Starting phenix.real_space_refine on Sat Sep 12 07:50:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uim_26549/09_2026/7uim_26549.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uim_26549/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7uim_26549/09_2026/7uim_26549.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uim_26549/09_2026/7uim_26549.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uim_26549/09_2026/7uim_26549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uim_26549/09_2026/7uim_26549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uim_26549/09_2026/7uim_26549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uim_26549/09_2026/7uim_26549.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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 Classifications: {'RNAv2': 541} Modifications used: {'rna2p_pur': 42, 'rna2p_pyr': 16, 'rna3p_pur': 286, 'rna3p_pyr': 197} Link IDs: {'rna2p': 57, 'rna3p': 483} Unresolved chain links: 5 Unresolved chain link angles: 20 Unresolved chain link dihedrals: 15 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 5 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: 2.87, per 1000 atoms: 0.19 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: 1.23 Conformation dependent library (CDL) restraints added in 291.7 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: 2.01 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: 3.53 Time building geometry restraints manager: 1.72 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=" O3' C B 433 " pdb=" P C B 434 " ideal model delta sigma weight residual 1.607 1.626 -0.019 1.20e-02 6.94e+03 2.49e+00 ... (remaining 16209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 23413 2.69 - 5.38: 1103 5.38 - 8.08: 62 8.08 - 10.77: 8 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=" 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=" C3' G B 333 " pdb=" O3' G B 333 " pdb=" P C B 334 " ideal model delta sigma weight residual 119.70 125.42 -5.72 1.20e+00 6.94e-01 2.28e+01 angle pdb=" C3' C B 433 " pdb=" O3' C B 433 " pdb=" P C B 434 " ideal model delta sigma weight residual 119.70 125.42 -5.72 1.20e+00 6.94e-01 2.27e+01 ... (remaining 24584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.75: 7035 30.75 - 61.50: 1287 61.50 - 92.25: 99 92.25 - 123.01: 0 123.01 - 153.76: 5 Dihedral angle restraints: 8426 sinusoidal: 7302 harmonic: 1124 Sorted by residual: dihedral pdb=" C4' A B 438 " pdb=" C3' A B 438 " pdb=" C2' A B 438 " pdb=" C1' A B 438 " ideal model delta sinusoidal sigma weight residual 36.34 -40.79 77.13 1 3.10e+00 1.04e-01 7.76e+02 dihedral pdb=" C4' U B 325 " pdb=" C3' U B 325 " pdb=" C2' U B 325 " pdb=" C1' U B 325 " ideal model delta sinusoidal sigma weight residual 36.34 -39.99 76.34 1 3.10e+00 1.04e-01 7.63e+02 dihedral pdb=" C4' G B 340 " pdb=" C3' G B 340 " pdb=" C2' G B 340 " pdb=" C1' G B 340 " ideal model delta sinusoidal sigma weight residual 36.34 -39.13 75.47 1 3.10e+00 1.04e-01 7.48e+02 ... (remaining 8423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2308 0.085 - 0.169: 196 0.169 - 0.254: 537 0.254 - 0.339: 122 0.339 - 0.424: 2 Chirality restraints: 3165 Sorted by residual: chirality pdb=" P C B 434 " pdb=" OP1 C B 434 " pdb=" OP2 C B 434 " pdb=" O5' C B 434 " both_signs ideal model delta sigma weight residual True 2.17 -2.60 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" P U B 207 " pdb=" OP1 U B 207 " pdb=" OP2 U B 207 " pdb=" O5' U B 207 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C2' C B 183 " pdb=" C3' C B 183 " pdb=" O2' C B 183 " pdb=" C1' C B 183 " both_signs ideal model delta sigma weight residual False -2.79 -2.46 -0.33 2.00e-01 2.50e+01 2.76e+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: 5.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.410 Find NCS groups from input model: 0.170 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- 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= 0.260 Angle : 1.139 13.462 24589 Z= 0.475 Chirality : 0.114 0.424 3165 Planarity : 0.007 0.096 1084 Dihedral : 23.181 153.757 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 0.00530 / 0.26 (16214) covalent geometry : angle 1.13857 / 0.48 (24589) hydrogen bonds : bond 0.18650 / 9.84 ( 583) hydrogen bonds : angle 7.68906 / 3.09 ( 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 : 0.186 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: 0.1503 time to fit residues: 25.9464 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 : 0.165 ------------------------------------------------------------------------------- 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: 8.9990 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: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 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 = 0.4102 r_free = 0.4102 target = 0.072664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.058655 restraints weight = 106517.036| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.97 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 16215 Z= 0.438 Angle : 1.589 17.673 24589 Z= 0.633 Chirality : 0.106 1.030 3165 Planarity : 0.007 0.075 1084 Dihedral : 20.879 164.072 6897 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 32.