Starting phenix.real_space_refine on Fri Jul 3 14:30:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uim_26549/07_2026/7uim_26549.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uim_26549/07_2026/7uim_26549.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 { model { file = "/net/cci-nas-00/data/ceres_data/7uim_26549/07_2026/7uim_26549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uim_26549/07_2026/7uim_26549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uim_26549/07_2026/7uim_26549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uim_26549/07_2026/7uim_26549.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uim_26549/07_2026/7uim_26549.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uim_26549/07_2026/7uim_26549.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= 0.015 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 P 536 5.49 5 Mg 13 5.21 5 S 21 5.16 5 C 7184 2.51 5 N 2736 2.21 5 O 4282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14772 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 11624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 11624 Inner-chain residues flagged as termini: ['pdbres=" G B 171 "', 'pdbres=" G B 220 "', 'pdbres=" A B 298 "', 'pdbres=" A B 401 "', 'pdbres=" G B 551 "'] Classifications: {'RNA': 541} Modifications used: {'5*END': 5, 'rna2p_pur': 42, 'rna2p_pyr': 16, 'rna3p_pur': 286, 'rna3p_pyr': 197} Link IDs: {'rna2p': 57, 'rna3p': 483} Chain: "D" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3133 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 10, 'TRANS': 376} Chain breaks: 2 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' MG': 13, 'NH4': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Time building chain proxies: 2.93, per 1000 atoms: 0.20 Number of scatterers: 14772 At special positions: 0 Unit cell: (100.672, 153.92, 154.752, 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) S 21 16.00 P 536 15.00 Mg 13 11.99 O 4282 8.00 N 2736 7.00 C 7184 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 262.7 milliseconds 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 72.4% alpha, 4.1% beta 159 base pairs and 290 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 36 through 58 removed outlier: 6.359A pdb=" N GLU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N THR D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 106 Proline residue: D 100 - end of helix removed outlier: 6.256A pdb=" N GLU D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 133 removed outlier: 3.649A 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 Processing helix chain 'D' and resid 164 through 177 removed outlier: 4.064A pdb=" N ILE D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 218 removed outlier: 3.870A 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 266 through 270 removed outlier: 3.566A pdb=" N LEU D 270 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 313 through 332 Processing helix chain 'D' and resid 337 through 361 removed outlier: 4.159A pdb=" N GLU D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 3.622A 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 387 Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'D' and resid 397 through 403 removed outlier: 3.732A pdb=" N ILE D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 412 Processing helix chain 'D' and resid 415 through 423 Processing sheet with id=AA1, first strand: chain 'D' and resid 220 through 223 removed outlier: 4.571A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D 265 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 275 through 277 200 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 383 hydrogen bonds 574 hydrogen bond angles 0 basepair planarities 159 basepair parallelities 290 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 1.38 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: 1918 1.33 - 1.45: 7477 1.45 - 1.57: 5712 1.57 - 1.70: 1072 1.70 - 1.82: 35 Bond restraints: 16214 Sorted by residual: bond pdb=" CB GLU D 39 " pdb=" CG GLU D 39 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.76e+00 bond pdb=" CB ILE D 325 " pdb=" CG2 ILE D 325 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.35e+00 bond pdb=" CD2 TYR D 174 " pdb=" CE2 TYR D 174 " ideal model delta sigma weight residual 1.382 1.329 0.053 3.00e-02 1.11e+03 