Starting phenix.real_space_refine on Thu Aug 6 11:04:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t2r_40985/08_2026/8t2r_40985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2r_40985/08_2026/8t2r_40985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8t2r_40985/08_2026/8t2r_40985.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t2r_40985/08_2026/8t2r_40985.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t2r_40985/08_2026/8t2r_40985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2r_40985/08_2026/8t2r_40985.map" model { file = "/net/cci-nas-00/data/ceres_data/8t2r_40985/08_2026/8t2r_40985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2r_40985/08_2026/8t2r_40985.cif" } resolution = 3.1 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= 0.001 sd= 0.028 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 Ca 13 9.91 5 P 552 5.49 5 S 21 5.16 5 C 7314 2.51 5 N 2782 2.21 5 O 4381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 15063 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 3184 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 388, 3142 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 10, 'TRANS': 377} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 388, 3142 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 10, 'TRANS': 377} Chain breaks: 2 bond proxies already assigned to first conformer: 3149 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 3} Chain: "B" Number of atoms: 11724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 11724 Classifications: {'RNAv2': 545} Modifications used: {'rna2p_pur': 39, 'rna2p_pyr': 10, 'rna3p_pur': 291, 'rna3p_pyr': 205} Link IDs: {'rna2p': 48, 'rna3p': 496} Chain breaks: 6 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' CA': 13, 'NH4': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG D 347 " occ=0.25 ... (20 atoms not shown) pdb=" NH2BARG D 347 " occ=0.75 residue: pdb=" N AGLN D 359 " occ=0.72 ... (16 atoms not shown) pdb=" NE2BGLN D 359 " occ=0.28 residue: pdb=" N AARG D 382 " occ=0.67 ... (20 atoms not shown) pdb=" NH2BARG D 382 " occ=0.33 residue: pdb=" N AARG D 407 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG D 407 " occ=0.52 Time building chain proxies: 3.55, per 1000 atoms: 0.24 Number of scatterers: 15063 At special positions: 0 Unit cell: (97.904, 134.196, 160.36, 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) Ca 13 19.99 S 21 16.00 P 552 15.00 O 4381 8.00 N 2782 7.00 C 7314 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: 1.13 Conformation dependent library (CDL) restraints added in 375.8 milliseconds 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 70.9% alpha, 5.9% beta 177 base pairs and 312 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'D' and resid 4 through 11 Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 36 through 57 removed outlier: 6.619A pdb=" N GLU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 118 through 132 removed outlier: 3.601A pdb=" N ALA D 122 " --> pdb=" O CYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 150 through 162 removed outlier: 3.589A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.681A pdb=" N ILE D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 218 removed outlier: 4.304A pdb=" N LEU D 201 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU D 210 " --> pdb=" O MET D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 252 Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 313 through 333 Processing helix chain 'D' and resid 337 through 361 removed outlier: 3.658A pdb=" N LYS D 361 " --> pdb=" O TRP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 374 Processing helix chain 'D' and resid 376 through 385 removed outlier: 4.381A pdb=" N AARG D 382 " --> pdb=" O ASN D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 396 removed outlier: 4.032A pdb=" N LYS D 396 " --> pdb=" O TYR D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 415 through 424 Processing sheet with id=AA1, first strand: chain 'D' and resid 220 through 224 removed outlier: 4.374A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS D 228 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 275 through 279 205 hydrogen bonds defined for protein. 