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 7.04 % Allowed : 28.15 % Favored : 64.81 % 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: -1.14 (0.40), residues: 381 helix: -0.34 (0.29), residues: 267 sheet: -1.01 (1.01), residues: 24 loop : -1.51 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 349 TYR 0.021 0.003 TYR D 392 PHE 0.013 0.003 PHE D 298 TRP 0.024 0.003 TRP D 328 HIS 0.005 0.002 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00870 / 0.44 (16214) covalent geometry : angle 1.58927 / 0.63 (24589) hydrogen bonds : bond 0.13618 / 7.26 ( 583) hydrogen bonds : angle 4.75166 / 1.92 ( 1165) Misc. bond : bond 0.00027 / 0.01 ( 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: 24 poor density : 68 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: D 30 GLU cc_start: 0.3307 (mm-30) cc_final: 0.2532 (pt0) REVERT: D 35 MET cc_start: 0.5927 (ptt) cc_final: 0.5546 (pmm) REVERT: D 173 LYS cc_start: 0.8748 (ptpt) cc_final: 0.8286 (mttt) REVERT: D 206 MET cc_start: 0.8123 (tpp) cc_final: 0.7770 (tpt) REVERT: D 235 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8427 (tm-30) REVERT: D 236 MET cc_start: -0.0052 (ttt) cc_final: -0.0727 (tpt) REVERT: D 310 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.7615 (t60) REVERT: D 337 MET cc_start: 0.6719 (ptt) cc_final: 0.6329 (ptm) outliers start: 24 outliers final: 11 residues processed: 86 average time/residue: 0.1253 time to fit residues: 15.6173 Evaluate side-chains 68 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP 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 315 SER 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: 7.9990 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 107 HIS 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 = 0.4051 r_free = 0.4051 target = 0.070139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.056423 restraints weight = 109942.705| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.73 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.7936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 16215 Z= 0.378 Angle : 1.407 16.471 24589 Z= 0.562 Chirality : 0.099 0.863 3165 Planarity : 0.007 0.065 1084 Dihedral : 21.060 169.354 6897 Min Nonbonded Distance : 0.868 Molprobity Statistics. All-atom Clashscore : 31.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 8.21 % Allowed : 30.21 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.39), residues: 381 helix: -0.50 (0.29), residues: 270 sheet: -0.47 (0.92), residues: 24 loop : -2.30 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 56 TYR 0.024 0.003 TYR D 392 PHE 0.014 0.003 PHE D 221 TRP 0.029 0.003 TRP D 328 HIS 0.004 0.001 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00760 / 0.38 (16214) covalent geometry : angle 1.40697 / 0.56 (24589) hydrogen bonds : bond 0.12473 / 6.76 ( 583) hydrogen bonds : angle 4.73864 / 1.88 ( 1165) Misc. bond : bond 0.00005 / 0.00 ( 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 88 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: D 30 GLU cc_start: 0.3165 (OUTLIER) cc_final: 0.2863 (pt0) REVERT: D 130 MET cc_start: 0.7429 (mpp) cc_final: 0.6795 (mpp) REVERT: D 155 MET cc_start: 0.9271 (mmt) cc_final: 0.8982 (mmt) REVERT: D 172 ARG cc_start: 0.9179 (tpp80) cc_final: 0.8701 (ttp80) REVERT: D 173 LYS cc_start: 0.8786 (ptpt) cc_final: 0.7919 (mmtt) REVERT: D 175 LEU cc_start: 0.8490 (mt) cc_final: 0.7816 (tt) REVERT: D 310 TRP cc_start: 0.8036 (OUTLIER) cc_final: 0.7193 (t60) REVERT: D 323 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: D 350 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7443 (t80) REVERT: D 354 MET cc_start: 0.6982 (ptm) cc_final: 0.6754 (ptm) outliers start: 28 outliers final: 13 residues processed: 83 average time/residue: 0.1306 time to fit residues: 16.0517 Evaluate side-chains 67 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 40 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 138 VAL 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 264 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 350 TYR 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: 7.9990 chunk 34 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.068891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.055386 restraints weight = 108250.071| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.76 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.9181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 16215 Z= 0.368 Angle : 1.385 15.975 24589 Z= 0.551 Chirality : 0.094 0.848 3165 Planarity : 0.006 0.062 1084 Dihedral : 20.953 173.805 6897 Min Nonbonded Distance : 1.033 Molprobity Statistics. All-atom Clashscore : 32.