Starting phenix.real_space_refine on Tue Aug 4 13:27:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu9_60894/08_2026/9iu9_60894.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu9_60894/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9iu9_60894/08_2026/9iu9_60894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu9_60894/08_2026/9iu9_60894.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iu9_60894/08_2026/9iu9_60894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu9_60894/08_2026/9iu9_60894.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 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-2.2rc3-6140/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: 0.92, per 1000 atoms: 0.28 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: 0.31 Conformation dependent library (CDL) restraints added in 81.5 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: 0.63 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: 0.61 Time building geometry restraints manager: 0.40 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: 4459 2.76 - 5.53: 360 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=" 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=" 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 1.90e+00 2.77e-01 3.93e+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: 0.910 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.450 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.370 ------------------------------------------------------------------------------- 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= 0.663 Angle : 1.649 21.141 4873 Z= 1.080 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 1.60870 / 1.08 ( 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 : 0.116 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: 0.1477 time to fit residues: 10.8030 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 : 0.135 ------------------------------------------------------------------------------- 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: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.175005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.138599 restraints weight = 3612.712| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.45 r_work: 0.3206 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3451 Z= 0.203 Angle : 0.761 13.572 4873 Z= 0.415 Chirality : 0.050 0.209 528 Planarity : 0.006 0.044 463 Dihedral : 26.025 88.604 843 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.50 % Allowed : 10.42 % Favored : 87.08 % 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: 1.86 (0.50), residues: 282 helix: 1.95 (0.45), residues: 124 sheet: -0.59 (0.64), residues: 49 loop : 1.56 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 472 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 0.00405 / 0.20 ( 3447) covalent geometry : angle 0.72350 / 0.41 ( 4867) hydrogen bonds : bond 0.04949 / 3.19 ( 169) hydrogen bonds : angle 3.82647 / 2.84 ( 422) metal coordination : bond 0.00989 / 0.49 ( 4) metal coordination : angle 6.77444 / 6.49 ( 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 48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: B 219 GLN cc_start: 0.8091 (tt0) cc_final: 0.7785 (tp-100) REVERT: B 253 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.6992 (mtmt) REVERT: B 283 VAL cc_start: 0.8467 (p) cc_final: 0.8214 (m) REVERT: B 351 GLU cc_start: 0.7826 (tt0) cc_final: 0.7379 (tp30) REVERT: B 366 VAL cc_start: 0.8353 (t) cc_final: 0.7943 (m) REVERT: B 431 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7449 (mt-10) REVERT: B 441 ASP cc_start: 0.6921 (m-30) cc_final: 0.5376 (m-30) REVERT: B 444 ARG cc_start: 0.8226 (mtm110) cc_final: 0.7866 (mtm110) REVERT: B 445 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7900 (mp0) outliers start: 6 outliers final: 2 residues processed: 45 average time/residue: 0.1222 time to fit residues: 6.2012 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 : 0.097 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.172325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.136609 restraints weight = 3629.994| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.46 r_work: 0.3200 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3451 Z= 0.168 Angle : 0.665 7.534 4873 Z= 0.371 Chirality : 0.044 0.192 528 Planarity : 0.005 0.035 463 Dihedral : 26.395 89.535 841 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.92 % Allowed : 13.75 % Favored : 83.33 % 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: 1.86 (0.51), residues: 282 helix: 1.96 (0.47), residues: 124 sheet: -1.02 (0.64), residues: 49 loop : 1.79 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 190 TYR 0.010 0.002 TYR B 154 PHE 0.007 0.001 PHE B 464 TRP 0.010 0.001 TRP B 230 HIS 0.002 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 ( 3447) covalent geometry : angle 0.64451 / 0.37 ( 4867) hydrogen bonds : bond 0.04162 / 2.69 ( 169) hydrogen bonds : angle 3.62050 / 2.75 ( 422) metal coordination : bond 0.00827 / 0.41 ( 4) metal coordination : angle 4.72566 / 4.41 ( 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 