 (pt0) cc_final: 0.6973 (mm110) REVERT: A 439 LYS cc_start: 0.7673 (ttmt) cc_final: 0.6825 (ttpp) REVERT: A 528 PHE cc_start: 0.7921 (m-80) cc_final: 0.7691 (m-80) REVERT: A 541 LYS cc_start: 0.7927 (mmmm) cc_final: 0.7670 (mtmt) REVERT: A 543 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 581 GLN cc_start: 0.7918 (tt0) cc_final: 0.7664 (mt0) outliers start: 12 outliers final: 5 residues processed: 61 average time/residue: 0.6949 time to fit residues: 45.1022 Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 598 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110699 restraints weight = 15122.748| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.76 r_work: 0.3319 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4570 Z= 0.146 Angle : 0.561 8.899 6233 Z= 0.280 Chirality : 0.040 0.431 690 Planarity : 0.005 0.040 754 Dihedral : 11.008 137.771 611 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.16 % Allowed : 19.26 % Favored : 78.57 % 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: 1.43 (0.37), residues: 544 helix: 1.53 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.44 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 440 TYR 0.017 0.001 TYR A 84 PHE 0.014 0.001 PHE A 316 TRP 0.007 0.001 TRP A 80 HIS 0.003 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 4569) covalent geometry : angle 0.56024 / 0.28 ( 6231) SS BOND : bond 0.00124 / 0.08 ( 1) SS BOND : angle 1.96637 / 0.68 ( 2) hydrogen bonds : bond 0.04875 / 3.20 ( 295) hydrogen bonds : angle 4.72170 / 3.33 ( 852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.241 Fit side-chains REVERT: A 66 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6759 (mt) REVERT: A 205 TYR cc_start: 0.4454 (OUTLIER) cc_final: 0.3236 (t80) REVERT: A 206 LYS cc_start: 0.7346 (ptpp) cc_final: 0.6703 (pmmt) REVERT: A 301 ARG cc_start: 0.7423 (tpt90) cc_final: 0.6579 (ttt180) REVERT: A 436 GLN cc_start: 0.7744 (pt0) cc_final: 0.6979 (mm110) REVERT: A 439 LYS cc_start: 0.7692 (ttmt) cc_final: 0.6860 (ttpp) REVERT: A 541 LYS cc_start: 0.7875 (mmmm) cc_final: 0.7620 (mtmt) REVERT: A 543 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8023 (tt) outliers start: 10 outliers final: 2 residues processed: 55 average time/residue: 0.7219 time to fit residues: 42.4844 Evaluate side-chains 54 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 543 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111695 restraints weight = 14904.684| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.73 r_work: 0.3331 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4570 Z= 0.131 Angle : 0.549 8.889 6233 Z= 0.273 Chirality : 0.040 0.428 690 Planarity : 0.005 0.040 754 Dihedral : 10.961 138.112 611 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.95 % Allowed : 20.56 % Favored : 77.49 % 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: 1.50 (0.37), residues: 544 helix: 1.58 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.43 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 440 TYR 0.016 0.001 TYR A 84 PHE 0.013 0.001 PHE A 316 TRP 0.006 0.001 TRP A 80 HIS 0.003 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4569) covalent geometry : angle 0.54795 / 0.27 ( 6231) SS BOND : bond 0.00141 / 0.09 ( 1) SS BOND : angle 1.81874 / 0.63 ( 2) hydrogen bonds : bond 0.04647 / 3.04 ( 295) hydrogen bonds : angle 4.65959 / 3.28 ( 852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.235 Fit side-chains REVERT: A 66 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6755 (mt) REVERT: A 205 TYR cc_start: 0.4336 (OUTLIER) cc_final: 0.3195 (t80) REVERT: A 206 LYS cc_start: 0.7221 (ptpp) cc_final: 0.6621 (pmmt) REVERT: A 266 THR cc_start: 0.8125 (m) cc_final: 0.7367 (t) REVERT: A 301 ARG cc_start: 0.7477 (tpt90) cc_final: 0.6656 (ttt180) REVERT: A 436 GLN cc_start: 0.7703 (pt0) cc_final: 0.6985 (mm110) REVERT: A 439 LYS cc_start: 0.7677 (ttmt) cc_final: 0.6851 (ttpp) REVERT: A 543 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8037 (tt) outliers start: 9 outliers final: 3 residues processed: 56 average time/residue: 0.6583 time to fit residues: 39.6796 Evaluate side-chains 56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 463 LYS Chi-restraints excluded: chain A residue 543 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.133186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111960 restraints weight = 14986.801| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.74 r_work: 0.3333 