Starting phenix.real_space_refine on Thu Sep 18 06:10:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uim_26549/09_2025/7uim_26549.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uim_26549/09_2025/7uim_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_26549/09_2025/7uim_26549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uim_26549/09_2025/7uim_26549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uim_26549/09_2025/7uim_26549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uim_26549/09_2025/7uim_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-2.0-5805/lib/python3.9/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: 3.30, per 1000 atoms: 0.22 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: 1.09 Conformation dependent library (CDL) restraints added in 239.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.60 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: 3.64 Time building geometry restraints manager: 1.48 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: 8654 33.89 - 67.78: 1431 67.78 - 101.67: 157 101.67 - 135.57: 2 135.57 - 169.46: 6 Dihedral angle restraints: 10250 sinusoidal: 9126 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 10247 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: 4.770 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.550 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4534 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 : 24.926 169.458 9526 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 aren 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 covalent geometry : bond 0.00487 (16214) covalent geometry : angle 0.87102 (24589) hydrogen bonds : bond 0.18650 ( 583) hydrogen bonds : angle 7.68906 ( 1165) Misc. bond : bond 0.00140 ( 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 : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 26 ASN cc_start: 0.8204 (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: 0.1777 time to fit residues: 30.2777 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 : 0.333 ------------------------------------------------------------------------------- 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: 10.0000 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: 10.9990 chunk 74 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.071031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.057106 restraints weight = 109221.208| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.31 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 16215 Z= 0.421 Angle : 1.040 10.815 24589 Z= 0.516 Chirality : 0.050 0.265 3165 Planarity : 0.007 0.080 1084 Dihedral : 25.941 176.500 8721 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 36.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 8.21 % Allowed : 29.03 % Favored : 62.76 % 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 aren not related in a simple way. whole: -1.47 (0.38), residues: 381 helix: -0.53 (0.29), residues: 262 sheet: -1.30 (0.97), residues: 24 loop : -1.72 (0.57), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG D 56 TYR 0.024 0.003 TYR D 392 PHE 0.017 0.003 PHE D 298 TRP 0.031 0.003 TRP D 328 HIS 0.007 0.002 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.00749 (16214) covalent geometry : angle 1.03982 (24589) hydrogen bonds : bond 0.14100 ( 583) hydrogen bonds : angle 4.96589 ( 1165) Misc. bond : bond 0.00035 ( 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 97 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.3198 (mm-30) cc_final: 0.2564 (pt0) REVERT: D 35 MET cc_start: 0.6017 (ptt) cc_final: 0.5707 (pmm) REVERT: D 130 MET cc_start: 0.7218 (mpp) cc_final: 0.6300 (mpp) REVERT: D 135 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: D 173 LYS cc_start: 0.8801 (ptpt) cc_final: 0.8096 (mmtm) REVERT: D 175 LEU cc_start: 0.8630 (mt) cc_final: 0.8216 (tt) REVERT: D 310 TRP cc_start: 0.8098 (OUTLIER) cc_final: 0.7343 (t60) outliers start: 28 outliers final: 13 residues processed: 91 average time/residue: 0.1410 time to fit residues: 18.3250 Evaluate side-chains 72 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 135 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 221 PHE 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: 10.0000 chunk 23 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 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: 9.9990 chunk 4 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 HIS ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN D 204 ASN D 244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.069013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.055173 restraints weight = 109854.433| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.90 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.8071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 16215 Z= 0.382 Angle : 0.899 10.287 24589 Z= 0.451 Chirality : 0.045 0.321 3165 Planarity : 0.007 0.074 1084 Dihedral : 26.027 178.763 8721 Min Nonbonded Distance : 0.819 Molprobity Statistics. All-atom Clashscore : 32.