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 8.50 % Allowed : 29.62 % Favored : 61.88 % 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: -1.00 (0.39), residues: 381 helix: -0.08 (0.29), residues: 262 sheet: -0.76 (0.78), residues: 29 loop : -2.03 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 56 TYR 0.022 0.003 TYR D 392 PHE 0.013 0.003 PHE D 146 TRP 0.032 0.004 TRP D 328 HIS 0.006 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.37 (16214) covalent geometry : angle 1.38451 / 0.55 (24589) hydrogen bonds : bond 0.12181 / 6.65 ( 583) hydrogen bonds : angle 4.61392 / 1.83 ( 1165) Misc. bond : bond 0.00019 / 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 : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.3900 (mm-30) cc_final: 0.3443 (pt0) REVERT: D 35 MET cc_start: 0.6273 (ptt) cc_final: 0.6048 (pmm) REVERT: D 125 THR cc_start: 0.8889 (m) cc_final: 0.8653 (p) REVERT: D 130 MET cc_start: 0.7603 (mpp) cc_final: 0.7032 (mpp) REVERT: D 173 LYS cc_start: 0.8929 (ptpt) cc_final: 0.8064 (mmtt) REVERT: D 175 LEU cc_start: 0.8550 (mt) cc_final: 0.8039 (tt) REVERT: D 214 MET cc_start: 0.8874 (mmm) cc_final: 0.8608 (mmm) REVERT: D 280 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8052 (p0) REVERT: D 310 TRP cc_start: 0.7940 (OUTLIER) cc_final: 0.7068 (t60) REVERT: D 323 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.6499 (tm-30) outliers start: 29 outliers final: 17 residues processed: 78 average time/residue: 0.1322 time to fit residues: 15.1905 Evaluate side-chains 69 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 27 LYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 249 ILE 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 315 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 338 LYS Chi-restraints excluded: chain D residue 375 ILE 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: 8.9990 chunk 53 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.069087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.055862 restraints weight = 109710.029| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.64 r_work: 0.3598 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.9508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 16215 Z= 0.333 Angle : 1.322 16.569 24589 Z= 0.526 Chirality : 0.091 0.754 3165 Planarity : 0.006 0.046 1084 Dihedral : 20.864 170.357 6897 Min Nonbonded Distance : 1.036 Molprobity Statistics. All-atom Clashscore : 29.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.72 % Favored : 95.01 % Rotamer: Outliers : 7.33 % Allowed : 31.38 % 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: -0.66 (0.41), residues: 381 helix: 0.24 (0.31), residues: 262 sheet: -0.18 (0.83), residues: 24 loop : -2.22 (0.59), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 381 TYR 0.021 0.003 TYR D 392 PHE 0.013 0.003 PHE D 221 TRP 0.012 0.002 TRP D 328 HIS 0.007 0.002 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.33 (16214) covalent geometry : angle 1.32177 / 0.53 (24589) hydrogen bonds : bond 0.11393 / 6.18 ( 583) hydrogen bonds : angle 4.55521 / 1.79 ( 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 80 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: D 30 GLU cc_start: 0.3721 (OUTLIER) cc_final: 0.3359 (pt0) REVERT: D 35 MET cc_start: 0.6158 (ptt) cc_final: 0.5811 (pmm) REVERT: D 125 THR cc_start: 0.8975 (m) cc_final: 0.8722 (p) REVERT: D 130 MET cc_start: 0.7526 (mpp) cc_final: 0.7035 (mpp) REVERT: D 152 ASP cc_start: 0.8709 (t0) cc_final: 0.7844 (t0) REVERT: D 172 ARG cc_start: 0.9022 (tpp80) cc_final: 0.8646 (ttp80) REVERT: D 173 LYS cc_start: 0.8933 (ptpt) cc_final: 0.8133 (mptt) REVERT: D 175 LEU cc_start: 0.8600 (mt) cc_final: 0.8123 (tt) REVERT: D 272 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.6137 (t80) REVERT: D 280 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8237 (p0) REVERT: D 299 LYS cc_start: 0.8248 (pptt) cc_final: 0.7930 (mttp) REVERT: D 310 TRP cc_start: 0.7918 (OUTLIER) cc_final: 0.6979 (t60) REVERT: D 323 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7007 (tm-30) outliers start: 25 outliers final: 16 residues processed: 74 average time/residue: 0.1296 time to fit residues: 14.4825 Evaluate side-chains 73 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER 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 138 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 222 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 315 