3.16e+00 bond pdb=" CB LYS D 36 " pdb=" CG LYS D 36 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" CB ARG D 377 " pdb=" CG ARG D 377 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.48e+00 ... (remaining 16209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 24165 2.69 - 5.38: 368 5.38 - 8.08: 47 8.08 - 10.77: 6 10.77 - 13.46: 3 Bond angle restraints: 24589 Sorted by residual: angle pdb=" CA LYS D 36 " pdb=" CB LYS D 36 " pdb=" CG LYS D 36 " ideal model delta sigma weight residual 114.10 127.56 -13.46 2.00e+00 2.50e-01 4.53e+01 angle pdb=" CA PRO D 281 " pdb=" N PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 112.00 104.42 7.58 1.40e+00 5.10e-01 2.93e+01 angle pdb=" O3' G B 123 " pdb=" C3' G B 123 " pdb=" C2' G B 123 " ideal model delta sigma weight residual 113.70 121.42 -7.72 1.50e+00 4.44e-01 2.65e+01 angle pdb=" CA ARG D 377 " pdb=" CB ARG D 377 " pdb=" CG ARG D 377 " ideal model delta sigma weight residual 114.10 124.17 -10.07 2.00e+00 2.50e-01 2.54e+01 angle pdb=" CB LYS D 263 " pdb=" CG LYS D 263 " pdb=" CD LYS D 263 " ideal model delta sigma weight residual 111.30 121.59 -10.29 2.30e+00 1.89e-01 2.00e+01 ... (remaining 24584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 7769 33.89 - 67.78: 593 67.78 - 101.67: 56 101.67 - 135.57: 2 135.57 - 169.46: 6 Dihedral angle restraints: 8426 sinusoidal: 7302 harmonic: 1124 Sorted by residual: dihedral pdb=" O4' C B 439 " pdb=" C1' C B 439 " pdb=" N1 C B 439 " pdb=" C2 C B 439 " ideal model delta sinusoidal sigma weight residual 232.00 62.54 169.46 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O4' C B 440 " pdb=" C1' C B 440 " pdb=" N1 C B 440 " pdb=" C2 C B 440 " ideal model delta sinusoidal sigma weight residual -128.00 35.88 -163.88 1 1.70e+01 3.46e-03 6.51e+01 dihedral pdb=" CA PRO D 281 " pdb=" C PRO D 281 " pdb=" N ARG D 282 " pdb=" CA ARG D 282 " ideal model delta harmonic sigma weight residual 180.00 148.62 31.38 0 5.00e+00 4.00e-02 3.94e+01 ... (remaining 8423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2769 0.062 - 0.124: 324 0.124 - 0.186: 56 0.186 - 0.248: 9 0.248 - 0.310: 7 Chirality restraints: 3165 Sorted by residual: chirality pdb=" C3' G B 123 " pdb=" C4' G B 123 " pdb=" O3' G B 123 " pdb=" C2' G B 123 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' G B 333 " pdb=" C4' G B 333 " pdb=" O3' G B 333 " pdb=" C2' G B 333 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C3' U B 46 " pdb=" C4' U B 46 " pdb=" O3' U B 46 " pdb=" C2' U B 46 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 3162 not shown) Planarity restraints: 1084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 280 " -0.066 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO D 281 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 281 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 281 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 39 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" CD GLU D 39 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU D 39 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU D 39 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 289 " 0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO D 290 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 290 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 290 " 0.044 5.00e-02 4.00e+02 ... (remaining 1081 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 82 2.50 - 3.10: 9414 3.10 - 3.70: 29724 3.70 - 4.30: 41728 4.30 - 4.90: 53740 Nonbonded interactions: 134688 Sorted by model distance: nonbonded pdb=" OP1 C B 581 " pdb="MG MG B 701 " model vdw 1.903 2.170 nonbonded pdb=" O3' U B 638 " pdb="MG MG B 701 " model vdw 1.943 2.170 nonbonded pdb=" OP2 G B 158 " pdb="MG MG B 708 " model vdw 1.984 2.170 nonbonded pdb=" OP2 A B 560 " pdb="MG MG B 705 " model vdw 1.992 2.170 nonbonded pdb=" OP2 A B 323 " pdb="MG MG B 709 " model vdw 2.016 2.170 ... (remaining 134683 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: 3.680 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: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.040 Find NCS groups from input model: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4745 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 : 0.005 0.068 16215 Z= 0.257 Angle : 0.871 13.462 24589 Z= 0.437 Chirality : 0.045 0.310 3165 Planarity : 0.007 