Starting phenix.real_space_refine on Wed Jul 1 22:15:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu9_60894/07_2026/9iu9_60894.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu9_60894/07_2026/9iu9_60894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iu9_60894/07_2026/9iu9_60894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu9_60894/07_2026/9iu9_60894.map" model { file = "/net/cci-nas-00/data/ceres_data/9iu9_60894/07_2026/9iu9_60894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu9_60894/07_2026/9iu9_60894.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 47 5.49 5 S 10 5.16 5 C 1916 2.51 5 N 606 2.21 5 O 697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3277 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2312 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 16, 'TRANS': 273} Chain breaks: 3 Chain: "E" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 473 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 491 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1221 SG CYS B 304 40.717 28.517 37.508 1.00123.35 S ATOM 1239 SG CYS B 307 40.635 30.005 34.038 1.00120.16 S ATOM 1390 SG CYS B 326 37.782 29.702 35.393 1.00113.50 S ATOM 1462 SG CYS B 335 39.396 26.331 34.884 1.00123.42 S Time building chain proxies: 0.85, per 1000 atoms: 0.26 Number of scatterers: 3277 At special positions: 0 Unit cell: (65.8465, 96.4181, 74.0773, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 10 16.00 P 47 15.00 O 697 8.00 N 606 7.00 C 1916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 95.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 335 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 307 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 326 " pdb="ZN ZN B1000 " - pdb=" SG CYS B 304 " Number of angles added : 6 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 532 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 5 sheets defined 46.2% alpha, 14.1% beta 23 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 197 through 208 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 271 through 283 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 342 through 358 Processing helix chain 'B' and resid 371 through 389 removed outlier: 3.912A pdb=" N VAL B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 446 removed outlier: 3.516A pdb=" N GLN B 446 " --> pdb=" O TRP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 Processing sheet with id=AA1, first strand: chain 'B' and resid 163 through 165 Processing sheet with id=AA2, first strand: chain 'B' and resid 249 through 250 Processing sheet with id=AA3, first strand: chain 'B' and resid 302 through 304 Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 315 Processing sheet with id=AA5, first strand: chain 'B' and resid 361 through 368 removed outlier: 7.063A pdb=" N ARG B 362 " --> pdb=" O THR B 435 " (cutoff:3.500A) 111 hydrogen bonds defined for protein. 306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 0.56 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 692 1.33 - 1.45: 1119 1.45 - 1.57: 1529 1.57 - 1.69: 92 1.69 - 1.81: 15 Bond restraints: 3447 Sorted by residual: bond pdb=" N1 DC F 21 " pdb=" C6 DC F 21 " ideal model delta sigma weight residual 1.367 1.328 0.039 6.00e-03 2.78e+04 4.28e+01 bond pdb=" CA PRO B 159 " pdb=" CB PRO B 159 " ideal model delta sigma weight residual 1.539 1.499 0.040 9.30e-03 1.16e+04 1.84e+01 bond pdb=" P DC E 30 " pdb=" O5' DC E 30 " ideal model delta sigma weight residual 1.593 1.632 -0.039 1.00e-02 1.00e+04 1.50e+01 bond pdb=" CA SER B 157 " pdb=" CB SER B 157 " ideal model delta sigma weight residual 1.530 1.474 0.056 1.69e-02 3.50e+03 1.09e+01 bond pdb=" C4 DC F 21 " pdb=" C5 DC F 21 " ideal model delta sigma weight residual 1.425 1.399 0.026 8.00e-03 1.56e+04 1.08e+01 ... (remaining 3442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 4467 2.76 - 5.53: 352 5.53 - 8.29: 42 8.29 - 11.05: 3 11.05 - 13.81: 3 Bond angle restraints: 4867 Sorted by residual: angle pdb=" O5' DT E 33 " pdb=" C5' DT E 33 " pdb=" C4' DT E 33 " ideal model delta sigma weight residual 109.40 115.88 -6.48 8.00e-01 1.56e+00 6.55e+01 angle pdb=" O3' DT E 36 " pdb=" P DG E 37 " pdb=" O5' DG E 37 " ideal model delta sigma weight residual 104.00 92.09 11.91 1.50e+00 4.44e-01 6.31e+01 angle pdb=" CB GLU B 445 " pdb=" CG GLU B 445 " pdb=" CD GLU B 445 " ideal model delta sigma weight residual 112.60 123.76 -11.16 1.70e+00 3.46e-01 4.31e+01 angle pdb=" O4' DA E 31 " pdb=" C1' DA E 31 " pdb=" C2' DA E 31 " ideal model delta sigma weight residual 105.90 100.81 5.09 8.00e-01 1.56e+00 4.05e+01 angle pdb=" O4' DT E 33 " pdb=" C1' DT E 33 " pdb=" N1 DT E 33 " ideal model delta sigma weight residual 108.00 112.22 -4.22 7.00e-01 2.04e+00 3.63e+01 ... (remaining 4862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 1464 17.34 - 34.68: 244 34.68 - 52.01: 150 52.01 - 69.35: 58 69.35 - 86.69: 5 Dihedral angle restraints: 1921 sinusoidal: 1096 harmonic: 825 Sorted by residual: dihedral pdb=" CA TYR B 154 " pdb=" C TYR B 154 " pdb=" N ARG B 155 " pdb=" CA ARG B 155 " ideal model delta harmonic sigma weight residual -180.00 -162.30 -17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LEU B 470 " pdb=" C LEU B 470 " pdb=" N THR B 471 " pdb=" CA THR B 471 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CG ARG B 208 " pdb=" CD ARG B 208 " pdb=" NE ARG B 208 " pdb=" CZ ARG B 208 " ideal model delta sinusoidal sigma weight residual 180.00 135.39 44.61 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 1918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 467 0.133 - 0.265: 51 0.265 - 0.398: 4 0.398 - 0.530: 4 0.530 - 0.662: 2 Chirality restraints: 528 Sorted by residual: chirality pdb=" P DC E 30 " pdb=" OP1 DC E 30 " pdb=" OP2 DC E 30 " pdb=" O5' DC E 30 " both_signs ideal model delta sigma weight residual True 2.34 -3.00 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" P DT F 1 " pdb=" OP1 DT F 1 " pdb=" OP2 DT F 1 " pdb=" O5' DT F 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DT F 22 " pdb=" OP1 DT F 22 " pdb=" OP2 DT F 22 " pdb=" O5' DT F 22 " both_signs ideal model delta sigma weight residual True 2.34 -2.83 -0.49 2.00e-01 2.50e+01 6.02e+00 ... (remaining 525 not shown) Planarity restraints: 463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC F 21 " -0.085 2.00e-02 2.50e+03 4.21e-02 3.99e+01 pdb=" N1 DC F 21 " 0.067 2.00e-02 2.50e+03 pdb=" C2 DC F 21 " 0.036 2.00e-02 2.50e+03 pdb=" O2 DC F 21 " 0.014 2.00e-02 2.50e+03 pdb=" N3 DC F 21 " -0.028 2.00e-02 2.50e+03 pdb=" C4 DC F 21 " -0.029 2.00e-02 2.50e+03 pdb=" N4 DC F 21 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC F 21 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC F 21 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG E 42 " 0.060 2.00e-02 2.50e+03 2.43e-02 1.77e+01 pdb=" N9 DG E 42 " -0.050 2.00e-02 2.50e+03 pdb=" C8 DG E 42 " -0.011 2.00e-02 2.50e+03 pdb=" N7 DG E 42 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DG E 42 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG E 42 " 0.011 2.00e-02 2.50e+03 pdb=" O6 DG E 42 " 0.016 2.00e-02 2.50e+03 pdb=" N1 DG E 42 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DG E 42 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG E 42 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG E 42 " -0.015 2.00e-02 2.50e+03 pdb=" C4 DG E 42 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 472 " 0.327 9.50e-02 1.11e+02 1.47e-01 1.65e+01 pdb=" NE ARG B 472 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 472 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG B 472 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 472 " 0.001 2.00e-02 2.50e+03 ... (remaining 460 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 459 2.77 - 3.30: 2867 3.30 - 3.84: 6293 3.84 - 4.37: 7045 4.37 - 4.90: 10946 Nonbonded interactions: 27610 Sorted by model distance: nonbonded pdb=" OH TYR B 312 " pdb=" OP2 DT E 43 " model vdw 2.238 3.040 nonbonded pdb=" NH1 ARG B 223 " pdb=" OP1 DG F 23 " model vdw 2.401 3.120 nonbonded pdb=" OG SER B 157 " pdb=" O2 DT F 22 " model vdw 2.407 3.040 nonbonded pdb=" NH2 ARG B 190 " pdb=" OE2 GLU B 196 " model vdw 2.410 3.120 nonbonded pdb=" NE1 TRP B 161 " pdb=" OE1 GLN B 180 " model vdw 2.446 3.120 ... (remaining 27605 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: 1.130 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.400 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 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 : 0.010 0.078 3451 Z= 0.662 Angle : 1.644 21.141 4873 Z= 1.087 Chirality : 0.099 0.662 528 Planarity : 0.017 0.147 463 Dihedral : 22.835 86.685 1389 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.13 % Favored : 97.52 % Rotamer: Outliers : 3.75 % Allowed : 6.67 % Favored : 89.58 % 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: 0.54 (0.47), residues: 282 helix: 0.50 (0.41), residues: 124 sheet: -0.40 (0.67), residues: 49 loop : 0.88 (0.62), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.004 ARG B 472 TYR 0.034 0.007 TYR B 312 PHE 0.028 0.004 PHE B 439 TRP 0.021 0.005 TRP B 367 HIS 0.008 0.003 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00967 / 0.66 ( 3447) covalent geometry : angle 1.60353 / 1.09 ( 4867) hydrogen bonds : bond 0.14482 / 9.29 ( 169) hydrogen bonds : angle 5.91496 / 4.22 ( 422) metal coordination : bond 0.05838 / 2.91 ( 4) metal coordination : angle 10.41935 / 9.