613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 439 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 177 basepair parallelities 312 stacking parallelities Total time for adding SS restraints: 4.04 Time building geometry restraints manager: 1.55 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: 1878 1.33 - 1.45: 7659 1.45 - 1.57: 5863 1.57 - 1.69: 1096 1.69 - 1.82: 35 Bond restraints: 16531 Sorted by residual: bond pdb=" C ASP D 265 " pdb=" N ARG D 266 " ideal model delta sigma weight residual 1.335 1.250 0.084 3.04e-02 1.08e+03 7.69e+00 bond pdb=" CB MET D 354 " pdb=" CG MET D 354 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.90e+00 bond pdb=" SD MET D 354 " pdb=" CE MET D 354 " ideal model delta sigma weight residual 1.791 1.743 0.048 2.50e-02 1.60e+03 3.75e+00 bond pdb=" C3' A B 67 " pdb=" O3' A B 67 " ideal model delta sigma weight residual 1.415 1.449 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" SD MET D 337 " pdb=" CE MET D 337 " ideal model delta sigma weight residual 1.791 1.749 0.042 2.50e-02 1.60e+03 2.78e+00 ... (remaining 16526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 24887 4.84 - 9.68: 174 9.68 - 14.52: 4 14.52 - 19.36: 0 19.36 - 24.20: 1 Bond angle restraints: 25066 Sorted by residual: angle pdb=" C3' A B 67 " pdb=" O3' A B 67 " pdb=" P U B 68 " ideal model delta sigma weight residual 119.70 127.49 -7.79 1.20e+00 6.94e-01 4.21e+01 angle pdb=" C ASP D 265 " pdb=" N ARG D 266 " pdb=" CA ARG D 266 " ideal model delta sigma weight residual 121.95 146.15 -24.20 3.74e+00 7.15e-02 4.19e+01 angle pdb=" C3' G B 348 " pdb=" O3' G B 348 " pdb=" P A B 349 " ideal model delta sigma weight residual 119.70 127.23 -7.53 1.20e+00 6.94e-01 3.93e+01 angle pdb=" C ALA D 225 " pdb=" N ASP D 226 " pdb=" CA ASP D 226 " ideal model delta sigma weight residual 122.61 131.23 -8.62 1.56e+00 4.11e-01 3.05e+01 angle pdb=" C3' G B 369 " pdb=" O3' G B 369 " pdb=" P A B 370 " ideal model delta sigma weight residual 119.70 126.21 -6.51 1.20e+00 6.94e-01 2.94e+01 ... (remaining 25061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 8059 34.74 - 69.49: 1768 69.49 - 104.23: 163 104.23 - 138.97: 2 138.97 - 173.72: 6 Dihedral angle restraints: 9998 sinusoidal: 8853 harmonic: 1145 Sorted by residual: dihedral pdb=" C4' G B 432 " pdb=" C3' G B 432 " pdb=" C2' G B 432 " pdb=" C1' G B 432 " ideal model delta sinusoidal sigma weight residual 36.34 -44.07 80.41 1 3.10e+00 1.04e-01 8.33e+02 dihedral pdb=" C4' A B 426 " pdb=" C3' A B 426 " pdb=" C2' A B 426 " pdb=" C1' A B 426 " ideal model delta sinusoidal sigma weight residual 36.34 -40.26 76.61 1 3.10e+00 1.04e-01 7.68e+02 dihedral pdb=" C4' G B 592 " pdb=" C3' G B 592 " pdb=" C2' G B 592 " pdb=" C1' G B 592 " ideal model delta sinusoidal sigma weight residual 36.35 -39.58 75.92 1 3.10e+00 1.04e-01 7.56e+02 ... (remaining 9995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2391 0.082 - 0.164: 181 0.164 - 0.246: 497 0.246 - 0.327: 145 0.327 - 0.409: 18 Chirality restraints: 3232 Sorted by residual: chirality pdb=" P G B 223 " pdb=" OP1 G B 223 " pdb=" OP2 G B 223 " pdb=" O5' G B 223 " both_signs ideal model delta sigma weight residual True 2.17 -2.58 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" P C B 439 " pdb=" OP1 C B 439 " pdb=" OP2 C B 439 " pdb=" O5' C B 439 " both_signs ideal model delta sigma weight residual True 2.17 -2.57 -0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" C2' A B 426 " pdb=" C3' A B 426 " pdb=" O2' A B 426 " pdb=" C1' A B 426 " both_signs ideal model delta sigma weight residual False -2.79 -2.40 -0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 3229 not shown) Planarity restraints: 1108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 99 " -0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO D 100 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 51 " 0.038 2.00e-02 2.50e+03 1.81e-02 9.05e+00 pdb=" N9 A B 51 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A B 51 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 51 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A B 51 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 51 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 51 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A B 51 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 51 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 51 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A B 51 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 436 " 0.037 2.00e-02 2.50e+03 1.93e-02 8.37e+00 pdb=" N1 U B 436 " -0.040 2.00e-02 2.50e+03 pdb=" C2 U B 436 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U B 436 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U B 436 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U B 436 " 0.008 2.00e-02 2.50e+03 pdb=" O4 U B 436 " 0.012 2.00e-02 2.50e+03 pdb=" C5 U B 436 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 436 " -0.007 2.00e-02 