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4570 Z= 0.128 Angle : 0.545 8.819 6233 Z= 0.271 Chirality : 0.040 0.428 690 Planarity : 0.005 0.039 754 Dihedral : 10.908 138.281 611 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.73 % Allowed : 21.21 % Favored : 77.06 % 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: 1.53 (0.37), residues: 544 helix: 1.61 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.42 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 440 TYR 0.016 0.001 TYR A 84 PHE 0.013 0.001 PHE A 316 TRP 0.006 0.001 TRP A 553 HIS 0.002 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 4569) covalent geometry : angle 0.54448 / 0.27 ( 6231) SS BOND : bond 0.00138 / 0.09 ( 1) SS BOND : angle 1.74353 / 0.61 ( 2) hydrogen bonds : bond 0.04557 / 2.98 ( 295) hydrogen bonds : angle 4.62497 / 3.25 ( 852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6800 (mt) REVERT: A 205 TYR cc_start: 0.4371 (OUTLIER) cc_final: 0.3245 (t80) REVERT: A 206 LYS cc_start: 0.7170 (ptpp) cc_final: 0.6574 (pmmt) REVERT: A 266 THR cc_start: 0.8121 (m) cc_final: 0.7379 (t) REVERT: A 301 ARG cc_start: 0.7460 (tpt90) cc_final: 0.6642 (ttt180) REVERT: A 436 GLN cc_start: 0.7682 (pt0) cc_final: 0.6986 (mm110) REVERT: A 439 LYS cc_start: 0.7674 (ttmt) cc_final: 0.6849 (ttpp) REVERT: A 543 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8037 (tt) outliers start: 8 outliers final: 3 residues processed: 55 average time/residue: 0.6319 time to fit residues: 37.1268 Evaluate side-chains 57 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 543 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112669 restraints weight = 15058.848| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.74 r_work: 0.3348 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4570 Z= 0.118 Angle : 0.536 8.639 6233 Z= 0.266 Chirality : 0.039 0.427 690 Planarity : 0.005 0.039 754 Dihedral : 10.839 138.596 611 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.30 % Allowed : 21.86 % Favored : 76.84 % 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: 1.57 (0.37), residues: 544 helix: 1.67 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.50 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 440 TYR 0.015 0.001 TYR A 84 PHE 0.012 0.001 PHE A 94 TRP 0.006 0.001 TRP A 553 HIS 0.002 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4569) covalent geometry : angle 0.53571 / 0.27 ( 6231) SS BOND : bond 0.00130 / 0.08 ( 1) SS BOND : angle 1.62577 / 0.57 ( 2) hydrogen bonds : bond 0.04368 / 2.85 ( 295) hydrogen bonds : angle 4.56279 / 3.21 ( 852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6763 (mt) REVERT: A 204 LYS cc_start: 0.5756 (mmmt) cc_final: 0.5440 (mmmt) REVERT: A 266 THR cc_start: 0.8137 (m) cc_final: 0.7427 (t) REVERT: A 301 ARG cc_start: 0.7445 (tpt90) cc_final: 0.6641 (ttt180) REVERT: A 436 GLN cc_start: 0.7680 (pt0) cc_final: 0.6998 (mm110) REVERT: A 439 LYS cc_start: 0.7669 (ttmt) cc_final: 0.6844 (ttpp) REVERT: A 612 GLN cc_start: 0.7295 (mp10) cc_final: 0.7091 (mp10) outliers start: 6 outliers final: 3 residues processed: 55 average time/residue: 0.6947 time to fit residues: 40.8010 Evaluate side-chains 56 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN A 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.133558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112505 restraints weight = 14958.385| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.73 r_work: 0.3344 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4570 Z= 0.121 Angle : 0.539 8.588 6233 Z= 0.267 Chirality : 0.039 0.428 690 Planarity : 0.005 0.038 754 Dihedral : 10.771 138.494 610 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.08 % Allowed : 22.08 % Favored : 76.84 % 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: 1.61 (0.37), residues: 544 helix: 1.68 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -0.42 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 440 TYR 0.016 0.001 TYR A 84 PHE 0.013 0.001 PHE A 316 TRP 0.006 0.001 TRP A 553 HIS 0.002 0.001 HIS A 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 4569) covalent geometry : angle 0.53842 / 0.27 ( 6231) SS BOND : bond 0.00138 / 0.09 ( 1) SS BOND : angle 1.63972 / 0.57 ( 2) hydrogen bonds : bond 0.04400 / 2.87 ( 295) hydrogen bonds : angle 4.56754 / 3.21 ( 852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2820.59 seconds wall clock time: 48 minutes 34.88 seconds (2914.88 seconds total)