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 338 LYS 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: 0.9980 chunk 81 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 overall best weight: 5.1986 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.069209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.055957 restraints weight = 108860.827| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.69 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.9826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16215 Z= 0.316 Angle : 1.295 15.248 24589 Z= 0.513 Chirality : 0.089 0.757 3165 Planarity : 0.006 0.049 1084 Dihedral : 20.832 172.818 6897 Min Nonbonded Distance : 1.015 Molprobity Statistics. All-atom Clashscore : 28.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.46 % Favored : 95.28 % Rotamer: Outliers : 7.92 % Allowed : 32.84 % Favored : 59.24 % 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: -0.52 (0.41), residues: 381 helix: 0.41 (0.31), residues: 261 sheet: -0.10 (0.91), residues: 24 loop : -2.35 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 381 TYR 0.020 0.003 TYR D 392 PHE 0.013 0.002 PHE D 221 TRP 0.012 0.002 TRP D 328 HIS 0.003 0.001 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.32 (16214) covalent geometry : angle 1.29546 / 0.51 (24589) hydrogen bonds : bond 0.11046 / 5.93 ( 583) hydrogen bonds : angle 4.55453 / 1.78 ( 1165) Misc. bond : bond 0.00019 / 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 82 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.3761 (OUTLIER) cc_final: 0.3423 (pt0) REVERT: D 35 MET cc_start: 0.6210 (ptt) cc_final: 0.5944 (pmm) REVERT: D 130 MET cc_start: 0.7442 (mpp) cc_final: 0.7006 (mpp) REVERT: D 173 LYS cc_start: 0.8891 (ptpt) cc_final: 0.8010 (mptt) REVERT: D 175 LEU cc_start: 0.8611 (mt) cc_final: 0.8133 (tt) REVERT: D 214 MET cc_start: 0.8813 (mmm) cc_final: 0.8473 (mmm) REVERT: D 265 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7437 (p0) REVERT: D 280 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8234 (p0) REVERT: D 310 TRP cc_start: 0.7824 (OUTLIER) cc_final: 0.6909 (t60) REVERT: D 323 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.6787 (tm-30) REVERT: D 367 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8351 (tt0) outliers start: 27 outliers final: 15 residues processed: 77 average time/residue: 0.1199 time to fit residues: 13.9633 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 : 0.257 ------------------------------------------------------------------------------- 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 30 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 229 ILE 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 313 SER Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 LYS Chi-restraints excluded: chain D residue 367 GLU 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: 10.0000 chunk 49 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 38 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 = 0.4018 r_free = 0.4018 target = 0.067907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.054672 restraints weight = 109775.470| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.64 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 1.0512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 16215 Z= 0.376 Angle : 1.413 14.792 24589 Z= 0.559 Chirality : 0.096 0.907 3165 Planarity : 0.006 0.052 1084 Dihedral : 21.167 170.817 6897 Min Nonbonded Distance : 0.975 Molprobity Statistics. All-atom Clashscore : 34.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.51 % Favored : 94.23 % Rotamer: Outliers : 8.80 % Allowed : 34.02 % 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: -0.89 (0.42), residues: 381 helix: 0.05 (0.31), residues: 264 sheet: 0.21 (0.96), residues: 24 loop : -2.47 (0.59), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 389 TYR 0.026 0.004 TYR D 392 PHE 0.021 0.003 PHE D 248 TRP 0.012 0.002 TRP D 328 HIS 0.005 0.002 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.38 (16214) covalent geometry : angle 1.41295 / 0.56 (24589) hydrogen bonds : bond 0.12752 / 6.72 ( 583) hydrogen bonds : angle 4.77196 / 1.85 ( 1165) Misc. bond : bond 0.00026 / 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 86 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 56 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 MET cc_start: 0.6215 (ptt) cc_final: 0.5932 (pmm) REVERT: D 130 MET cc_start: 0.7554 (mpp) cc_final: 0.7317 (mpp) REVERT: D 136 TRP cc_start: 0.8449 (m100) cc_final: 0.8243 (m100) REVERT: D 173 LYS cc_start: 0.9061 (ptpt) cc_final: 0.8246 (mptt) REVERT: D 175 LEU cc_start: 0.8777 (mt) cc_final: 0.8293 (tt) REVERT: D 214 MET cc_start: 0.8897 (mmm) cc_final: 0.8625 (mmm) REVERT: D 265 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7553 (p0) REVERT: D 272 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.6161 (t80) REVERT: D 280 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8438 (p0) REVERT: D 299 LYS cc_start: 0.8231 (pptt) cc_final: 0.8021 (mttm) REVERT: D 310 TRP cc_start: 0.8003 (OUTLIER) cc_final: 0.7453 (t60) outliers start: 30 outliers final: 20 residues processed: 77 average time/residue: 0.1227 time to fit residues: 14.1355 Evaluate side-chains 78 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 99 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 221 PHE 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 272 TYR Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 375 ILE 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: 0.0270 chunk 1 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 overall best weight: 5.6046 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.068754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.055553 restraints weight = 107715.071| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.75 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 1.0586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 16215 Z= 0.330 Angle : 1.323 15.151 24589 Z= 0.524 Chirality : 0.090 0.776 3165 Planarity : 0.006 0.051 1084 Dihedral : 21.065 172.489 6897 Min Nonbonded Distance : 1.048 Molprobity Statistics. All-atom Clashscore : 30.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.77 % Favored : 93.96 % 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: -0.80 (0.41), residues: 381 helix: 0.22 (0.31), residues: 262 sheet: 0.04 (0.95), residues: 24 loop : -2.66 (0.56), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 349 TYR 0.025 0.003 TYR D 392 PHE 0.015 0.003 PHE D 221 TRP 0.009 0.002 TRP D 328 HIS 0.005 0.002 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.33 (16214) covalent geometry : angle 1.32334 / 0.52 (24589) hydrogen bonds : bond 0.11399 / 6.00 ( 583) hydrogen bonds : angle 4.58999 / 1.79 ( 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 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 35 MET cc_start: 0.6466 (ptt) cc_final: 0.6087 (pmm) REVERT: D 130 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7148 (mpp) REVERT: D 172 ARG cc_start: 0.8995 (tpp80) cc_final: 0.8645 (ttp80) REVERT: D 173 LYS cc_start: 0.8981 (ptpt) cc_final: 0.8224 (mptt) REVERT: D 175 LEU cc_start: 0.8716 (mt) cc_final: 0.8272 (tt) REVERT: D 214 MET cc_start: 0.8878 (mmm) cc_final: 0.8516 (mmm) REVERT: D 272 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.6499 (t80) REVERT: D 299 LYS cc_start: 0.8145 (pptt) cc_final: 0.7876 (mtmt) REVERT: D 310 TRP cc_start: 0.7859 (OUTLIER) cc_final: 0.7243 (t60) outliers start: 24 outliers final: 17 residues processed: 72 average time/residue: 0.1229 time to fit residues: 13.3812 Evaluate side-chains 72 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 101 ILE Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 219 LEU 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 309 SER Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 315 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 76 optimal weight: 0.0980 chunk 38 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 overall best weight: 6.2188 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.067986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.054816 restraints weight = 109565.244| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.75 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 1.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 16215 Z= 0.365 Angle : 1.383 15.400 24589 Z= 0.547 Chirality : 0.094 0.846 3165 Planarity : 0.006 0.045 1084 Dihedral : 21.166 171.986 6897 Min Nonbonded Distance : 1.033 Molprobity Statistics. All-atom Clashscore : 33.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.56 % Favored : 93.18 % Rotamer: Outliers : 8.21 % Allowed : 34.60 % 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: -0.92 (0.41), residues: 381 helix: 0.14 (0.32), residues: 262 sheet: -0.39 (0.89), residues: 24 loop : -2.62 (0.56), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 381 TYR 0.023 0.003 TYR D 392 PHE 0.020 0.003 PHE D 248 TRP 0.010 0.002 TRP D 310 HIS 0.013 0.003 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.37 (16214) covalent geometry : angle 1.38300 / 0.55 (24589) hydrogen bonds : bond 0.12394 / 6.48 ( 583) hydrogen bonds : angle 4.73228 / 1.84 ( 1165) Misc. bond : bond 0.00024 / 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 84 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7122 (mpp) REVERT: D 132 ASP cc_start: 0.9010 (t0) cc_final: 0.8762 (m-30) REVERT: D 136 TRP cc_start: 0.8365 (m100) cc_final: 0.7886 (m100) REVERT: D 172 ARG cc_start: 0.8995 (tpp80) cc_final: 0.8538 (tpp80) REVERT: D 173 LYS cc_start: 