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.078 Fit side-chains REVERT: B 164 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7941 (pt) REVERT: B 204 ASP cc_start: 0.7943 (t70) cc_final: 0.7605 (t0) REVERT: B 215 ASP cc_start: 0.7825 (m-30) cc_final: 0.7417 (m-30) REVERT: B 219 GLN cc_start: 0.7112 (tt0) cc_final: 0.6633 (tp-100) REVERT: B 239 MET cc_start: 0.7890 (mmm) cc_final: 0.7528 (mmm) REVERT: B 250 LEU cc_start: 0.7396 (tp) cc_final: 0.7153 (tp) REVERT: B 253 LYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5114 (mtmm) REVERT: B 351 GLU cc_start: 0.6769 (tt0) cc_final: 0.6347 (tp30) REVERT: B 366 VAL cc_start: 0.5789 (t) cc_final: 0.5427 (m) REVERT: B 445 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7697 (mm-30) REVERT: B 472 ARG cc_start: 0.8078 (ptp-170) cc_final: 0.7174 (mtm110) REVERT: B 478 ASP cc_start: 0.7812 (m-30) cc_final: 0.7559 (m-30) outliers start: 9 outliers final: 0 residues processed: 65 average time/residue: 0.0888 time to fit residues: 6.5579 Evaluate side-chains 47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 445 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.174156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.138632 restraints weight = 3611.993| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.66 r_work: 0.3167 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3451 Z= 0.209 Angle : 0.753 13.736 4873 Z= 0.414 Chirality : 0.049 0.216 528 Planarity : 0.006 0.042 463 Dihedral : 26.067 88.515 843 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.92 % Allowed : 10.42 % Favored : 86.67 % 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: 1.83 (0.50), residues: 282 helix: 1.92 (0.45), residues: 124 sheet: -0.59 (0.64), residues: 49 loop : 1.54 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 444 TYR 0.009 0.002 TYR B 312 PHE 0.009 0.002 PHE B 464 TRP 0.011 0.002 TRP B 230 HIS 0.002 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.21 ( 3447) covalent geometry : angle 0.71415 / 0.41 ( 4867) hydrogen bonds : bond 0.04964 / 3.20 ( 169) hydrogen bonds : angle 3.82783 / 2.83 ( 422) metal coordination : bond 0.00967 / 0.48 ( 4) metal coordination : angle 6.81974 / 6.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.056 Fit side-chains revert: symmetry clash REVERT: B 253 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6947 (mtmt) REVERT: B 283 VAL cc_start: 0.8483 (p) cc_final: 0.8225 (m) REVERT: B 351 GLU cc_start: 0.7763 (tt0) cc_final: 0.7381 (tp30) REVERT: B 366 VAL cc_start: 0.8309 (t) cc_final: 0.7900 (m) REVERT: B 431 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7426 (mt-10) REVERT: B 441 ASP cc_start: 0.6927 (m-30) cc_final: 0.5319 (m-30) REVERT: B 445 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7837 (mp0) outliers start: 7 outliers final: 2 residues processed: 46 average time/residue: 0.0957 time to fit residues: 4.9477 Evaluate side-chains 35 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 445 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.0030 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.172294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.137557 restraints weight = 3604.635| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.56 r_work: 0.3166 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3451 Z= 0.167 Angle : 0.670 7.774 4873 Z= 0.375 Chirality : 0.044 0.194 528 Planarity : 0.006 0.061 463 Dihedral : 26.423 89.468 841 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.92 % Allowed : 15.00 % Favored : 82.08 % 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: 1.85 (0.51), residues: 282 helix: 1.95 (0.47), residues: 124 sheet: -0.99 (0.65), residues: 49 loop : 1.76 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 190 TYR 0.010 0.002 TYR B 154 PHE 0.010 0.002 PHE B 464 TRP 0.010 0.001 TRP B 230 HIS 0.002 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 ( 3447) covalent geometry : angle 0.64807 / 0.37 ( 4867) hydrogen bonds : bond 0.04156 / 2.70 ( 169) hydrogen bonds : angle 3.64803 / 2.77 ( 422) metal coordination : bond 0.00768 / 0.38 ( 4) metal coordination : angle 4.83688 / 4.