Starting phenix.real_space_refine on Fri Jun 13 03:02:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uim_26549/06_2025/7uim_26549.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uim_26549/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uim_26549/06_2025/7uim_26549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uim_26549/06_2025/7uim_26549.map" model { file = "/net/cci-nas-00/data/ceres_data/7uim_26549/06_2025/7uim_26549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uim_26549/06_2025/7uim_26549.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 536 5.49 5 Mg 13 5.21 5 S 21 5.16 5 C 7184 2.51 5 N 2736 2.21 5 O 4282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.43, per 1000 atoms: 0.64 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: 3.37 Conformation dependent library (CDL) restraints added in 446.7 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: 6.81 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: 7.02 Time building geometry restraints manager: 4.12 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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 39.820 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.003 TRP D 360 HIS 0.007 0.002 HIS D 291 PHE 0.032 0.003 PHE D 298 TYR 0.032 0.003 TYR D 278 ARG 0.010 0.001 ARG D 377 Details of bonding type rmsd hydrogen bonds : bond 0.18650 ( 583) hydrogen bonds : angle 7.68906 ( 1165) covalent geometry : bond 0.00487 (16214) covalent geometry : angle 0.87102 (24589) 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 : 0.779 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: 0.3452 time to fit residues: 58.6838 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 : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.071202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.057313 restraints weight = 110097.815| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 3.18 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 16215 Z= 0.412 Angle : 1.016 10.520 24589 Z= 0.499 Chirality : 0.050 0.293 3165 Planarity : 0.007 0.080 1084 Dihedral : 25.843 175.120 8721 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 34.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 7.92 % Allowed : 30.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.38), residues: 381 helix: -0.58 (0.29), residues: 268 sheet: -1.17 (0.98), residues: 24 loop : -1.93 (0.55), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 328 HIS 0.008 0.002 HIS D 109 PHE 0.019 0.004 PHE D 298 TYR 0.025 0.003 TYR D 392 ARG 0.019 0.002 ARG D 172 Details of bonding type rmsd hydrogen bonds : bond 0.13917 ( 583) hydrogen bonds : angle 4.91706 ( 1165) covalent geometry : bond 0.00763 (16214) covalent geometry : angle 1.01558 (24589) Misc. bond : bond 0.00042 ( 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 95 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.3168 (mm-30) cc_final: 0.2445 (pt0) REVERT: D 35 MET cc_start: 0.5919 (ptt) cc_final: 0.5615 (pmm) REVERT: D 130 MET cc_start: 0.7202 (mpp) cc_final: 0.6296 (mpp) REVERT: D 173 LYS cc_start: 0.8768 (ptpt) cc_final: 0.8087 (mmtm) REVERT: D 175 LEU cc_start: 0.8636 (mt) cc_final: 0.8207 (tt) REVERT: D 206 MET cc_start: 0.8287 (tpp) cc_final: 0.8043 (tpt) REVERT: D 235 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8307 (tm-30) REVERT: D 310 TRP cc_start: 0.8230 (OUTLIER) cc_final: 0.7471 (t60) REVERT: D 354 MET cc_start: 0.6852 (ptm) cc_final: 0.6622 (ptm) outliers start: 27 outliers final: 11 residues processed: 89 average time/residue: 0.2886 time to fit residues: 36.5704 Evaluate side-chains 69 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 341 CYS 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 87 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 HIS 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 = 0.4057 r_free = 0.4057 target = 0.070561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.056720 restraints weight = 106104.740| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.71 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.7468 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= 0.300 Angle : 0.783 9.976 24589 Z= 0.394 Chirality : 0.040 0.277 3165 Planarity : 0.006 0.066 1084 Dihedral : 25.715 172.082 8721 Min Nonbonded Distance : 0.886 Molprobity Statistics. All-atom Clashscore : 26.