2.50e+03 ... (remaining 1105 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1629 2.72 - 3.26: 12266 3.26 - 3.81: 32606 3.81 - 4.35: 39407 4.35 - 4.90: 50689 Nonbonded interactions: 136597 Sorted by model distance: nonbonded pdb=" O2' A B 370 " pdb=" O4' G B 371 " model vdw 2.174 3.040 nonbonded pdb=" O2' G B 136 " pdb=" OP1 U B 148 " model vdw 2.239 3.040 nonbonded pdb=" OG SER D 415 " pdb=" OD2 ASP D 418 " model vdw 2.285 3.040 nonbonded pdb=" OP2 A B 137 " pdb=" O2' A B 147 " model vdw 2.290 3.040 nonbonded pdb=" OG SER D 110 " pdb=" OD2 ASP D 211 " model vdw 2.295 3.040 ... (remaining 136592 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=0.00 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: 5.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.690 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.006 0.084 16531 Z= 0.295 Angle : 1.203 24.199 25066 Z= 0.493 Chirality : 0.115 0.409 3232 Planarity : 0.007 0.086 1108 Dihedral : 26.959 173.716 9262 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.14 % Favored : 96.34 % Rotamer: Outliers : 1.15 % Allowed : 23.34 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.34), residues: 394 helix: -0.97 (0.26), residues: 272 sheet: -1.11 (1.04), residues: 20 loop : -2.29 (0.49), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 217 TYR 0.029 0.003 TYR D 350 PHE 0.018 0.003 PHE D 221 TRP 0.009 0.002 TRP D 328 HIS 0.003 0.001 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.30 (16531) covalent geometry : angle 1.20266 / 0.49 (25066) hydrogen bonds : bond 0.13901 / 8.70 ( 644) hydrogen bonds : angle 5.28168 / 3.78 ( 1305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.260 Fit side-chains REVERT: D 197 ASN cc_start: 0.6283 (t0) cc_final: 0.5914 (t0) REVERT: D 216 LYS cc_start: 0.8625 (tmtt) cc_final: 0.8217 (tttt) REVERT: D 236 MET cc_start: 0.5233 (ppp) cc_final: 0.4107 (ttp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1537 time to fit residues: 8.3759 Evaluate side-chains 33 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.177258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.140534 restraints weight = 47308.411| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 0.92 r_work: 0.3138 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (16 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16531 Z= 0.321 Angle : 1.291 17.114 25066 Z= 0.516 Chirality : 0.102 1.615 3232 Planarity : 0.006 0.080 1108 Dihedral : 25.492 168.775 8440 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.66 % Favored : 95.81 % Rotamer: Outliers : 3.17 % Allowed : 21.61 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.38 (0.40), residues: 394 helix: 0.50 (0.30), residues: 272 sheet: -1.08 (1.02), residues: 22 loop : -2.00 (0.55), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 247 TYR 0.024 0.002 TYR D 385 PHE 0.011 0.002 PHE D 145 TRP 0.011 0.002 TRP D 136 HIS 0.004 0.001 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.32 (16531) covalent geometry : angle 1.29067 / 0.52 (25066) hydrogen bonds : bond 0.07574 / 5.01 ( 644) hydrogen bonds : angle 3.52295 / 2.54 ( 1305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.199 Fit side-chains REVERT: D 88 ARG cc_start: 0.7645 (ttm110) cc_final: 0.7011 (mtm110) REVERT: D 197 ASN cc_start: 0.6659 (t0) cc_final: 0.6271 (t0) REVERT: D 216 LYS cc_start: 0.8669 (tmtt) cc_final: 0.8405 (tttt) REVERT: D 236 MET cc_start: 0.5724 (ppp) cc_final: 0.5364 (ttp) REVERT: D 247 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7363 (ttm170) outliers start: 7 outliers final: 7 residues processed: 32 average time/residue: 0.1450 time to fit residues: 6.7992 Evaluate side-chains 33 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.181631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142007 restraints weight = 53914.056| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.01 r_work: 0.3178 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16531 Z= 0.227 Angle : 1.109 17.032 25066 Z= 0.440 Chirality : 0.087 1.308 3232 Planarity : 0.005 0.079 1108 Dihedral : 25.253 176.250 8440 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.66 % Favored : 95.81 % Rotamer: Outliers : 3.17 % Allowed : 23.05 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.47 (0.42), residues: 394 helix: 1.22 (0.31), residues: 272 sheet: -0.96 (1.01), residues: 22 loop : -1.88 (0.57), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 247 TYR 0.023 0.002 TYR D 385 PHE 0.010 0.002 PHE D 145 TRP 0.008 0.001 TRP D 136 HIS 0.002 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.23 (16531) covalent