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: B 253 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.6957 (mtmt) REVERT: B 351 GLU cc_start: 0.7790 (tt0) cc_final: 0.7458 (tp30) REVERT: B 366 VAL cc_start: 0.8308 (t) cc_final: 0.7923 (m) REVERT: B 431 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7219 (mt-10) REVERT: B 445 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7841 (mp0) outliers start: 7 outliers final: 2 residues processed: 38 average time/residue: 0.0923 time to fit residues: 3.9794 Evaluate side-chains 37 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.169294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.132085 restraints weight = 3587.564| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.38 r_work: 0.3172 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3451 Z= 0.214 Angle : 0.677 7.838 4873 Z= 0.374 Chirality : 0.044 0.190 528 Planarity : 0.005 0.040 463 Dihedral : 26.607 88.936 841 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.17 % Allowed : 12.92 % Favored : 82.92 % 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: 1.60 (0.50), residues: 282 helix: 1.93 (0.47), residues: 123 sheet: -1.39 (0.63), residues: 49 loop : 1.53 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 444 TYR 0.010 0.002 TYR B 154 PHE 0.010 0.002 PHE B 439 TRP 0.011 0.001 TRP B 230 HIS 0.002 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 ( 3447) covalent geometry : angle 0.66018 / 0.37 ( 4867) hydrogen bonds : bond 0.04470 / 2.87 ( 169) hydrogen bonds : angle 3.70920 / 2.84 ( 422) metal coordination : bond 0.00884 / 0.44 ( 4) metal coordination : angle 4.31111 / 4.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: B 253 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7032 (mtmt) REVERT: B 351 GLU cc_start: 0.7867 (tt0) cc_final: 0.7505 (tp30) REVERT: B 431 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7342 (mt-10) REVERT: B 444 ARG cc_start: 0.8111 (mtm110) cc_final: 0.7765 (mtm110) REVERT: B 445 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7738 (mp0) outliers start: 10 outliers final: 5 residues processed: 38 average time/residue: 0.1038 time to fit residues: 4.5001 Evaluate side-chains 37 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 6 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.0070 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.174594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.136869 restraints weight = 3591.259| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.35 r_work: 0.3214 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3451 Z= 0.142 Angle : 0.610 6.188 4873 Z= 0.345 Chirality : 0.041 0.184 528 Planarity : 0.004 0.035 463 Dihedral : 26.483 88.518 841 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.17 % Allowed : 14.58 % Favored : 81.25 % 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: 1.71 (0.51), residues: 282 helix: 2.04 (0.47), residues: 123 sheet: -1.40 (0.66), residues: 49 loop : 1.60 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 433 TYR 0.008 0.001 TYR B 324 PHE 0.006 0.001 PHE B 464 TRP 0.009 0.001 TRP B 345 HIS 0.002 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 ( 3447) covalent geometry : angle 0.59584 / 0.34 ( 4867) hydrogen bonds : bond 0.03432 / 2.23 ( 169) hydrogen bonds : angle 3.50945 / 2.73 ( 422) metal coordination : bond 0.00611 / 0.31 ( 4) metal coordination : angle 3.83356 / 3.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.057 Fit side-chains revert: symmetry clash REVERT: B 155 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7543 (ptt90) REVERT: B 189 HIS cc_start: 0.7852 (m170) cc_final: 0.7545 (t70) REVERT: B 253 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.6997 (mtmt) REVERT: B 351 GLU cc_start: 0.7987 (tt0) cc_final: 0.7470 (tp30) REVERT: B 377 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6766 (mp) REVERT: B 431 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7109 (mt-10) REVERT: B 444 ARG cc_start: 0.8117 (mtm110) cc_final: 0.7672 (mtm110) REVERT: B 445 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: B 472 ARG cc_start: 0.8115 (ptp-110) cc_final: 0.7832 (ptp-110) outliers start: 10 outliers final: 5 residues processed: 41 average time/residue: 0.0883 time to fit residues: 4.0367 Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.172031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136730 restraints weight = 3627.324| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.29 r_work: 0.3198 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3451 