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 7.62 % Allowed : 29.03 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.39), residues: 381 helix: -0.23 (0.29), residues: 270 sheet: -0.25 (1.00), residues: 24 loop : -2.46 (0.56), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 328 HIS 0.005 0.001 HIS D 291 PHE 0.015 0.003 PHE D 106 TYR 0.019 0.003 TYR D 392 ARG 0.008 0.001 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.10436 ( 583) hydrogen bonds : angle 4.49249 ( 1165) covalent geometry : bond 0.00556 (16214) covalent geometry : angle 0.78255 (24589) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 MET cc_start: 0.5923 (ptt) cc_final: 0.5670 (pmm) REVERT: D 130 MET cc_start: 0.7389 (mpp) cc_final: 0.6688 (mpp) REVERT: D 135 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: D 155 MET cc_start: 0.9326 (mmt) cc_final: 0.9072 (mmt) REVERT: D 173 LYS cc_start: 0.8832 (ptpt) cc_final: 0.8045 (mmtm) REVERT: D 310 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.7165 (t60) REVERT: D 323 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: D 354 MET cc_start: 0.7242 (ptm) cc_final: 0.6972 (ptm) outliers start: 26 outliers final: 13 residues processed: 86 average time/residue: 0.2747 time to fit residues: 34.5258 Evaluate side-chains 69 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 228 CYS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 338 LYS 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 78 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.070880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.057214 restraints weight = 107298.483| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.63 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.8097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16215 Z= 0.222 Angle : 0.690 11.251 24589 Z= 0.350 Chirality : 0.036 0.247 3165 Planarity : 0.005 0.070 1084 Dihedral : 25.460 170.499 8721 Min Nonbonded Distance : 1.108 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 7.04 % Allowed : 30.50 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.42), residues: 381 helix: 0.81 (0.32), residues: 261 sheet: -0.74 (0.90), residues: 29 loop : -1.99 (0.59), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 328 HIS 0.003 0.001 HIS D 291 PHE 0.017 0.003 PHE D 221 TYR 0.016 0.002 TYR D 392 ARG 0.007 0.001 ARG D 172 Details of bonding type rmsd hydrogen bonds : bond 0.09098 ( 583) hydrogen bonds : angle 4.12357 ( 1165) covalent geometry : bond 0.00414 (16214) covalent geometry : angle 0.68997 (24589) Misc. bond : bond 0.00005 ( 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 81 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.4060 (OUTLIER) cc_final: 0.3480 (pt0) REVERT: D 125 THR cc_start: 0.8901 (m) cc_final: 0.8652 (p) REVERT: D 130 MET cc_start: 0.7147 (mpp) cc_final: 0.6532 (mpp) REVERT: D 155 MET cc_start: 0.9362 (mmt) cc_final: 0.9014 (mmt) REVERT: D 172 ARG cc_start: 0.9337 (ttm-80) cc_final: 0.8624 (tmt170) REVERT: D 173 LYS cc_start: 0.8841 (ptpt) cc_final: 0.7815 (mttt) REVERT: D 175 LEU cc_start: 0.8523 (mt) cc_final: 0.8254 (tp) REVERT: D 214 MET cc_start: 0.8874 (mmm) cc_final: 0.8634 (mmm) REVERT: D 285 GLN cc_start: 0.8224 (mp10) cc_final: 0.7996 (pm20) REVERT: D 299 LYS cc_start: 0.8299 (pptt) cc_final: 0.8053 (mttm) REVERT: D 323 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.6396 (tm-30) REVERT: D 354 MET cc_start: 0.7408 (ptm) cc_final: 0.7141 (ptm) outliers start: 24 outliers final: 15 residues processed: 77 average time/residue: 0.2968 time to fit residues: 32.8161 Evaluate side-chains 69 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 111 TYR Chi-restraints excluded: chain D residue 158 ILE 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 323 GLN Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 393 VAL 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 58 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4031 r_free = 0.4031 target = 0.068890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.055269 restraints weight = 110561.042| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.71 r_work: 0.3591 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.9006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16215 Z= 0.297 Angle : 0.791 12.218 24589 Z= 0.400 Chirality : 0.040 0.262 3165 Planarity : 0.006 0.067 1084 Dihedral : 25.734 169.094 8721 Min Nonbonded Distance : 0.997 Molprobity Statistics. All-atom Clashscore : 28.