geometry : angle 1.10899 / 0.44 (25066) hydrogen bonds : bond 0.06979 / 4.67 ( 644) hydrogen bonds : angle 3.32963 / 2.41 ( 1305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: D 88 ARG cc_start: 0.7497 (ttm110) cc_final: 0.6816 (mtm110) REVERT: D 197 ASN cc_start: 0.6616 (t0) cc_final: 0.6241 (t0) REVERT: D 216 LYS cc_start: 0.8664 (tmtt) cc_final: 0.8431 (tttt) REVERT: D 236 MET cc_start: 0.5822 (ppp) cc_final: 0.5088 (ttp) REVERT: D 247 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7629 (tmm-80) outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 0.1480 time to fit residues: 7.5618 Evaluate side-chains 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.184101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143210 restraints weight = 52024.326| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.21 r_work: 0.3186 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16531 Z= 0.178 Angle : 1.079 16.706 25066 Z= 0.427 Chirality : 0.084 1.179 3232 Planarity : 0.005 0.083 1108 Dihedral : 25.259 177.684 8440 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.14 % Favored : 96.34 % Rotamer: Outliers : 3.75 % Allowed : 22.19 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 1.02 (0.43), residues: 394 helix: 1.68 (0.32), residues: 272 sheet: -0.91 (1.02), residues: 22 loop : -1.79 (0.59), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 247 TYR 0.019 0.002 TYR D 385 PHE 0.010 0.001 PHE D 145 TRP 0.010 0.001 TRP D 136 HIS 0.002 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (16531) covalent geometry : angle 1.07866 / 0.43 (25066) hydrogen bonds : bond 0.06636 / 4.43 ( 644) hydrogen bonds : angle 3.18655 / 2.31 ( 1305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: D 88 ARG cc_start: 0.7299 (ttm110) cc_final: 0.6581 (mtm110) REVERT: D 197 ASN cc_start: 0.6539 (t0) cc_final: 0.6155 (t0) REVERT: D 216 LYS cc_start: 0.8667 (tmtt) cc_final: 0.8423 (tttt) REVERT: D 236 MET cc_start: 0.5849 (ppp) cc_final: 0.5249 (ttp) REVERT: D 247 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7637 (tmm-80) outliers start: 9 outliers final: 7 residues processed: 37 average time/residue: 0.1431 time to fit residues: 7.5733 Evaluate side-chains 40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 30.0000 chunk 16 optimal weight: 0.0570 chunk 87 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.184331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144192 restraints weight = 45476.528| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.00 r_work: 0.3228 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16531 Z= 0.183 Angle : 1.067 16.637 25066 Z= 0.423 Chirality : 0.083 1.148 3232 Planarity : 0.005 0.080 1108 Dihedral : 25.195 178.386 8440 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.40 % Favored : 96.07 % Rotamer: Outliers : 3.75 % Allowed : 23.05 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 1.25 (0.43), residues: 394 helix: 1.84 (0.32), residues: 272 sheet: -0.67 (1.06), residues: 22 loop : -1.71 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 247 TYR 0.039 0.002 TYR D 60 PHE 0.008 0.001 PHE D 145 TRP 0.008 0.001 TRP D 136 HIS 0.002 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (16531) covalent geometry : angle 1.06701 / 0.42 (25066) hydrogen bonds : bond 0.06620 / 4.42 ( 644) hydrogen bonds : angle 3.13229 / 2.28 ( 1305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: D 88 ARG cc_start: 0.7410 (ttm110) cc_final: 0.6678 (mtm110) REVERT: D 197 ASN cc_start: 0.6576 (t0) cc_final: 0.6225 (t0) REVERT: D 216 LYS cc_start: 0.8679 (tmtt) cc_final: 0.8459 (tttt) REVERT: D 236 MET cc_start: 0.5972 (ppp) cc_final: 0.5227 (ttp) REVERT: D 247 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7665 (tmm-80) REVERT: D 396 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7814 (pptt) outliers start: 9 outliers final: 8 residues processed: 39 average time/residue: 0.1488 time to fit residues: 8.2917 Evaluate side-chains 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 396 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 20 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.182485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140801 restraints weight = 59388.623| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.27 r_work: 0.3136 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16531 Z= 0.232 Angle : 1.096 16.764 25066 Z= 0.434 Chirality : 0.085 1.205 3232 Planarity : 0.005 0.080 1108 Dihedral : 25.082 178.196 8440 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.66 % Favored : 95.81 % Rotamer: Outliers : 