0.096 1084 Dihedral : 18.460 169.458 7702 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 31.67 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.28 (0.39), residues: 381 helix: -0.58 (0.28), residues: 256 sheet: -1.65 (0.92), residues: 24 loop : -0.87 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 377 TYR 0.032 0.003 TYR D 278 PHE 0.032 0.003 PHE D 298 TRP 0.018 0.003 TRP D 360 HIS 0.007 0.002 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.26 (16214) covalent geometry : angle 0.87102 / 0.44 (24589) hydrogen bonds : bond 0.18650 / 11.12 ( 583) hydrogen bonds : angle 7.68906 / 4.46 ( 1165) Misc. bond : bond 0.00140 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 26 ASN cc_start: 0.8205 (m-40) cc_final: 0.8002 (m-40) REVERT: D 175 LEU cc_start: 0.7673 (mt) cc_final: 0.7446 (tp) REVERT: D 270 LEU cc_start: 0.4275 (mt) cc_final: 0.2998 (mt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1563 time to fit residues: 26.8946 Evaluate side-chains 71 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.071672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.057945 restraints weight = 110391.366| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.14 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 16215 Z= 0.394 Angle : 0.966 10.350 24589 Z= 0.478 Chirality : 0.047 0.247 3165 Planarity : 0.007 0.075 1084 Dihedral : 19.211 174.356 6897 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 33.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 7.33 % Allowed : 30.21 % Favored : 62.46 % 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: -1.28 (0.39), residues: 381 helix: -0.43 (0.29), residues: 263 sheet: -1.18 (0.99), residues: 24 loop : -1.54 (0.59), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG D 381 TYR 0.023 0.003 TYR D 392 PHE 0.028 0.004 PHE D 298 TRP 0.067 0.005 TRP D 328 HIS 0.006 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.39 (16214) covalent geometry : angle 0.96634 / 0.48 (24589) hydrogen bonds : bond 0.13315 / 8.03 ( 583) hydrogen bonds : angle 4.81453 / 2.91 ( 1165) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.3208 (mm-30) cc_final: 0.2478 (pt0) REVERT: D 35 MET cc_start: 0.5973 (ptt) cc_final: 0.5539 (pmm) REVERT: D 96 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8222 (mt0) REVERT: D 130 MET cc_start: 0.7188 (mpp) cc_final: 0.6237 (mpp) REVERT: D 173 LYS cc_start: 0.8775 (ptpt) cc_final: 0.8234 (mttt) REVERT: D 175 LEU cc_start: 0.8656 (mt) cc_final: 0.8233 (tt) REVERT: D 206 MET cc_start: 0.8272 (tpp) cc_final: 0.8027 (tpt) REVERT: D 235 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8343 (tm-30) REVERT: D 310 TRP cc_start: 0.8271 (OUTLIER) cc_final: 0.7511 (t60) outliers start: 25 outliers final: 10 residues processed: 87 average time/residue: 0.1300 time to fit residues: 16.4206 Evaluate side-chains 69 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 107 HIS ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN D 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.068053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.054132 restraints weight = 111471.400| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.03 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.8810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.123 16215 Z= 0.447 Angle : 1.024 12.369 24589 Z= 0.511 Chirality : 0.051 0.362 3165 Planarity : 0.008 0.079 1084 Dihedral : 20.334 178.026 6897 Min Nonbonded Distance : 1.110 Molprobity Statistics. All-atom Clashscore : 39.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.20 % Favored : 95.54 % Rotamer: Outliers : 9.09 % Allowed : 29.62 % Favored : 61.29 % 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: -2.00 (0.39), residues: 381 helix: -0.89 (0.29), residues: 266 sheet: 0.06 (1.25), residues: 14 loop : -2.36 (0.59), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG D 353 TYR 0.030 0.004 TYR D 392 PHE 0.025 0.004 PHE D 106 TRP 0.035 0.004 TRP D 328 HIS 0.006 0.002 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00834 / 0.45 (16214) covalent geometry : angle 1.02362 / 0.51 (24589) hydrogen bonds : bond 0.14321 / 8.74 ( 583) hydrogen bonds : angle 5.14217 / 3.14 ( 1165) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: D 30 GLU cc_start: 0.3031 (OUTLIER) cc_final: 0.2753 (pt0) REVERT: D 130 MET cc_start: 0.7633 (mpp) cc_final: 