Starting phenix.real_space_refine on Fri May 16 18:39:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t2t_40987/05_2025/8t2t_40987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2t_40987/05_2025/8t2t_40987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t2t_40987/05_2025/8t2t_40987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2t_40987/05_2025/8t2t_40987.map" model { file = "/net/cci-nas-00/data/ceres_data/8t2t_40987/05_2025/8t2t_40987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2t_40987/05_2025/8t2t_40987.cif" } resolution = 3.0 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= 0.000 sd= 0.016 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 546 5.49 5 Mg 10 5.21 5 S 21 5.16 5 C 7226 2.51 5 N 2738 2.21 5 O 4335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14876 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 183 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 5} Chain: "B" Number of atoms: 11548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 11548 Classifications: {'RNA': 537} Modifications used: {'rna2p_pur': 37, 'rna2p_pyr': 11, 'rna3p_pur': 287, 'rna3p_pyr': 202} Link IDs: {'rna2p': 47, 'rna3p': 489} Chain breaks: 5 Chain: "D" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3133 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 10, 'TRANS': 376} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 9, 'NH4': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 9.12, per 1000 atoms: 0.61 Number of scatterers: 14876 At special positions: 0 Unit cell: (103.168, 133.12, 161.408, 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 546 15.00 Mg 10 11.99 O 4335 8.00 N 2738 7.00 C 7226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 472.2 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: 24 helices and 2 sheets defined 70.5% alpha, 5.7% beta 172 base pairs and 301 stacking pairs defined. Time for finding SS restraints: 7.03 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 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 100 through 106 removed outlier: 3.661A pdb=" N GLN D 105 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 131 removed outlier: 3.754A pdb=" N ALA D 122 " --> pdb=" O CYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.607A pdb=" N ASP D 147 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR D 148 " --> pdb=" O PHE D 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 148' Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.672A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.635A pdb=" N ILE D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 207 Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 234 through 252 Processing helix chain 'D' and resid 266 through 270 removed outlier: 3.803A 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: 3.555A pdb=" N LYS D 361 " --> pdb=" O TRP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 373 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 389 through 396 removed outlier: 4.161A pdb=" N LYS D 396 " --> pdb=" O TYR D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 404 through 412 Processing helix chain 'D' and resid 415 through 424 removed outlier: 3.607A pdb=" N TYR D 419 " --> pdb=" O SER D 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 220 through 223 removed outlier: 4.030A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS D 228 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 3.500A 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 279 183 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 416 hydrogen bonds 648 hydrogen bond angles 0 basepair planarities 172 basepair parallelities 301 stacking parallelities Total time for adding SS restraints: 7.38 Time building geometry restraints manager: 4.08 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: 2323 1.33 - 1.46: 7393 1.46 - 1.58: 5495 1.58 - 1.70: 1081 1.70 - 1.83: 35 Bond restraints: 16327 Sorted by residual: bond pdb=" CG1 ILE D 325 " pdb=" CD1 ILE D 325 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.27e+00 bond pdb=" C3' A B 204 " pdb=" O3' A B 204 " ideal model delta sigma weight residual 1.427 1.454 -0.027 1.50e-02 4.44e+03 3.16e+00 bond pdb=" CG LEU D 16 " pdb=" CD2 LEU D 16 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.09e+00 bond pdb=" CB CYS D 341 " pdb=" SG CYS D 341 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CA ASP D 265 " pdb=" CB ASP D 265 " ideal model delta sigma weight residual 1.532 1.558 -0.026 1.68e-02 3.54e+03 2.31e+00 ... (remaining 16322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 23986 2.39 - 4.79: 639 4.79 - 7.18: 103 7.18 - 9.57: 23 9.57 - 11.96: 5 Bond angle restraints: 24756 Sorted by residual: angle pdb=" C3' A B 204 " pdb=" O3' A B 204 " pdb=" P A B 205 " ideal model delta sigma weight residual 120.20 128.70 -8.50 1.50e+00 4.44e-01 3.21e+01 angle pdb=" O3' A B 204 " pdb=" C3' A B 204 " pdb=" C2' A B 204 " ideal model delta sigma weight residual 109.50 117.63 -8.13 1.50e+00 4.44e-01 2.94e+01 angle