Z= 0.163 Angle : 0.619 6.782 4873 Z= 0.344 Chirality : 0.041 0.184 528 Planarity : 0.005 0.035 463 Dihedral : 26.592 87.708 841 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.58 % Allowed : 13.75 % Favored : 81.67 % 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: 1.71 (0.51), residues: 282 helix: 2.05 (0.47), residues: 124 sheet: -1.45 (0.66), residues: 49 loop : 1.61 (0.61), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 438 TYR 0.007 0.001 TYR B 154 PHE 0.009 0.001 PHE B 464 TRP 0.008 0.001 TRP B 230 HIS 0.002 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 3447) covalent geometry : angle 0.60660 / 0.34 ( 4867) hydrogen bonds : bond 0.03806 / 2.48 ( 169) hydrogen bonds : angle 3.51208 / 2.75 ( 422) metal coordination : bond 0.00711 / 0.35 ( 4) metal coordination : angle 3.59810 / 3.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7454 (ptt90) REVERT: B 189 HIS cc_start: 0.7928 (m170) cc_final: 0.7653 (t70) REVERT: B 253 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7077 (mtmt) REVERT: B 351 GLU cc_start: 0.8007 (tt0) cc_final: 0.7505 (tp30) REVERT: B 361 GLU cc_start: 0.7656 (tt0) cc_final: 0.7170 (tt0) REVERT: B 431 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7393 (mt-10) REVERT: B 472 ARG cc_start: 0.8117 (ptp-110) cc_final: 0.7791 (ptp-110) outliers start: 11 outliers final: 5 residues processed: 39 average time/residue: 0.1037 time to fit residues: 4.5622 Evaluate side-chains 38 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.170982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.135803 restraints weight = 3680.078| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.31 r_work: 0.3181 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3451 Z= 0.166 Angle : 0.625 6.582 4873 Z= 0.346 Chirality : 0.041 0.182 528 Planarity : 0.005 0.060 463 Dihedral : 26.577 87.111 841 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.50 % Allowed : 16.25 % Favored : 81.25 % 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: 1.70 (0.51), residues: 282 helix: 2.01 (0.47), residues: 124 sheet: -1.40 (0.68), residues: 49 loop : 1.61 (0.61), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 444 TYR 0.007 0.001 TYR B 154 PHE 0.008 0.001 PHE B 439 TRP 0.009 0.001 TRP B 230 HIS 0.002 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 ( 3447) covalent geometry : angle 0.61336 / 0.35 ( 4867) hydrogen bonds : bond 0.03713 / 2.45 ( 169) hydrogen bonds : angle 3.51996 / 2.76 ( 422) metal coordination : bond 0.00726 / 0.36 ( 4) metal coordination : angle 3.45747 / 3.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7514 (ptt90) REVERT: B 253 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7056 (mtmt) REVERT: B 351 GLU cc_start: 0.7935 (tt0) cc_final: 0.7517 (tp30) REVERT: B 431 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7371 (mt-10) REVERT: B 472 ARG cc_start: 0.8119 (ptp-110) cc_final: 0.7805 (ptp-110) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.0990 time to fit residues: 4.0989 Evaluate side-chains 36 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 15 optimal weight: 0.0060 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.0670 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.173864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.138871 restraints weight = 3666.110| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.31 r_work: 0.3220 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3451 Z= 0.130 Angle : 0.587 5.633 4873 Z= 0.332 Chirality : 0.039 0.175 528 Planarity : 0.005 0.051 463 Dihedral : 26.449 88.011 841 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.08 % Allowed : 16.67 % Favored : 81.25 % 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: 1.83 (0.51), residues: 282 helix: 2.12 (0.48), residues: 124 sheet: -1.42 (0.67), residues: 49 loop : 1.73 (0.62), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 444 TYR 0.007 0.001 TYR B 324 PHE 0.006 0.001 PHE B 439 TRP 0.009 0.001 TRP B 345 HIS 0.002 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 ( 3447) covalent geometry : angle 0.57648 / 0.33 ( 4867) hydrogen bonds : bond 0.03213 / 2.11 ( 169) hydrogen bonds : angle 3.45544 / 2.73 ( 422) metal coordination : bond 0.00569 / 0.28 ( 4) metal coordination : angle 3.18025 / 3.