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.42), residues: 381 helix: 0.40 (0.31), residues: 262 sheet: -0.37 (0.90), residues: 24 loop : -2.24 (0.62), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP D 328 HIS 0.004 0.001 HIS D 291 PHE 0.016 0.003 PHE D 146 TYR 0.023 0.003 TYR D 392 ARG 0.005 0.001 ARG D 301 Details of bonding type rmsd hydrogen bonds : bond 0.11061 ( 583) hydrogen bonds : angle 4.43321 ( 1165) covalent geometry : bond 0.00549 (16214) covalent geometry : angle 0.79054 (24589) Misc. bond : bond 0.00018 ( 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 82 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: D 30 GLU cc_start: 0.4041 (mm-30) cc_final: 0.3585 (pt0) REVERT: D 130 MET cc_start: 0.7289 (mpp) cc_final: 0.6764 (mpp) REVERT: D 155 MET cc_start: 0.9438 (mmt) cc_final: 0.8796 (mmt) REVERT: D 173 LYS cc_start: 0.9001 (ptpt) cc_final: 0.8197 (mptt) REVERT: D 285 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8322 (pm20) REVERT: D 299 LYS cc_start: 0.8271 (pptt) cc_final: 0.7906 (mttm) REVERT: D 310 TRP cc_start: 0.7883 (OUTLIER) cc_final: 0.7023 (t60) outliers start: 25 outliers final: 15 residues processed: 78 average time/residue: 0.2632 time to fit residues: 30.3051 Evaluate side-chains 69 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 167 VAL 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 280 ASP Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 310 TRP 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 11 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 overall best weight: 6.7988 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.067672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.054232 restraints weight = 113994.386| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.74 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.9972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 16215 Z= 0.358 Angle : 0.864 12.017 24589 Z= 0.437 Chirality : 0.044 0.244 3165 Planarity : 0.007 0.076 1084 Dihedral : 25.927 168.095 8721 Min Nonbonded Distance : 0.995 Molprobity Statistics. All-atom Clashscore : 33.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 10.85 % Allowed : 30.50 % Favored : 58.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.41), residues: 381 helix: 0.05 (0.30), residues: 262 sheet: -0.16 (0.94), residues: 24 loop : -2.42 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP D 328 HIS 0.008 0.002 HIS D 151 PHE 0.022 0.003 PHE D 248 TYR 0.026 0.003 TYR D 392 ARG 0.012 0.001 ARG D 172 Details of bonding type rmsd hydrogen bonds : bond 0.11830 ( 583) hydrogen bonds : angle 4.63522 ( 1165) covalent geometry : bond 0.00668 (16214) covalent geometry : angle 0.86351 (24589) Misc. bond : bond 0.00025 ( 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 96 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 59 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: D 30 GLU cc_start: 0.3720 (OUTLIER) cc_final: 0.3301 (pt0) REVERT: D 37 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.7563 (p90) REVERT: D 130 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7194 (mpp) REVERT: D 155 MET cc_start: 0.9323 (mmt) cc_final: 0.8740 (mmt) REVERT: D 172 ARG cc_start: 0.9396 (ttm-80) cc_final: 0.8967 (ttm110) REVERT: D 173 LYS cc_start: 0.9189 (ptpt) cc_final: 0.8616 (mptt) REVERT: D 214 MET cc_start: 0.8911 (mmm) cc_final: 0.8612 (mmm) REVERT: D 272 TYR cc_start: 0.7649 (OUTLIER) cc_final: 0.6143 (t80) REVERT: D 280 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8504 (p0) REVERT: D 299 LYS cc_start: 0.8464 (pptt) cc_final: 0.8017 (mttm) REVERT: D 310 TRP cc_start: 0.7701 (OUTLIER) cc_final: 0.6751 (t60) outliers start: 37 outliers final: 21 residues processed: 88 average time/residue: 0.2692 time to fit residues: 34.9089 Evaluate side-chains 85 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 33 ASP Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 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 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 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 Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 23 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 9 optimal weight: 10.9990 chunk 82 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.068335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.055054 restraints weight = 113535.189| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.64 r_work: 0.3592 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 1.0127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16215 Z= 0.297 Angle : 0.784 12.615 24589 Z= 0.397 Chirality : 0.040 0.218 3165 Planarity : 0.006 0.048 1084 Dihedral : 25.838 166.328 8721 Min Nonbonded Distance : 1.001 Molprobity Statistics. All-atom Clashscore : 28.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.87 % Allowed : 34.02 % Favored : 60.