0.7137 (mpp) REVERT: D 173 LYS cc_start: 0.9037 (ptpt) cc_final: 0.8279 (mptt) REVERT: D 175 LEU cc_start: 0.8529 (mt) cc_final: 0.8250 (tt) REVERT: D 310 TRP cc_start: 0.8058 (OUTLIER) cc_final: 0.7222 (t60) REVERT: D 416 MET cc_start: 0.9018 (mmm) cc_final: 0.8784 (mmm) outliers start: 31 outliers final: 14 residues processed: 88 average time/residue: 0.1285 time to fit residues: 16.5447 Evaluate side-chains 65 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 9 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 overall best weight: 6.3788 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.068385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.055011 restraints weight = 113020.496| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.74 r_work: 0.3581 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.9086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16215 Z= 0.333 Angle : 0.824 10.138 24589 Z= 0.417 Chirality : 0.043 0.335 3165 Planarity : 0.006 0.061 1084 Dihedral : 19.717 177.676 6897 Min Nonbonded Distance : 0.939 Molprobity Statistics. All-atom Clashscore : 30.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 8.50 % Allowed : 32.55 % Favored : 58.94 % 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: -1.30 (0.41), residues: 381 helix: -0.21 (0.30), residues: 264 sheet: -1.03 (0.82), residues: 29 loop : -2.49 (0.62), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 172 TYR 0.023 0.003 TYR D 392 PHE 0.014 0.003 PHE D 298 TRP 0.034 0.004 TRP D 328 HIS 0.005 0.001 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.33 (16214) covalent geometry : angle 0.82364 / 0.42 (24589) hydrogen bonds : bond 0.11245 / 6.85 ( 583) hydrogen bonds : angle 4.68158 / 2.85 ( 1165) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.4151 (mm-30) cc_final: 0.3414 (pt0) REVERT: D 130 MET cc_start: 0.7322 (mpp) cc_final: 0.6820 (mpp) REVERT: D 173 LYS cc_start: 0.9096 (ptpt) cc_final: 0.8324 (mptt) REVERT: D 175 LEU cc_start: 0.8615 (mt) cc_final: 0.8413 (tt) REVERT: D 214 MET cc_start: 0.9019 (mmm) cc_final: 0.8786 (mmm) REVERT: D 285 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8379 (pm20) REVERT: D 299 LYS cc_start: 0.8411 (pptt) cc_final: 0.8030 (mtmt) REVERT: D 323 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.6901 (tm-30) outliers start: 29 outliers final: 15 residues processed: 76 average time/residue: 0.1252 time to fit residues: 14.0615 Evaluate side-chains 70 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 31 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 overall best weight: 5.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.068136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.054665 restraints weight = 112277.463| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.70 r_work: 0.3574 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.9616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 16215 Z= 0.321 Angle : 0.814 12.488 24589 Z= 0.413 Chirality : 0.042 0.238 3165 Planarity : 0.006 0.059 1084 Dihedral : 19.787 179.544 6897 Min Nonbonded Distance : 1.000 Molprobity Statistics. All-atom Clashscore : 29.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.20 % Favored : 95.54 % Rotamer: Outliers : 8.21 % Allowed : 30.50 % Favored : 61.29 % 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: -1.01 (0.41), residues: 381 helix: -0.03 (0.30), residues: 263 sheet: -0.18 (0.93), residues: 24 loop : -2.39 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 172 TYR 0.025 0.003 TYR D 392 PHE 0.012 0.003 PHE D 248 TRP 0.023 0.003 TRP D 328 HIS 0.003 0.001 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.32 (16214) covalent geometry : angle 0.81382 / 0.41 (24589) hydrogen bonds : bond 0.11234 / 6.80 ( 583) hydrogen bonds : angle 4.61531 / 2.85 ( 1165) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.3953 (OUTLIER) cc_final: 0.3711 (pt0) REVERT: D 130 MET cc_start: 0.7331 (mpp) cc_final: 0.6979 (mpp) REVERT: D 172 ARG cc_start: 0.9349 (ttm-80) cc_final: 0.9145 (mtm110) REVERT: D 173 LYS cc_start: 0.9172 (ptpt) cc_final: 0.8435 (mptt) REVERT: D 214 MET cc_start: 0.8971 (mmm) cc_final: 0.8708 (mmm) REVERT: D 280 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8268 (p0) REVERT: D 299 LYS cc_start: 0.8412 (pptt) cc_final: 0.7958 (mtmt) REVERT: D 310 TRP cc_start: 0.7819 (OUTLIER) cc_final: 