pdb=" O3' G B 123 " pdb=" C3' G B 123 " pdb=" C2' G B 123 " ideal model delta sigma weight residual 113.70 121.70 -8.00 1.50e+00 4.44e-01 2.84e+01 angle pdb=" C3' U B 89 " pdb=" O3' U B 89 " pdb=" P A B 90 " ideal model delta sigma weight residual 120.20 127.41 -7.21 1.50e+00 4.44e-01 2.31e+01 angle pdb=" CA ILE D 325 " pdb=" CB ILE D 325 " pdb=" CG1 ILE D 325 " ideal model delta sigma weight residual 110.40 118.14 -7.74 1.70e+00 3.46e-01 2.07e+01 ... (remaining 24751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 8873 35.49 - 70.98: 1308 70.98 - 106.48: 143 106.48 - 141.97: 4 141.97 - 177.46: 10 Dihedral angle restraints: 10338 sinusoidal: 9214 harmonic: 1124 Sorted by residual: dihedral pdb=" C4' C B 206 " pdb=" C3' C B 206 " pdb=" C2' C B 206 " pdb=" C1' C B 206 " ideal model delta sinusoidal sigma weight residual -35.00 29.06 -64.06 1 8.00e+00 1.56e-02 8.44e+01 dihedral pdb=" C5' C B 206 " pdb=" C4' C B 206 " pdb=" C3' C B 206 " pdb=" O3' C B 206 " ideal model delta sinusoidal sigma weight residual 147.00 84.54 62.46 1 8.00e+00 1.56e-02 8.06e+01 dihedral pdb=" O4' U B 2 " pdb=" C1' U B 2 " pdb=" N1 U B 2 " pdb=" C2 U B 2 " ideal model delta sinusoidal sigma weight residual 200.00 51.41 148.59 1 1.50e+01 4.44e-03 7.91e+01 ... (remaining 10335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2979 0.082 - 0.163: 192 0.163 - 0.245: 13 0.245 - 0.326: 3 0.326 - 0.408: 8 Chirality restraints: 3195 Sorted by residual: chirality pdb=" C1' A B 370 " pdb=" O4' A B 370 " pdb=" C2' A B 370 " pdb=" N9 A B 370 " both_signs ideal model delta sigma weight residual False 2.46 2.05 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" C3' C B 206 " pdb=" C4' C B 206 " pdb=" O3' C B 206 " pdb=" C2' C B 206 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.37 2.00e-01 2.50e+01 3.35e+00 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 -2.13 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 3192 not shown) Planarity restraints: 1089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 289 " 0.053 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO D 290 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 290 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 290 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 102 " -0.019 2.00e-02 2.50e+03 2.04e-02 8.35e+00 pdb=" CG TYR D 102 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 102 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR D 102 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR D 102 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR D 102 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR D 102 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 102 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 99 " -0.044 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO D 100 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " -0.038 5.00e-02 4.00e+02 ... (remaining 1086 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 142 2.57 - 3.15: 10129 3.15 - 3.73: 31199 3.73 - 4.32: 40526 4.32 - 4.90: 52341 Nonbonded interactions: 134337 Sorted by model distance: nonbonded pdb=" OP1 C B 581 " pdb="MG MG B 701 " model vdw 1.982 2.170 nonbonded pdb=" O2' U B 638 " pdb="MG MG B 701 " model vdw 2.005 2.170 nonbonded pdb=" OP2 G B 136 " pdb="MG MG B 709 " model vdw 2.013 2.170 nonbonded pdb=" OP2 G B 578 " pdb="MG MG B 708 " model vdw 2.020 2.170 nonbonded pdb=" O3' U B 638 " pdb="MG MG B 701 " model vdw 2.036 2.170 ... (remaining 134332 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: 3.000 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.490 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:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0531 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 16327 Z= 0.315 Angle : 0.975 11.964 24756 Z= 0.481 Chirality : 0.047 0.408 3195 Planarity : 0.007 0.081 1089 Dihedral : 24.844 177.461 9614 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.46 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 24.93 % Favored : 75.07 % 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: -1.78 (0.39), residues: 381 helix: -0.91 (0.29), residues: 244 sheet: -0.56 (1.06), residues: 28 loop : -1.59 (0.54), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 328 HIS 0.011 0.003 HIS D 151 PHE 0.027 0.003 PHE D 89 TYR 0.045 0.004 TYR D 102 ARG 0.014 0.001 ARG D 25 Details of bonding type rmsd hydrogen bonds : bond 0.16869 ( 599) hydrogen bonds : angle 7.10956 ( 1182) covalent geometry : bond 0.00588 (16327) covalent geometry : angle 0.97458 (24756) *********************** 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 76 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6329 (mttp) cc_final: 0.5684 (mtpp) REVERT: D 37 TYR cc_start: 0.4045 (p90) cc_final: 0.3790 (p90) REVERT: D 241 VAL cc_start: 0.2833 (t) cc_final: 0.2266 (p) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 1.3512 time to fit residues: 112.3408 Evaluate side-chains 35 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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: 1.