40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: B 253 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7021 (mtmt) REVERT: B 351 GLU cc_start: 0.7878 (tt0) cc_final: 0.7470 (tp30) REVERT: B 366 VAL cc_start: 0.8316 (t) cc_final: 0.7937 (m) REVERT: B 431 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7392 (mt-10) REVERT: B 444 ARG cc_start: 0.8225 (mtm110) cc_final: 0.7774 (mtm110) REVERT: B 445 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: B 472 ARG cc_start: 0.8159 (ptp-110) cc_final: 0.7880 (ptp-110) outliers start: 7 outliers final: 2 residues processed: 37 average time/residue: 0.0974 time to fit residues: 4.1466 Evaluate side-chains 36 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.099 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 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: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.170941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136407 restraints weight = 3604.515| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.51 r_work: 0.3146 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3451 Z= 0.201 Angle : 0.663 7.446 4873 Z= 0.368 Chirality : 0.044 0.193 528 Planarity : 0.005 0.036 463 Dihedral : 26.541 88.761 841 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.58 % Allowed : 12.50 % 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: 1.62 (0.50), residues: 282 helix: 1.93 (0.47), residues: 123 sheet: -1.45 (0.62), residues: 49 loop : 1.60 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 190 TYR 0.009 0.002 TYR B 154 PHE 0.009 0.002 PHE B 464 TRP 0.010 0.001 TRP B 230 HIS 0.002 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 ( 3447) covalent geometry : angle 0.64645 / 0.37 ( 4867) hydrogen bonds : bond 0.04345 / 2.79 ( 169) hydrogen bonds : angle 3.67061 / 2.82 ( 422) metal coordination : bond 0.00753 / 0.38 ( 4) metal coordination : angle 4.24652 / 4.00 ( 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 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: B 155 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7240 (ptt90) REVERT: B 253 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.6990 (mtmt) REVERT: B 351 GLU cc_start: 0.7877 (tt0) cc_final: 0.7475 (tp30) REVERT: B 431 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7303 (mt-10) REVERT: B 444 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7675 (mtm110) REVERT: B 445 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7681 (mp0) outliers start: 11 outliers final: 4 residues processed: 40 average time/residue: 0.0925 time to fit residues: 4.1940 Evaluate side-chains 36 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 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 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: 0.6980 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.0070 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.172669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.137759 restraints weight = 3611.353| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.37 r_work: 0.3201 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3451 Z= 0.149 Angle : 0.622 6.037 4873 Z= 0.348 Chirality : 0.041 0.187 528 Planarity : 0.004 0.037 463 Dihedral : 26.443 88.039 841 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.93 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: 1.69 (0.51), residues: 282 helix: 2.02 (0.47), residues: 123 sheet: -1.42 (0.66), residues: 49 loop : 1.61 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 433 TYR 0.008 0.001 TYR B 324 PHE 0.007 0.001 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 0.00284 / 0.15 ( 3447) covalent geometry : angle 0.60784 / 0.35 ( 4867) hydrogen bonds : bond 0.03537 / 2.30 ( 169) hydrogen bonds : angle 3.52169 / 2.74 ( 422) metal coordination : bond 0.00714 / 0.36 ( 4) metal coordination : angle 3.82943 / 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: 0.8091 (OUTLIER) cc_final: 0.7307 (ptt90) REVERT: B 189 HIS cc_start: 0.7892 (m170) cc_final: 0.7607 (t70) REVERT: B 253 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7027 (mtmt) REVERT: B 351 GLU cc_start: 0.7990 (tt0) cc_final: 0.7500 (tp30) REVERT: B 431 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7191 (mt-10) REVERT: B 444 ARG cc_start: 0.8078 (mtm110) cc_final: 0.7644 (mtm110) REVERT: B 445 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: B 472 ARG cc_start: 0.8099 (ptp-110) cc_final: 0.7805 (ptp-110) outliers start: 10 outliers final: 4 residues processed: 41 average time/residue: 0.0874 time to fit residues: 4.0030 Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.169954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.133902 restraints weight = 3637.555| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.29 r_work: 0.3182 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3451 Z= 0.189 Angle : 0.648 7.354 4873 Z= 0.354 Chirality : 0.042 0.189 528 Planarity : 0.005 0.036 463 Dihedral : 26.597 87.028 841 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.11 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: 1.60 (0.51), residues: 282 helix: 1.92 (0.47), residues: 124 sheet: -1.44 (0.67), residues: 