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % 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 aren not related in a simple way. whole: -1.64 (0.40), residues: 381 helix: -0.59 (0.29), residues: 266 sheet: -0.41 (0.99), residues: 24 loop : -2.38 (0.61), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 353 TYR 0.027 0.004 TYR D 392 PHE 0.019 0.003 PHE D 106 TRP 0.026 0.004 TRP D 328 HIS 0.005 0.001 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.00708 (16214) covalent geometry : angle 0.89937 (24589) hydrogen bonds : bond 0.12498 ( 583) hydrogen bonds : angle 4.80546 ( 1165) Misc. bond : bond 0.00012 ( 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 91 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: D 26 ASN cc_start: 0.9529 (m-40) cc_final: 0.9155 (m-40) REVERT: D 30 GLU cc_start: 0.3308 (OUTLIER) cc_final: 0.2922 (pt0) REVERT: D 35 MET cc_start: 0.5850 (ptt) cc_final: 0.5630 (pmm) REVERT: D 130 MET cc_start: 0.7560 (mpp) cc_final: 0.7034 (mpp) REVERT: D 172 ARG cc_start: 0.9341 (ttp-110) cc_final: 0.8728 (tmt170) REVERT: D 173 LYS cc_start: 0.8932 (ptpt) cc_final: 0.7834 (mttt) REVERT: D 310 TRP cc_start: 0.8105 (OUTLIER) cc_final: 0.7156 (t60) REVERT: D 345 ASP cc_start: 0.7197 (m-30) cc_final: 0.6820 (m-30) outliers start: 29 outliers final: 12 residues processed: 85 average time/residue: 0.1308 time to fit residues: 16.4258 Evaluate side-chains 67 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 ASN 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 158 ILE 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 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: 8.9990 chunk 12 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.068445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.054919 restraints weight = 112326.563| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.83 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.8905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16215 Z= 0.337 Angle : 0.832 11.443 24589 Z= 0.421 Chirality : 0.043 0.307 3165 Planarity : 0.006 0.075 1084 Dihedral : 26.004 175.685 8721 Min Nonbonded Distance : 0.972 Molprobity Statistics. All-atom Clashscore : 31.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 10.56 % Allowed : 29.03 % Favored : 60.41 % 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 aren not related in a simple way. whole: -1.12 (0.41), residues: 381 helix: -0.09 (0.30), residues: 264 sheet: -1.06 (0.80), residues: 29 loop : -2.31 (0.62), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 301 TYR 0.023 0.003 TYR D 392 PHE 0.013 0.003 PHE D 146 TRP 0.023 0.003 TRP D 328 HIS 0.005 0.001 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.00624 (16214) covalent geometry : angle 0.83239 (24589) hydrogen bonds : bond 0.11490 ( 583) hydrogen bonds : angle 4.61275 ( 1165) Misc. bond : bond 0.00027 ( 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 90 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 54 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.3814 (OUTLIER) cc_final: 0.3209 (pt0) REVERT: D 125 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8678 (p) REVERT: D 130 MET cc_start: 0.7366 (mpp) cc_final: 0.6881 (mpp) REVERT: D 155 MET cc_start: 0.9346 (mmt) cc_final: 0.9131 (mtt) REVERT: D 172 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.9044 (ttm110) REVERT: D 173 LYS cc_start: 0.9030 (ptpt) cc_final: 0.8174 (mptt) REVERT: D 285 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: D 299 LYS cc_start: 0.8349 (pptt) cc_final: 0.7975 (mtmt) REVERT: D 310 TRP cc_start: 0.7969 (OUTLIER) cc_final: 0.7099 (t60) outliers start: 36 outliers final: 17 residues processed: 81 average time/residue: 0.1339 time to fit residues: 16.0562 Evaluate side-chains 72 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 30 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 231 MET 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 375 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 415 SER 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: 0.9990 chunk 71 optimal weight: 0.9990 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: 8.9990 overall best weight: 6.