3.75 % Allowed : 23.05 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 1.31 (0.43), residues: 394 helix: 1.92 (0.31), residues: 272 sheet: -0.67 (1.06), residues: 22 loop : -1.78 (0.59), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 266 TYR 0.023 0.002 TYR D 385 PHE 0.009 0.001 PHE D 298 TRP 0.007 0.001 TRP D 136 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.23 (16531) covalent geometry : angle 1.09605 / 0.43 (25066) hydrogen bonds : bond 0.07055 / 4.72 ( 644) hydrogen bonds : angle 3.15527 / 2.29 ( 1305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.244 Fit side-chains REVERT: D 88 ARG cc_start: 0.7255 (ttm110) cc_final: 0.6509 (mtm110) REVERT: D 197 ASN cc_start: 0.6679 (t0) cc_final: 0.6263 (t0) REVERT: D 216 LYS cc_start: 0.8713 (tmtt) cc_final: 0.8477 (tttt) REVERT: D 236 MET cc_start: 0.6140 (ppp) cc_final: 0.5668 (ttp) REVERT: D 247 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7657 (tmm-80) REVERT: D 396 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.7954 (pttm) outliers start: 9 outliers final: 8 residues processed: 34 average time/residue: 0.1447 time to fit residues: 7.1291 Evaluate side-chains 37 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 396 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.176219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126808 restraints weight = 59083.330| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.01 r_work: 0.3031 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.061 16531 Z= 0.496 Angle : 1.359 20.750 25066 Z= 0.539 Chirality : 0.106 1.873 3232 Planarity : 0.006 0.076 1108 Dihedral : 25.196 174.455 8440 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.97 % Favored : 94.50 % Rotamer: Outliers : 4.03 % Allowed : 23.05 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.65 (0.41), residues: 394 helix: 1.38 (0.31), residues: 272 sheet: -0.64 (0.98), residues: 22 loop : -1.95 (0.56), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 353 TYR 0.030 0.003 TYR D 385 PHE 0.014 0.003 PHE D 145 TRP 0.012 0.002 TRP D 136 HIS 0.005 0.002 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.01016 / 0.50 (16531) covalent geometry : angle 1.35852 / 0.54 (25066) hydrogen bonds : bond 0.09206 / 6.15 ( 644) hydrogen bonds : angle 3.47099 / 2.50 ( 1305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.214 Fit side-chains REVERT: D 88 ARG cc_start: 0.7364 (ttm110) cc_final: 0.6714 (mtm110) REVERT: D 216 LYS cc_start: 0.8678 (tmtt) cc_final: 0.8433 (tttt) REVERT: D 247 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7622 (tmm-80) REVERT: D 396 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8458 (pttm) outliers start: 10 outliers final: 8 residues processed: 32 average time/residue: 0.1340 time to fit residues: 6.1302 Evaluate side-chains 34 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 396 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 69 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 8 optimal weight: 0.0970 chunk 49 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.186183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147458 restraints weight = 44619.485| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 0.88 r_work: 0.3273 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16531 Z= 0.159 Angle : 1.050 17.270 25066 Z= 0.413 Chirality : 0.079 0.904 3232 Planarity : 0.005 0.080 1108 Dihedral : 25.130 175.362 8440 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.52 % Allowed : 2.88 % Favored : 96.60 % Rotamer: Outliers : 3.46 % Allowed : 23.63 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 1.29 (0.43), residues: 394 helix: 1.91 (0.31), residues: 272 sheet: -0.95 (1.00), residues: 22 loop : -1.73 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 247 TYR 0.017 0.002 TYR D 385 PHE 0.010 0.001 PHE D 145 TRP 0.007 0.001 TRP D 136 HIS 0.001 0.000 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (16531) covalent geometry : angle 1.04954 / 0.41 (25066) hydrogen bonds : bond 0.06914 / 4.60 ( 644) hydrogen bonds : angle 3.12697 / 2.26 ( 1305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.236 Fit side-chains REVERT: D 88 ARG cc_start: 0.7342 (ttm110) cc_final: 0.6872 (mtp180) REVERT: D 197 ASN cc_start: 0.6317 (t0) cc_final: 0.6002 (t0) REVERT: D 216 LYS cc_start: 0.8706 (tmtt) cc_final: 0.8498 (tttt) REVERT: D 247 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7650 (tmm-80) REVERT: D 396 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7907 (pptt) outliers start: 8 outliers final: 6 residues processed: 34 average time/residue: 