49 loop : 1.57 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 438 TYR 0.007 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 0.00399 / 0.19 ( 3447) covalent geometry : angle 0.63538 / 0.35 ( 4867) hydrogen bonds : bond 0.04111 / 2.69 ( 169) hydrogen bonds : angle 3.59203 / 2.81 ( 422) metal coordination : bond 0.00813 / 0.41 ( 4) metal coordination : angle 3.61276 / 3.39 ( 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 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.056 Fit side-chains revert: symmetry clash REVERT: B 155 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7297 (ptt90) REVERT: B 189 HIS cc_start: 0.7859 (m170) cc_final: 0.7551 (t70) REVERT: B 253 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7035 (mtmt) REVERT: B 351 GLU cc_start: 0.7970 (tt0) cc_final: 0.7462 (tp30) REVERT: B 431 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7344 (mt-10) REVERT: B 444 ARG cc_start: 0.8056 (mtm110) cc_final: 0.7625 (mtm110) REVERT: B 445 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: B 472 ARG cc_start: 0.8153 (ptp-110) cc_final: 0.7803 (ptp-110) outliers start: 11 outliers final: 5 residues processed: 41 average time/residue: 0.0828 time to fit residues: 3.8251 Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 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 364 GLU 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: 3.9990 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.170188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.134963 restraints weight = 3675.406| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.28 r_work: 0.3178 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3451 Z= 0.173 Angle : 0.632 6.824 4873 Z= 0.349 Chirality : 0.042 0.184 528 Planarity : 0.005 0.036 463 Dihedral : 26.545 86.560 841 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 1.59 (0.51), residues: 282 helix: 1.92 (0.48), residues: 124 sheet: -1.43 (0.68), residues: 49 loop : 1.55 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 433 TYR 0.007 0.001 TYR B 324 PHE 0.007 0.001 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 0.00356 / 0.17 ( 3447) covalent geometry : angle 0.62062 / 0.35 ( 4867) hydrogen bonds : bond 0.03762 / 2.49 ( 169) hydrogen bonds : angle 3.60529 / 2.83 ( 422) metal coordination : bond 0.00751 / 0.38 ( 4) metal coordination : angle 3.47693 / 3.28 ( 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: 7 poor density : 32 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: B 155 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7461 (ptt90) REVERT: B 189 HIS cc_start: 0.7863 (m170) cc_final: 0.7607 (t70) REVERT: B 253 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7105 (mtmt) REVERT: B 351 GLU cc_start: 0.8035 (tt0) cc_final: 0.7498 (tp30) REVERT: B 431 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7384 (mt-10) REVERT: B 444 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7619 (mtm110) REVERT: B 445 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: B 472 ARG cc_start: 0.8150 (ptp-110) cc_final: 0.7820 (ptp-110) outliers start: 7 outliers final: 4 residues processed: 37 average time/residue: 0.1656 time to fit residues: 6.8203 Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.0670 overall best weight: 0.8920 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.169402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.133383 restraints weight = 3666.417| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.29 r_work: 0.3167 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3451 Z= 0.190 Angle : 0.650 7.502 4873 Z= 0.356 Chirality : 0.042 0.181 528 Planarity : 0.005 0.036 463 Dihedral : 26.602 86.194 841 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.75 % Allowed : 14.17 % 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: 1.50 (0.51), residues: 282 helix: 1.86 (0.48), residues: 124 sheet: -1.48 (0.68), residues: 49 loop : 1.48 (0.59), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 433 TYR 0.006 0.001 TYR B 324 PHE 0.011 0.002 PHE B 464 TRP 0.010 0.001 TRP B 230 HIS 0.003 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 ( 3447) covalent geometry : angle 0.63922 / 0.36 ( 4867) hydrogen bonds : bond 0.04122 / 2.75 ( 169) hydrogen bonds : angle 3.68126 / 2.90 ( 422) metal coordination : bond 0.00792 / 0.40 ( 4) metal coordination : angle 3.48384 / 3.26 ( 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 41 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: B 155 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7303 (ptt90) REVERT: B 189 HIS cc_start: 0.7844 (m170) cc_final: 0.7593 (t70) REVERT: B 253 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7115 (mtmt) REVERT: B 351 GLU cc_start: 0.8006 (tt0) cc_final: 0.7502 (tp30) REVERT: B 431 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7410 (mt-10) REVERT: B 444 ARG cc_start: 0.7976 (mtm110) cc_final: 0.7541 (mtm110) REVERT: B 445 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7629 (mp0) outliers start: 9 outliers final: 4 residues processed: 39 average time/residue: 0.1411 time to fit residues: 6.1590 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 : 0.107 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 1 optimal weight: 0.2980 chunk 31 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.171036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.136168 restraints weight = 3635.013| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.57 r_work: 0.3151 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3451 Z= 0.160 Angle : 0.624 7.094 4873 Z= 0.346 Chirality : 0.041 0.177 528 Planarity : 0.005 0.037 463 Dihedral : 26.520 86.364 841 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: 1.58 (0.51), residues: 282 helix: 1.90 (0.48), residues: 124 sheet: -1.47 (0.68), residues: 49 loop : 1.59 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 438 TYR 0.007 0.001 TYR B 324 PHE 0.008 0.001 PHE B 464 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 0.00320 / 0.16 ( 3447) covalent geometry : angle 0.61220 / 0.35 ( 4867) hydrogen bonds : bond 0.03623 / 2.42 ( 169) hydrogen bonds : angle 3.65378 / 2.89 ( 422) metal coordination : bond 0.00684 / 0.34 ( 4) metal coordination : angle 3.42460 / 3.25 ( 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 41 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.060 Fit side-chains REVERT: B 155 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7176 (ptt90) REVERT: B 253 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7063 (mtmt) REVERT: B 361 GLU cc_start: 0.7557 (tt0) cc_final: 0.7055 (tt0) REVERT: B 431 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7288 (mt-10) REVERT: B 444 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7472 (mtm110) REVERT: B 445 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7545 (mp0) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 0.0951 time to fit residues: 4.1787 Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.060 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.170975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.136055 restraints weight = 3638.436| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.33 r_work: 0.3186 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3495 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= 0.152 Angle : 0.624 7.766 4873 Z= 0.347 Chirality : 0.040 0.174 528 Planarity : 0.004 0.035 463 Dihedral : 26.523 86.536 841 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 1.64 (0.51), residues: 282 helix: 1.94 (0.48), residues: 124 sheet: -1.48 (0.68), residues: 49 loop : 1.65 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 438 TYR 0.007 0.001 TYR B 154 PHE 0.009 0.001 PHE B 464 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 0.00298 / 0.15 ( 3447) covalent geometry : angle 0.61351 / 0.35 ( 4867) hydrogen bonds : bond 0.03544 / 2.36 ( 169) hydrogen bonds : angle 3.63126 / 2.88 ( 422) metal coordination : bond 0.00631 / 0.32 ( 4) metal coordination : angle 3.29655 / 3.12 ( 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 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.065 Fit side-chains REVERT: B 155 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7335 (ptt90) REVERT: B 253 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7139 (mtmt) REVERT: B 361 GLU cc_start: 0.7623 (tt0) cc_final: 0.7112 (tt0) REVERT: B 431 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7453 (mt-10) REVERT: B 444 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7546 (mtm110) REVERT: B 445 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7630 (mp0) outliers start: 7 outliers final: 3 residues processed: 36 average time/residue: 0.0897 time to fit residues: 3.6592 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 : 0.058 ------------------------------------------------------------------------------- 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 445 GLU Chi-restraints excluded: chain B residue 457 SER 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: 0.9980 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 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 = 0.3818 r_free = 0.3818 target = 0.170875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.132134 restraints weight = 3686.704| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.42 r_work: 0.3181 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3451 Z= 0.166 Angle : 0.640 8.011 4873 Z= 0.352 Chirality : 0.041 0.174 528 Planarity : 0.005 0.036 463 Dihedral : 26.588 86.272 841 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.50 % Allowed : 15.42 % 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: 1.61 (0.51), residues: 282 helix: 1.91 (0.48), residues: 124 sheet: -1.50 (0.68), residues: 49 loop : 1.63 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 438 TYR 0.006 0.001 TYR B 154 PHE 0.009 0.001 PHE B 464 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 0.00340 / 0.17 ( 3447) covalent geometry : angle 0.62985 / 0.35 ( 4867) hydrogen bonds : bond 0.03773 / 2.53 ( 169) hydrogen bonds : angle 3.67266 / 2.91 ( 422) metal coordination : bond 0.00700 / 0.35 ( 4) metal coordination : angle 3.29792 / 3.11 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 960.49 seconds wall clock time: 17 minutes 2.85 seconds (1022.85 seconds total)