0.6967 (t60) REVERT: D 324 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6108 (tt) REVERT: D 416 MET cc_start: 0.9172 (mmm) cc_final: 0.8562 (mmm) outliers start: 28 outliers final: 17 residues processed: 79 average time/residue: 0.1259 time to fit residues: 14.5958 Evaluate side-chains 70 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 58 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.068421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.055081 restraints weight = 110408.387| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.61 r_work: 0.3588 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.9902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16215 Z= 0.289 Angle : 0.772 12.480 24589 Z= 0.392 Chirality : 0.040 0.231 3165 Planarity : 0.006 0.066 1084 Dihedral : 19.597 179.710 6897 Min Nonbonded Distance : 0.993 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.72 % Favored : 95.01 % Rotamer: Outliers : 7.33 % Allowed : 33.72 % Favored : 58.94 % 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: -0.72 (0.41), residues: 381 helix: 0.21 (0.31), residues: 264 sheet: -0.04 (0.97), residues: 24 loop : -2.38 (0.58), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 301 TYR 0.022 0.003 TYR D 392 PHE 0.012 0.002 PHE D 113 TRP 0.015 0.002 TRP D 328 HIS 0.015 0.002 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.29 (16214) covalent geometry : angle 0.77190 / 0.39 (24589) hydrogen bonds : bond 0.10460 / 6.35 ( 583) hydrogen bonds : angle 4.51536 / 2.80 ( 1165) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 130 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6901 (mpp) REVERT: D 153 LYS cc_start: 0.9750 (mtmm) cc_final: 0.9475 (tppt) REVERT: D 173 LYS cc_start: 0.9063 (ptpt) cc_final: 0.8330 (mptt) REVERT: D 214 MET cc_start: 0.8988 (mmm) cc_final: 0.8702 (mmm) REVERT: D 285 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8449 (pm20) REVERT: D 299 LYS cc_start: 0.8344 (pptt) cc_final: 0.7945 (mtpt) REVERT: D 310 TRP cc_start: 0.7737 (OUTLIER) cc_final: 0.6838 (t60) outliers start: 25 outliers final: 15 residues processed: 74 average time/residue: 0.1124 time to fit residues: 12.3660 Evaluate side-chains 68 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.067542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.054023 restraints weight = 112707.553| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.68 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 1.0419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16215 Z= 0.331 Angle : 0.852 15.373 24589 Z= 0.428 Chirality : 0.043 0.232 3165 Planarity : 0.006 0.055 1084 Dihedral : 19.887 177.903 6897 Min Nonbonded Distance : 0.981 Molprobity Statistics. All-atom Clashscore : 31.97 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.56 % Favored : 93.18 % Rotamer: Outliers : 7.92 % Allowed : 34.02 % Favored : 58.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.40), residues: 381 helix: -0.20 (0.30), residues: 264 sheet: -0.25 (0.93), residues: 24 loop : -2.62 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 172 TYR 0.029 0.003 TYR D 392 PHE 0.018 0.003 PHE D 248 TRP 0.011 0.002 TRP D 328 HIS 0.008 0.002 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.33 (16214) covalent geometry : angle 0.85183 / 0.43 (24589) hydrogen bonds : bond 0.11748 / 7.11 ( 583) hydrogen bonds : angle 4.68076 / 2.88 ( 1165) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7160 (mpp) REVERT: D 136 TRP cc_start: 0.8493 (m100) cc_final: 0.8267 (m100) REVERT: D 172 ARG cc_start: 0.9201 (ttm-80) cc_final: 0.8959 (ttm170) REVERT: D 173 LYS cc_start: 0.9142 (ptpt) cc_final: 0.8501 (mptt) REVERT: D 214 MET cc_start: 0.8997 (mmm) cc_final: 0.8728 (mmm) REVERT: D 219 LEU cc_start: 0.7886 (mm) cc_final: 0.7606 (mm) REVERT: D 272 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6654 (t80) REVERT: D 280 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8460 (p0) REVERT: D 285 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8592 (mp10) REVERT: D 299 LYS cc_start: 0.8355 (pptt) cc_final: 0.7989 (mtpt) REVERT: D 310 TRP cc_start: 0.7712 (OUTLIER) cc_final: 0.6831 (t60) outliers start: 27 outliers final: 17 residues processed: 80 average time/residue: 0.1045 time to fit residues: 12.6164 Evaluate side-chains 79 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 272 TYR Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 57 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.067534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.054326 restraints weight = 113861.586| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.70 r_work: 0.3573 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 1.0664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16215 Z= 0.333 Angle : 0.832 12.755 24589 Z= 0.419 Chirality : 0.043 0.233 3165 Planarity : 0.006 0.049 1084 Dihedral : 19.732 177.316 6897 Min Nonbonded Distance : 1.000 Molprobity Statistics. All-atom Clashscore : 30.