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.41), residues: 381 helix: 0.30 (0.31), residues: 262 sheet: 0.08 (0.97), residues: 24 loop : -2.62 (0.58), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 328 HIS 0.004 0.001 HIS D 109 PHE 0.015 0.003 PHE D 113 TYR 0.025 0.003 TYR D 392 ARG 0.005 0.001 ARG D 347 Details of bonding type rmsd hydrogen bonds : bond 0.10420 ( 583) hydrogen bonds : angle 4.48249 ( 1165) covalent geometry : bond 0.00549 (16214) covalent geometry : angle 0.78446 (24589) Misc. bond : bond 0.00017 ( 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 83 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: D 130 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6866 (mpp) REVERT: D 136 TRP cc_start: 0.8517 (m100) cc_final: 0.7985 (m100) REVERT: D 155 MET cc_start: 0.9402 (mmt) cc_final: 0.8958 (mmt) REVERT: D 173 LYS cc_start: 0.9175 (ptpt) cc_final: 0.8450 (mptt) REVERT: D 214 MET cc_start: 0.8775 (mmm) cc_final: 0.8553 (mmm) REVERT: D 299 LYS cc_start: 0.8344 (pptt) cc_final: 0.8015 (mttm) REVERT: D 310 TRP cc_start: 0.7620 (OUTLIER) cc_final: 0.6713 (t60) outliers start: 20 outliers final: 14 residues processed: 80 average time/residue: 0.2590 time to fit residues: 30.9352 Evaluate side-chains 73 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP 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 116 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 221 PHE 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 339 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4038 r_free = 0.4038 target = 0.068975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.055659 restraints weight = 112048.540| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.62 r_work: 0.3607 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 1.0209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16215 Z= 0.237 Angle : 0.723 12.621 24589 Z= 0.368 Chirality : 0.038 0.213 3165 Planarity : 0.005 0.045 1084 Dihedral : 25.712 165.559 8721 Min Nonbonded Distance : 1.000 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.04 % Favored : 93.70 % Rotamer: Outliers : 7.04 % Allowed : 35.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.42), residues: 381 helix: 0.51 (0.31), residues: 261 sheet: 0.17 (0.96), residues: 24 loop : -2.68 (0.57), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 328 HIS 0.003 0.001 HIS D 291 PHE 0.016 0.003 PHE D 113 TYR 0.019 0.002 TYR D 392 ARG 0.004 0.001 ARG D 347 Details of bonding type rmsd hydrogen bonds : bond 0.09597 ( 583) hydrogen bonds : angle 4.35954 ( 1165) covalent geometry : bond 0.00438 (16214) covalent geometry : angle 0.72270 (24589) Misc. bond : bond 0.00011 ( 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 83 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7430 (p90) REVERT: D 130 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6842 (mpp) REVERT: D 136 TRP cc_start: 0.8489 (m100) cc_final: 0.7985 (m100) REVERT: D 155 MET cc_start: 0.9353 (mmt) cc_final: 0.8846 (mmt) REVERT: D 173 LYS cc_start: 0.9131 (ptpt) cc_final: 0.8393 (mptt) REVERT: D 214 MET cc_start: 0.8801 (mmm) cc_final: 0.8485 (mmm) REVERT: D 299 LYS cc_start: 0.8344 (pptt) cc_final: 0.8018 (mttm) REVERT: D 310 TRP cc_start: 0.7561 (OUTLIER) cc_final: 0.6644 (t60) REVERT: D 415 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8218 (t) REVERT: D 416 MET cc_start: 0.9201 (mmm) cc_final: 0.8940 (mmm) outliers start: 24 outliers final: 20 residues processed: 80 average time/residue: 0.2413 time to fit residues: 29.3711 Evaluate side-chains 80 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 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 151 HIS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 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 339 THR Chi-restraints excluded: chain D residue 359 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.068358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.055054 restraints weight = 112845.633| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.63 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 1.0308 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= 0.289 Angle : 0.775 13.865 24589 Z= 0.391 Chirality : 0.040 0.222 3165 Planarity : 0.005 0.047 1084 Dihedral : 25.754 166.212 8721 Min Nonbonded Distance : 1.002 Molprobity Statistics. All-atom Clashscore : 28.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.30 % Favored : 93.44 % Rotamer: Outliers : 7.33 % Allowed : 35.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.41), residues: 381 helix: 0.42 (0.31), residues: 261 sheet: 0.05 (0.96), residues: 24 loop : -2.71 (0.57), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 328 HIS 0.031 0.004 HIS D 43 PHE 0.017 0.003 PHE D 113 TYR 0.022 0.003 TYR D 392 ARG 0.004 0.001 ARG D 223 Details of bonding type rmsd hydrogen bonds : bond 0.10270 ( 583) hydrogen bonds : angle 4.40628 ( 1165) covalent geometry : bond 0.00536 (16214) covalent geometry : angle 0.77468 (24589) Misc. bond : bond 0.00020 ( 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 85 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7373 (p90) REVERT: D 130 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7023 (mpp) REVERT: D 136 TRP cc_start: 0.8524 (m100) cc_final: 0.7867 (m100) REVERT: D 155 MET cc_start: 0.9277 (mmt) cc_final: 0.8707 (mmt) REVERT: D 173 LYS cc_start: 0.9167 (ptpt) cc_final: 0.8437 (mptt) REVERT: D 214 MET cc_start: 0.8861 (mmm) cc_final: 0.8516 (mmm) REVERT: D 299 LYS cc_start: 0.8346 (pptt) cc_final: 0.8010 (mtmt) REVERT: D 310 TRP cc_start: 0.7536 (OUTLIER) cc_final: 0.6615 (t60) outliers start: 25 outliers final: 19 residues processed: 80 average time/residue: 0.2559 time to fit residues: 30.8870 Evaluate side-chains 80 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 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 167 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 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 339 THR Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 34 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 overall best weight: 9.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.065749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.052304 restraints weight = 115194.428| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.13 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 1.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 16215 Z= 0.504 Angle : 1.066 13.651 24589 Z= 0.528 Chirality : 0.053 0.269 3165 Planarity : 0.007 0.056 1084 Dihedral : 26.355 172.250 8721 Min Nonbonded Distance : 0.918 Molprobity Statistics. All-atom Clashscore : 45.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 7.33 % Allowed : 34.60 % Favored : 58.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.39), residues: 381 helix: -0.33 (0.30), residues: 259 sheet: -0.53 (1.07), residues: 14 loop : -2.71 (0.50), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 328 HIS 0.009 0.002 HIS D 43 PHE 0.032 0.004 PHE D 248 TYR 0.036 0.004 TYR D 392 ARG 0.010 0.001 ARG D 347 Details of bonding type rmsd hydrogen bonds : bond 0.14678 ( 583) hydrogen bonds : angle 5.05161 ( 1165) covalent geometry : bond 0.00934 (16214) covalent geometry : angle 1.06634 (24589) Misc. bond : bond 0.00051 ( 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 79 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: D 130 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7335 (mpp) REVERT: D 155 MET cc_start: 0.9315 (mmt) cc_final: 0.8982 (mmt) REVERT: D 172 ARG cc_start: 0.9424 (ttm-80) cc_final: 0.9016 (ttm170) REVERT: D 173 LYS cc_start: 0.9324 (ptpt) cc_final: 0.8726 (mptt) REVERT: D 214 MET cc_start: 0.8833 (mmm) cc_final: 0.8608 (mmm) REVERT: D 272 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.6437 (t80) REVERT: D 299 LYS cc_start: 0.8517 (pptt) cc_final: 0.8105 (mtmt) REVERT: D 310 TRP cc_start: 0.7737 (OUTLIER) cc_final: 0.6813 (t60) outliers start: 25 outliers final: 19 residues processed: 73 average time/residue: 0.2693 time to fit residues: 30.2312 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 : 0.865 ------------------------------------------------------------------------------- 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 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 130 MET Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 151 HIS 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 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 339 THR Chi-restraints excluded: chain D residue 375 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 18 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 = 0.067708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.054621 restraints weight = 113906.193| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.60 r_work: 0.3583 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 1.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16215 Z= 0.284 Angle : 0.802 14.052 24589 Z= 0.406 Chirality : 0.041 0.224 3165 Planarity : 0.006 0.046 1084 Dihedral : 25.981 166.827 8721 Min Nonbonded Distance : 1.004 Molprobity Statistics. All-atom Clashscore : 29.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.77 % Favored : 93.96 % Rotamer: Outliers : 7.33 % Allowed : 34.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.40), residues: 381 helix: -0.11 (0.30), residues: 264 sheet: -0.28 (0.93), residues: 24 loop : -2.62 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 328 HIS 0.010 0.002 HIS D 43 PHE 0.017 0.003 PHE D 113 TYR 0.023 0.003 TYR D 392 ARG 0.005 0.001 ARG D 347 Details of bonding type rmsd hydrogen bonds : bond 0.10549 ( 583) hydrogen bonds : angle 4.59613 ( 1165) covalent geometry : bond 0.00528 (16214) covalent geometry : angle 0.80227 (24589) Misc. bond : bond 0.00022 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7423.02 seconds wall clock time: 129 minutes 23.61 seconds (7763.61 seconds total)