0.9044 (ptpt) cc_final: 0.8279 (mptt) REVERT: D 175 LEU cc_start: 0.8808 (mt) cc_final: 0.8348 (tt) REVERT: D 214 MET cc_start: 0.8875 (mmm) cc_final: 0.8590 (mmm) REVERT: D 272 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.6567 (t80) REVERT: D 299 LYS cc_start: 0.8185 (pptt) cc_final: 0.7917 (mtmt) REVERT: D 310 TRP cc_start: 0.7969 (OUTLIER) cc_final: 0.7315 (t60) REVERT: D 367 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8516 (tt0) outliers start: 28 outliers final: 21 residues processed: 77 average time/residue: 0.1186 time to fit residues: 13.9595 Evaluate side-chains 79 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 43 HIS Chi-restraints excluded: chain D residue 101 ILE 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 158 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 219 LEU 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 309 SER Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 367 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 overall best weight: 4.3986 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.069430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.056372 restraints weight = 105196.725| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.66 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 1.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 16215 Z= 0.275 Angle : 1.248 15.721 24589 Z= 0.495 Chirality : 0.086 0.684 3165 Planarity : 0.005 0.047 1084 Dihedral : 20.990 172.005 6897 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.25 % Favored : 94.49 % Rotamer: Outliers : 6.16 % Allowed : 36.95 % 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: -0.62 (0.42), residues: 381 helix: 0.33 (0.32), residues: 262 sheet: -0.37 (0.92), residues: 24 loop : -2.37 (0.57), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 56 TYR 0.018 0.002 TYR D 392 PHE 0.017 0.003 PHE D 113 TRP 0.010 0.002 TRP D 328 HIS 0.013 0.002 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.27 (16214) covalent geometry : angle 1.24761 / 0.50 (24589) hydrogen bonds : bond 0.10575 / 5.52 ( 583) hydrogen bonds : angle 4.52432 / 1.77 ( 1165) Misc. bond : bond 0.00017 / 0.01 ( 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 74 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 MET cc_start: 0.6434 (ptt) cc_final: 0.6068 (pmm) REVERT: D 130 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6935 (mpp) REVERT: D 132 ASP cc_start: 0.8970 (t0) cc_final: 0.8722 (m-30) REVERT: D 173 LYS cc_start: 0.8969 (ptpt) cc_final: 0.8222 (mptt) REVERT: D 175 LEU cc_start: 0.8794 (mt) cc_final: 0.8301 (tt) REVERT: D 214 MET cc_start: 0.8890 (mmm) cc_final: 0.8493 (mmm) REVERT: D 272 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.6529 (t80) REVERT: D 299 LYS cc_start: 0.8153 (pptt) cc_final: 0.7925 (mtmt) outliers start: 21 outliers final: 16 residues processed: 70 average time/residue: 0.1228 time to fit residues: 13.1486 Evaluate side-chains 70 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 101 ILE 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 158 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 272 TYR Chi-restraints excluded: chain D residue 309 SER Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 324 LEU 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 73 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 63 optimal weight: 0.0470 overall best weight: 4.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 43 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.069763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.056587 restraints weight = 107753.784| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.73 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 1.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16215 Z= 0.261 Angle : 1.228 16.577 24589 Z= 0.487 Chirality : 0.084 0.651 3165 Planarity : 0.005 0.048 1084 Dihedral : 20.869 175.840 6897 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 25.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.30 % Favored : 93.44 % Rotamer: Outliers : 6.16 % Allowed : 36.07 % Favored : 57.77 % 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: -0.46 (0.42), residues: 381 helix: 0.48 (0.32), residues: 261 sheet: -0.34 (0.96), residues: 24 loop : -2.36 (0.58), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 377 TYR 0.017 0.003 TYR D 392 PHE 0.016 0.003 PHE D 221 TRP 0.009 0.002 TRP D 310 HIS 0.004 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.26 (16214) covalent geometry : angle 1.22776 / 0.49 (24589) hydrogen bonds : bond 0.10464 / 5.46 ( 583) hydrogen bonds : angle 4.44713 / 1.75 ( 1165) Misc. bond : bond 0.00014 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3474.03 seconds wall clock time: 60 minutes 49.10 seconds (3649.10 seconds total)