0.1382 time to fit residues: 6.5533 Evaluate side-chains 34 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 396 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.184387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.138412 restraints weight = 49189.710| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.22 r_work: 0.3188 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16531 Z= 0.202 Angle : 1.061 15.875 25066 Z= 0.419 Chirality : 0.078 0.775 3232 Planarity : 0.005 0.080 1108 Dihedral : 25.062 175.543 8440 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.14 % Favored : 96.34 % Rotamer: Outliers : 3.75 % Allowed : 23.34 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 1.45 (0.43), residues: 394 helix: 2.06 (0.31), residues: 272 sheet: -0.94 (1.00), residues: 22 loop : -1.77 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 247 TYR 0.021 0.002 TYR D 385 PHE 0.009 0.001 PHE D 145 TRP 0.007 0.001 TRP D 136 HIS 0.002 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (16531) covalent geometry : angle 1.06095 / 0.42 (25066) hydrogen bonds : bond 0.07147 / 4.76 ( 644) hydrogen bonds : angle 3.12701 / 2.28 ( 1305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.196 Fit side-chains REVERT: D 88 ARG cc_start: 0.7226 (ttm110) cc_final: 0.6652 (mtm110) REVERT: D 197 ASN cc_start: 0.6537 (t0) cc_final: 0.6094 (t0) REVERT: D 216 LYS cc_start: 0.8720 (tmtt) cc_final: 0.8487 (tttt) REVERT: D 396 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7842 (pptt) outliers start: 9 outliers final: 8 residues processed: 33 average time/residue: 0.1254 time to fit residues: 6.2135 Evaluate side-chains 36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 396 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 59 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.181906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.134136 restraints weight = 44060.900| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.34 r_work: 0.3156 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 16531 Z= 0.280 Angle : 1.126 18.466 25066 Z= 0.446 Chirality : 0.083 0.931 3232 Planarity : 0.005 0.079 1108 Dihedral : 25.053 174.952 8440 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.93 % Favored : 95.55 % Rotamer: Outliers : 3.75 % Allowed : 23.05 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 1.30 (0.42), residues: 394 helix: 1.94 (0.31), residues: 272 sheet: -0.91 (0.96), residues: 22 loop : -1.82 (0.58), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 247 TYR 0.026 0.002 TYR D 385 PHE 0.010 0.002 PHE D 145 TRP 0.006 0.001 TRP D 136 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.28 (16531) covalent geometry : angle 1.12575 / 0.45 (25066) hydrogen bonds : bond 0.07784 / 5.19 ( 644) hydrogen bonds : angle 3.19821 / 2.32 ( 1305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.185 Fit side-chains REVERT: D 88 ARG cc_start: 0.7261 (ttm110) cc_final: 0.6642 (mtm110) REVERT: D 197 ASN cc_start: 0.6650 (t0) cc_final: 0.6208 (t0) REVERT: D 216 LYS cc_start: 0.8724 (tmtt) cc_final: 0.8501 (tttt) REVERT: D 396 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8048 (pttp) outliers start: 9 outliers final: 8 residues processed: 33 average time/residue: 0.1263 time to fit residues: 6.1830 Evaluate side-chains 35 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 396 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 64 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.181979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135267 restraints weight = 39454.851| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.15 r_work: 0.3176 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 16531 Z= 0.277 Angle : 1.121 18.152 25066 Z= 0.444 Chirality : 0.083 0.928 3232 Planarity : 0.005 0.079 1108 Dihedral : 25.053 174.874 8440 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.93 % Favored : 95.55 % Rotamer: Outliers : 3.75 % Allowed : 23.05 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 1.29 (0.42), residues: 394 helix: 1.93 (0.31), residues: 272 sheet: -0.88 (0.96), residues: 22 loop : -1.82 (0.58), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 247 TYR 0.025 0.002 TYR D 385 PHE 0.011 0.002 PHE D 145 TRP 0.007 0.001 TRP D 136 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.28 (16531) covalent geometry : angle 1.12076 / 0.44 (25066) hydrogen bonds : bond 0.07727 / 5.15 ( 644) hydrogen bonds : angle 3.19959 / 2.33 ( 1305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3391.44 seconds wall clock time: 58 minutes 54.92 seconds (3534.92 seconds total)