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.068010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.054315 restraints weight = 110880.546| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.69 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.9653 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= 0.329 Angle : 0.831 13.153 24589 Z= 0.420 Chirality : 0.042 0.229 3165 Planarity : 0.006 0.073 1084 Dihedral : 26.001 166.273 8721 Min Nonbonded Distance : 0.983 Molprobity Statistics. All-atom Clashscore : 29.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.72 % Favored : 95.01 % Rotamer: Outliers : 9.09 % Allowed : 31.96 % 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 aren not related in a simple way. whole: -0.96 (0.41), residues: 381 helix: -0.01 (0.30), residues: 264 sheet: -0.18 (0.91), residues: 24 loop : -2.32 (0.63), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 223 TYR 0.025 0.003 TYR D 392 PHE 0.011 0.003 PHE D 113 TRP 0.016 0.003 TRP D 328 HIS 0.004 0.001 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.00610 (16214) covalent geometry : angle 0.83070 (24589) hydrogen bonds : bond 0.11326 ( 583) hydrogen bonds : angle 4.55353 ( 1165) Misc. bond : bond 0.00023 ( 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: 31 poor density : 53 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: D 30 GLU cc_start: 0.4008 (mm-30) cc_final: 0.3453 (pt0) REVERT: D 37 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7435 (p90) REVERT: D 125 THR cc_start: 0.9021 (m) cc_final: 0.8796 (p) REVERT: D 130 MET cc_start: 0.7556 (mpp) cc_final: 0.7232 (mpp) REVERT: D 155 MET cc_start: 0.9354 (mmt) cc_final: 0.8992 (mmm) REVERT: D 173 LYS cc_start: 0.9128 (ptpt) cc_final: 0.8506 (mttt) REVERT: D 214 MET cc_start: 0.9052 (mmm) cc_final: 0.8724 (mmm) REVERT: D 280 ASP cc_start: 0.8966 (OUTLIER) cc_final: 0.8492 (p0) REVERT: D 299 LYS cc_start: 0.8334 (pptt) cc_final: 0.7964 (mtpt) REVERT: D 310 TRP cc_start: 0.7750 (OUTLIER) cc_final: 0.6824 (t60) outliers start: 31 outliers final: 18 residues processed: 79 average time/residue: 0.1313 time to fit residues: 15.2319 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 : 0.237 ------------------------------------------------------------------------------- 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 37 TYR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 109 HIS 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 209 GLU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 222 VAL 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 310 TRP Chi-restraints excluded: chain D residue 313 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.067806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.054279 restraints weight = 109964.288| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.64 r_work: 0.3576 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 1.0048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16215 Z= 0.326 Angle : 0.821 13.778 24589 Z= 0.416 Chirality : 0.042 0.238 3165 Planarity : 0.006 0.059 1084 Dihedral : 26.033 166.875 8721 Min Nonbonded Distance : 0.977 Molprobity Statistics. All-atom Clashscore : 30.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.51 % Favored : 94.23 % Rotamer: Outliers : 7.92 % Allowed : 32.55 % Favored : 59.53 % 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 aren not related in a simple way. whole: -0.96 (0.41), residues: 381 helix: 0.14 (0.31), residues: 261 sheet: -0.28 (0.90), residues: 24 loop : -2.73 (0.57), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 25 TYR 0.023 0.003 TYR D 392 PHE 0.012 0.003 PHE D 113 TRP 0.013 0.002 TRP D 328 HIS 0.007 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00604 (16214) covalent geometry : angle 0.82121 (24589) hydrogen bonds : bond 0.11305 ( 583) hydrogen bonds : angle 4.58391 ( 1165) Misc. bond : bond 0.00022 ( 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 79 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: D 130 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6975 (mpp) REVERT: D 136 TRP cc_start: 0.8520 (m100) cc_final: 0.8302 (m100) REVERT: D 172 ARG cc_start: 0.9374 (OUTLIER) cc_final: 0.8721 (tmt170) REVERT: D 173 LYS cc_start: 0.9105 (ptpt) cc_final: 0.8088 (mttt) REVERT: D 214 MET cc_start: 0.9067 (mmm) cc_final: 0.8717 (mmm) REVERT: D 265 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7405 (p0) REVERT: D 272 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.6764 (t80) REVERT: D 299 LYS cc_start: 0.8374 (pptt) cc_final: 0.7966 (mtpt) REVERT: D 310 TRP cc_start: 0.7717 (OUTLIER) cc_final: 0.6790 (t60) outliers start: 27 outliers final: 17 residues processed: 73 average time/residue: 0.1258 time to fit residues: 13.3727 Evaluate side-chains 71 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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 172 ARG 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 310 TRP Chi-restraints excluded: chain D residue 313 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=2.50 ------------------------------------------------------------------------------- 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: 9.9990 chunk 89 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 overall best weight: 7.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3983 r_free = 0.3983 target = 0.066491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.053166 restraints weight = 114128.233| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.77 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 1.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 16215 Z= 0.409 Angle : 0.945 12.959 24589 Z= 0.474 Chirality : 0.048 0.248 3165 Planarity : 0.006 0.058 1084 Dihedral : 26.320 169.519 8721 Min Nonbonded Distance : 0.850 Molprobity Statistics. All-atom Clashscore : 38.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.56 % Favored : 93.18 % Rotamer: Outliers : 7.62 % Allowed : 34.02 % Favored : 58.36 % 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 aren not related in a simple way. whole: -1.46 (0.40), residues: 381 helix: -0.32 (0.31), residues: 265 sheet: -0.36 (0.89), residues: 24 loop : -2.81 (0.57), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 381 TYR 0.026 0.003 TYR D 392 PHE 0.024 0.003 PHE D 248 TRP 0.012 0.003 TRP D 310 HIS 0.004 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00758 (16214) covalent geometry : angle 0.94516 (24589) hydrogen bonds : bond 0.13574 ( 583) hydrogen bonds : angle 4.89535 ( 1165) Misc. bond : bond 0.00041 ( 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 82 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: D 130 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7403 (mpp) REVERT: D 136 TRP cc_start: 0.8554 (m100) cc_final: 0.8235 (m100) REVERT: D 172 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9142 (ttm-80) REVERT: D 173 LYS cc_start: 0.9179 (ptpt) cc_final: 0.8456 (mptt) REVERT: D 219 LEU cc_start: 0.7880 (mm) cc_final: 0.7658 (mm) REVERT: D 265 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7881 (p0) REVERT: D 272 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6658 (t80) REVERT: D 299 LYS cc_start: 0.8431 (pptt) cc_final: 0.8055 (mtpt) REVERT: D 310 TRP cc_start: 0.7815 (OUTLIER) cc_final: 0.6917 (t60) REVERT: D 324 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5934 (tp) outliers start: 26 outliers final: 17 residues processed: 74 average time/residue: 0.1296 time to fit residues: 13.8958 Evaluate side-chains 76 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 125 THR 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 172 ARG 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 273 LEU Chi-restraints excluded: chain D residue 280 ASP 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 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: 10.0000 chunk 1 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 49 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4007 r_free = 0.4007 target = 0.067499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.054196 restraints weight = 112908.126| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.68 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 1.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16215 Z= 0.324 Angle : 0.829 12.495 24589 Z= 0.419 Chirality : 0.043 0.229 3165 Planarity : 0.006 0.052 1084 Dihedral : 26.151 167.795 8721 Min Nonbonded Distance : 0.966 Molprobity Statistics. All-atom Clashscore : 31.