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.82 % Favored : 92.91 % Rotamer: Outliers : 8.50 % Allowed : 34.31 % Favored : 57.18 % 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: -1.17 (0.41), residues: 381 helix: -0.07 (0.31), residues: 265 sheet: -0.34 (0.89), residues: 24 loop : -2.76 (0.53), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 172 TYR 0.028 0.003 TYR D 392 PHE 0.018 0.003 PHE D 248 TRP 0.011 0.002 TRP D 328 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.33 (16214) covalent geometry : angle 0.83204 / 0.42 (24589) hydrogen bonds : bond 0.11207 / 6.78 ( 583) hydrogen bonds : angle 4.67586 / 2.87 ( 1165) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 56 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7567 (p90) REVERT: D 130 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.7026 (mpp) REVERT: D 151 HIS cc_start: 0.8844 (OUTLIER) cc_final: 0.8538 (m-70) REVERT: D 153 LYS cc_start: 0.9726 (mtmm) cc_final: 0.9462 (tppt) REVERT: D 172 ARG cc_start: 0.9263 (ttm-80) cc_final: 0.8835 (ttm170) REVERT: D 173 LYS cc_start: 0.9083 (ptpt) cc_final: 0.8398 (mptt) REVERT: D 214 MET cc_start: 0.9019 (mmm) cc_final: 0.8753 (mmm) REVERT: D 219 LEU cc_start: 0.7925 (mm) cc_final: 0.7622 (mm) REVERT: D 272 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7055 (t80) REVERT: D 285 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8433 (pm20) REVERT: D 297 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7279 (mmtm) REVERT: D 299 LYS cc_start: 0.8399 (pptt) cc_final: 0.8009 (mtpt) REVERT: D 310 TRP cc_start: 0.7721 (OUTLIER) cc_final: 0.6775 (t60) outliers start: 29 outliers final: 19 residues processed: 78 average time/residue: 0.1117 time to fit residues: 13.0488 Evaluate side-chains 82 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 272 TYR Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 375 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 76 optimal weight: 0.0050 chunk 38 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 overall best weight: 5.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 43 HIS D 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.067700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.054370 restraints weight = 112787.148| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.67 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 1.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16215 Z= 0.307 Angle : 0.821 16.368 24589 Z= 0.411 Chirality : 0.042 0.233 3165 Planarity : 0.005 0.046 1084 Dihedral : 19.607 177.765 6897 Min Nonbonded Distance : 1.012 Molprobity Statistics. All-atom Clashscore : 28.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.56 % Favored : 93.18 % Rotamer: Outliers : 8.21 % Allowed : 34.90 % Favored : 56.89 % 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: -1.20 (0.40), residues: 381 helix: -0.09 (0.31), residues: 264 sheet: -0.58 (0.90), residues: 24 loop : -2.68 (0.54), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 172 TYR 0.021 0.003 TYR D 392 PHE 0.016 0.003 PHE D 113 TRP 0.010 0.002 TRP D 328 HIS 0.004 0.001 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.31 (16214) covalent geometry : angle 0.82108 / 0.41 (24589) hydrogen bonds : bond 0.10908 / 6.62 ( 583) hydrogen bonds : angle 4.62986 / 2.84 ( 1165) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7489 (p90) REVERT: D 130 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6947 (mpp) REVERT: D 136 TRP cc_start: 0.8617 (m100) cc_final: 0.8140 (m100) REVERT: D 172 ARG cc_start: 0.9205 (ttm-80) cc_final: 0.8908 (ttm170) REVERT: D 173 LYS cc_start: 0.9100 (ptpt) cc_final: 0.8549 (mptt) REVERT: D 214 MET cc_start: 0.8991 (mmm) cc_final: 0.8736 (mmm) REVERT: D 219 LEU cc_start: 0.7801 (mm) cc_final: 0.7456 (mm) REVERT: D 272 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.6954 (t80) REVERT: D 285 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8618 (pm20) REVERT: D 299 LYS cc_start: 0.8359 (pptt) cc_final: 0.8014 (mtpt) REVERT: D 310 TRP cc_start: 0.7574 (OUTLIER) cc_final: 0.6676 (t60) outliers start: 28 outliers final: 17 residues processed: 77 average time/residue: 0.1235 time to fit residues: 14.1855 Evaluate side-chains 76 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 272 TYR Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 375 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 43 HIS D 323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.065982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.052623 restraints weight = 114821.559| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.87 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 1.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 16215 Z= 0.457 Angle : 1.013 15.986 24589 Z= 0.500 Chirality : 0.050 0.260 3165 Planarity : 0.006 0.045 1084 Dihedral : 20.250 177.191 6897 Min Nonbonded Distance : 0.960 Molprobity Statistics. All-atom Clashscore : 41.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.82 % Favored : 92.91 % Rotamer: Outliers : 7.04 % Allowed : 35.48 % Favored : 57.48 % 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 (0.40), residues: 381 helix: -0.51 (0.31), residues: 264 sheet: -1.63 (0.79), residues: 29 loop : -2.96 (0.52), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 56 TYR 0.031 0.004 TYR D 392 PHE 0.029 0.004 PHE D 248 TRP 0.013 0.003 TRP D 310 HIS 0.033 0.005 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00850 / 0.46 (16214) covalent geometry : angle 1.01262 / 0.50 (24589) hydrogen bonds : bond 0.13953 / 8.40 ( 583) hydrogen bonds : angle 5.00687 / 3.08 ( 1165) Misc. bond : bond 0.00052 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7531 (p90) REVERT: D 130 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7097 (mpp) REVERT: D 136 TRP cc_start: 0.8481 (m100) cc_final: 0.7938 (m100) REVERT: D 153 LYS cc_start: 0.9631 (mtmm) cc_final: 0.9295 (tppt) REVERT: D 173 LYS cc_start: 0.9151 (ptpt) cc_final: 0.8467 (mmtm) REVERT: D 214 MET cc_start: 0.9014 (mmm) cc_final: 0.8751 (mmm) REVERT: D 219 LEU cc_start: 0.7672 (mm) cc_final: 0.7335 (mm) REVERT: D 272 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7074 (t80) REVERT: D 285 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8742 (pm20) REVERT: D 310 TRP cc_start: 0.7742 (OUTLIER) cc_final: 0.6806 (t60) outliers start: 24 outliers final: 16 residues processed: 71 average time/residue: 0.1168 time to fit residues: 12.4385 Evaluate side-chains 74 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 272 TYR Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 381 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 73 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 43 HIS D 323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.068863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.055558 restraints weight = 110054.221| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.60 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 1.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16215 Z= 0.218 Angle : 0.748 17.980 24589 Z= 0.374 Chirality : 0.038 0.239 3165 Planarity : 0.005 0.048 1084 Dihedral : 19.329 178.234 6897 Min Nonbonded Distance : 1.035 Molprobity Statistics. All-atom Clashscore : 23.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.25 % Favored : 94.49 % Rotamer: Outliers : 6.74 % Allowed : 36.36 % Favored : 56.89 % 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: -1.09 (0.41), residues: 381 helix: 0.05 (0.32), residues: 256 sheet: -0.77 (0.87), residues: 24 loop : -2.53 (0.51), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 301 TYR 0.016 0.003 TYR D 350 PHE 0.016 0.002 PHE D 113 TRP 0.010 0.001 TRP D 357 HIS 0.015 0.003 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.22 (16214) covalent geometry : angle 0.74770 / 0.37 (24589) hydrogen bonds : bond 0.09429 / 5.77 ( 583) hydrogen bonds : angle 4.49064 / 2.73 ( 1165) Misc. bond : bond 0.00011 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3371.48 seconds wall clock time: 59 minutes 15.33 seconds (3555.33 seconds total)