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7546 (ptt90) REVERT: B 253 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7093 (mtmt) REVERT: B 351 GLU cc_start: 0.8041 (tt0) cc_final: 0.7532 (tp30) REVERT: B 431 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7428 (mt-10) outliers start: 5 outliers final: 2 residues processed: 36 average time/residue: 0.0935 time to fit residues: 3.7805 Evaluate side-chains 34 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 445 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 1 optimal weight: 0.0040 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.170877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.135771 restraints weight = 3657.610| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.31 r_work: 0.3196 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3451 Z= 0.165 Angle : 0.627 6.818 4873 Z= 0.346 Chirality : 0.040 0.175 528 Planarity : 0.005 0.048 463 Dihedral : 26.537 86.892 841 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.50 % Allowed : 16.67 % Favored : 80.83 % 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: 1.71 (0.51), residues: 282 helix: 2.03 (0.48), residues: 124 sheet: -1.35 (0.68), residues: 49 loop : 1.59 (0.61), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 444 TYR 0.006 0.001 TYR B 154 PHE 0.009 0.001 PHE B 464 TRP 0.008 0.001 TRP B 230 HIS 0.003 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 3447) covalent geometry : angle 0.61767 / 0.35 ( 4867) hydrogen bonds : bond 0.03770 / 2.53 ( 169) hydrogen bonds : angle 3.53961 / 2.79 ( 422) metal coordination : bond 0.00664 / 0.33 ( 4) metal coordination : angle 3.14892 / 2.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7552 (ptt90) REVERT: B 253 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7053 (mtmt) REVERT: B 431 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7317 (mt-10) outliers start: 6 outliers final: 4 residues processed: 36 average time/residue: 0.1268 time to fit residues: 5.1013 Evaluate side-chains 35 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 6 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.171356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136380 restraints weight = 3651.712| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.30 r_work: 0.3212 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3451 Z= 0.148 Angle : 0.617 7.376 4873 Z= 0.344 Chirality : 0.039 0.169 528 Planarity : 0.004 0.044 463 Dihedral : 26.469 87.118 841 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.50 % Allowed : 17.08 % Favored : 80.42 % 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: 1.73 (0.51), residues: 282 helix: 2.03 (0.48), residues: 124 sheet: -1.36 (0.68), residues: 49 loop : 1.62 (0.61), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 444 TYR 0.006 0.001 TYR B 154 PHE 0.008 0.001 PHE B 464 TRP 0.008 0.001 TRP B 345 HIS 0.002 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 ( 3447) covalent geometry : angle 0.60755 / 0.34 ( 4867) hydrogen bonds : bond 0.03438 / 2.29 ( 169) hydrogen bonds : angle 3.54332 / 2.80 ( 422) metal coordination : bond 0.00613 / 0.31 ( 4) metal coordination : angle 3.18670 / 2.99 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7567 (ptt90) REVERT: B 253 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7105 (mtmt) REVERT: B 431 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7393 (mt-10) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 0.1373 time to fit residues: 5.3768 Evaluate side-chains 35 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.171131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.136081 restraints weight = 3678.095| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.32 r_work: 0.3209 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3451 Z= 0.155 Angle : 0.629 7.955 4873 Z= 0.348 Chirality : 0.040 0.166 528 Planarity : 0.005 0.041 463 Dihedral : 26.486 87.093 841 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.92 % Allowed : 17.50 % Favored : 79.58 % 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: 1.73 (0.51), residues: 282 helix: 2.04 (0.48), residues: 124 sheet: -1.36 (0.67), residues: 49 loop : 1.63 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 444 TYR 0.006 0.001 TYR B 154 PHE 0.009 0.001 PHE B 464 TRP 0.008 0.001 TRP B 230 HIS 0.002 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 ( 3447) covalent geometry : angle 0.61920 / 0.35 ( 4867) hydrogen bonds : bond 0.03538 / 2.38 ( 169) hydrogen bonds : angle 3.56463 / 2.81 ( 422) metal coordination : bond 0.00611 / 0.30 ( 4) metal coordination : angle 3.17610 / 2.97 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 907.89 seconds wall clock time: 16 minutes 9.91 seconds (969.91 seconds total)