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.30 % Favored : 93.44 % Rotamer: Outliers : 7.62 % Allowed : 34.60 % 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 aren not related in a simple way. whole: -1.18 (0.41), residues: 381 helix: -0.04 (0.31), residues: 263 sheet: -0.54 (0.88), residues: 24 loop : -2.76 (0.54), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 301 TYR 0.025 0.003 TYR D 392 PHE 0.018 0.003 PHE D 248 TRP 0.009 0.002 TRP D 328 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00600 (16214) covalent geometry : angle 0.82867 (24589) hydrogen bonds : bond 0.11290 ( 583) hydrogen bonds : angle 4.71631 ( 1165) Misc. bond : bond 0.00024 ( 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 80 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: D 130 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7080 (mpp) REVERT: D 136 TRP cc_start: 0.8615 (m100) cc_final: 0.8319 (m100) REVERT: D 173 LYS cc_start: 0.9117 (ptpt) cc_final: 0.8336 (mptt) REVERT: D 214 MET cc_start: 0.8993 (mmm) cc_final: 0.8709 (mmm) REVERT: D 219 LEU cc_start: 0.7818 (mm) cc_final: 0.7559 (mm) REVERT: D 272 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.6633 (t80) REVERT: D 299 LYS cc_start: 0.8338 (pptt) cc_final: 0.7973 (mtpt) REVERT: D 310 TRP cc_start: 0.7583 (OUTLIER) cc_final: 0.6668 (t60) outliers start: 26 outliers final: 19 residues processed: 73 average time/residue: 0.1191 time to fit residues: 13.2884 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 : 0.239 ------------------------------------------------------------------------------- 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 32 VAL 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 125 THR Chi-restraints excluded: chain D residue 130 MET 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 222 VAL Chi-restraints excluded: chain D residue 272 TYR Chi-restraints excluded: chain D residue 280 ASP 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 334 ILE Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 420 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.3980 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: 10.0000 chunk 27 optimal weight: 10.0000 chunk 59 optimal weight: 0.3980 chunk 76 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 overall best weight: 5.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.067894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.054578 restraints weight = 115141.949| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.67 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 1.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16215 Z= 0.290 Angle : 0.798 15.238 24589 Z= 0.402 Chirality : 0.041 0.230 3165 Planarity : 0.005 0.052 1084 Dihedral : 26.018 168.347 8721 Min Nonbonded Distance : 0.995 Molprobity Statistics. All-atom Clashscore : 28.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.30 % Favored : 93.44 % Rotamer: Outliers : 5.87 % Allowed : 36.66 % 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 aren not related in a simple way. whole: -1.03 (0.41), residues: 381 helix: 0.04 (0.31), residues: 263 sheet: -0.56 (0.88), residues: 24 loop : -2.58 (0.56), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 301 TYR 0.021 0.003 TYR D 392 PHE 0.017 0.003 PHE D 113 TRP 0.008 0.002 TRP D 310 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00537 (16214) covalent geometry : angle 0.79752 (24589) hydrogen bonds : bond 0.10734 ( 583) hydrogen bonds : angle 4.64445 ( 1165) Misc. bond : bond 0.00019 ( 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 76 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: D 130 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7200 (mpp) REVERT: D 136 TRP cc_start: 0.8536 (m100) cc_final: 0.8284 (m100) REVERT: D 155 MET cc_start: 0.9372 (mtt) cc_final: 0.8759 (mtt) REVERT: D 172 ARG cc_start: 0.9323 (ttm-80) cc_final: 0.8931 (ttm110) REVERT: D 173 LYS cc_start: 0.9049 (ptpt) cc_final: 0.8276 (mptt) REVERT: D 214 MET cc_start: 0.8955 (mmm) cc_final: 0.8675 (mmm) REVERT: D 219 LEU cc_start: 0.7605 (mm) cc_final: 0.7300 (mm) REVERT: D 272 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.6635 (t80) REVERT: D 299 LYS cc_start: 0.8309 (pptt) cc_final: 0.7966 (mtpt) REVERT: D 310 TRP cc_start: 0.7593 (OUTLIER) cc_final: 0.6637 (t60) REVERT: D 420 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7686 (t80) outliers start: 20 outliers final: 15 residues processed: 72 average time/residue: 0.1213 time to fit residues: 13.1107 Evaluate side-chains 73 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 32 VAL 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 221 PHE Chi-restraints excluded: chain D residue 272 TYR Chi-restraints excluded: chain D residue 280 ASP 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 334 ILE Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 420 TYR 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: 3.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.067781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.054535 restraints weight = 111781.097| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.63 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 1.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16215 Z= 0.301 Angle : 0.817 20.040 24589 Z= 0.409 Chirality : 0.041 0.229 3165 Planarity : 0.005 0.051 1084 Dihedral : 26.019 168.315 8721 Min Nonbonded Distance : 0.994 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.30 % Favored : 93.44 % Rotamer: Outliers : 6.74 % Allowed : 37.54 % Favored : 55.72 % 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 aren not related in a simple way. whole: -1.08 (0.41), residues: 381 helix: 0.00 (0.31), residues: 263 sheet: -0.67 (0.88), residues: 24 loop : -2.56 (0.56), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 301 TYR 0.022 0.003 TYR D 392 PHE 0.015 0.003 PHE D 248 TRP 0.008 0.002 TRP D 310 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00559 (16214) covalent geometry : angle 0.81730 (24589) hydrogen bonds : bond 0.10913 ( 583) hydrogen bonds : angle 4.63009 ( 1165) Misc. bond : bond 0.00022 ( 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 78 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: D 46 LYS cc_start: 0.8910 (pttm) cc_final: 0.8051 (pttt) REVERT: D 130 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7209 (mpp) REVERT: D 136 TRP cc_start: 0.8564 (m100) cc_final: 0.8305 (m100) REVERT: D 173 LYS cc_start: 0.9041 (ptpt) cc_final: 0.8270 (mptt) REVERT: D 214 MET cc_start: 0.8980 (mmm) cc_final: 0.8701 (mmm) REVERT: D 219 LEU cc_start: 0.7680 (mm) cc_final: 0.7346 (mm) REVERT: D 272 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.6656 (t80) REVERT: D 299 LYS cc_start: 0.8316 (pptt) cc_final: 0.7972 (mtpt) REVERT: D 310 TRP cc_start: 0.7598 (OUTLIER) cc_final: 0.6667 (t60) REVERT: D 337 MET cc_start: 0.6822 (ptt) cc_final: 0.6497 (ptt) REVERT: D 420 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7681 (t80) outliers start: 23 outliers final: 16 residues processed: 72 average time/residue: 0.1256 time to fit residues: 13.3600 Evaluate side-chains 73 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 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 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 221 PHE Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 272 TYR Chi-restraints excluded: chain D residue 280 ASP 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 375 ILE Chi-restraints excluded: chain D residue 420 TYR 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: 7.9990 chunk 11 optimal weight: 10.0000 chunk 86 optimal weight: 0.0870 chunk 62 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 overall best weight: 4.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4027 r_free = 0.4027 target = 0.068335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.055037 restraints weight = 112695.539| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.61 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 1.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16215 Z= 0.254 Angle : 0.761 14.488 24589 Z= 0.384 Chirality : 0.039 0.228 3165 Planarity : 0.005 0.052 1084 Dihedral : 25.921 168.629 8721 Min Nonbonded Distance : 1.009 Molprobity Statistics. All-atom Clashscore : 26.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.04 % Favored : 93.70 % Rotamer: Outliers : 5.57 % Allowed : 38.71 % Favored : 55.72 % 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 aren not related in a simple way. whole: -0.82 (0.41), residues: 381 helix: 0.21 (0.32), residues: 263 sheet: -0.67 (0.88), residues: 24 loop : -2.47 (0.56), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 301 TYR 0.019 0.002 TYR D 392 PHE 0.017 0.003 PHE D 113 TRP 0.008 0.002 TRP D 357 HIS 0.004 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00471 (16214) covalent geometry : angle 0.76145 (24589) hydrogen bonds : bond 0.10126 ( 583) hydrogen bonds : angle 4.50291 ( 1165) Misc. bond : bond 0.00016 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3600.20 seconds wall clock time: 62 minutes 47.16 seconds (3767.16 seconds total)