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 96 GLN D 107 HIS D 121 GLN D 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.145058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.129934 restraints weight = 51605.781| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 1.50 r_work: 0.4295 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2203 moved from start: 0.7098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 16327 Z= 0.355 Angle : 1.292 11.847 24756 Z= 0.634 Chirality : 0.062 0.413 3195 Planarity : 0.009 0.096 1089 Dihedral : 26.109 176.881 8809 Min Nonbonded Distance : 1.259 Molprobity Statistics. All-atom Clashscore : 35.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.51 % Favored : 94.23 % Rotamer: Outliers : 8.50 % Allowed : 26.69 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -1.87 (0.37), residues: 381 helix: -0.75 (0.29), residues: 238 sheet: 0.91 (1.63), residues: 14 loop : -2.27 (0.46), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP D 328 HIS 0.009 0.004 HIS D 107 PHE 0.030 0.005 PHE D 145 TYR 0.024 0.003 TYR D 102 ARG 0.014 0.002 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.18261 ( 599) hydrogen bonds : angle 4.63691 ( 1182) covalent geometry : bond 0.00654 (16327) covalent geometry : angle 1.29235 (24756) *********************** 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 72 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 43 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6316 (mttp) cc_final: 0.5791 (tttm) REVERT: D 102 TYR cc_start: 0.2573 (OUTLIER) cc_final: 0.1190 (t80) REVERT: D 106 PHE cc_start: 0.1660 (OUTLIER) cc_final: 0.1347 (m-80) REVERT: D 236 MET cc_start: 0.4137 (mtt) cc_final: 0.0970 (ptm) REVERT: D 347 ARG cc_start: 0.3116 (OUTLIER) cc_final: 0.1655 (tpt170) REVERT: D 424 CYS cc_start: -0.2428 (OUTLIER) cc_final: -0.2759 (p) outliers start: 29 outliers final: 3 residues processed: 68 average time/residue: 0.9682 time to fit residues: 74.2365 Evaluate side-chains 41 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 424 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 42 optimal weight: 9.9990 chunk 59 optimal weight: 0.0050 chunk 91 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.143168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.127472 restraints weight = 50437.999| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 1.43 r_work: 0.4255 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2040 moved from start: 0.7344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16327 Z= 0.174 Angle : 0.734 8.508 24756 Z= 0.376 Chirality : 0.039 0.284 3195 Planarity : 0.006 0.082 1089 Dihedral : 25.414 178.266 8809 Min Nonbonded Distance : 1.120 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.94 % Favored : 95.80 % Rotamer: Outliers : 5.57 % Allowed : 31.09 % Favored : 63.34 % 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: -0.91 (0.40), residues: 381 helix: 0.24 (0.31), residues: 240 sheet: -0.57 (1.06), residues: 29 loop : -2.37 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 328 HIS 0.007 0.002 HIS D 284 PHE 0.034 0.003 PHE D 411 TYR 0.010 0.002 TYR D 385 ARG 0.007 0.001 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.08520 ( 599) hydrogen bonds : angle 3.62145 ( 1182) covalent geometry : bond 0.00315 (16327) covalent geometry : angle 0.73400 (24756) *********************** 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 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6444 (mttp) cc_final: 0.5882 (tttm) outliers start: 19 outliers final: 5 residues processed: 53 average time/residue: 1.0027 time to fit residues: 59.8952 Evaluate side-chains 39 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 395 ASN Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.151176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.137982 restraints weight = 57629.314| |-----------------------------------------------------------------------------| r_work (start): 0.4487 rms_B_bonded: 1.56 r_work: 0.4407 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3112 moved from start: 1.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.151 16327 Z= 0.317 Angle : 1.136 17.635 24756 Z= 0.574 Chirality : 0.058 0.414 3195 Planarity : 0.009 0.090 1089 Dihedral : 26.343 177.754 8809 Min Nonbonded Distance : 0.850 Molprobity Statistics. All-atom Clashscore : 34.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.51 % Favored : 94.23 % Rotamer: Outliers : 8.50 % Allowed : 31.09 % 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 (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: -2.28 (0.37), residues: 381 helix: -0.91 (0.29), residues: 239 sheet: -1.00 (1.80), residues: 10 loop : -2.53 (0.45), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP D 328 HIS 0.056 0.007 HIS D 43 PHE 0.026 0.005 PHE D 106 TYR 0.078 0.005 TYR D 420 ARG 0.011 0.002 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.16730 ( 599) hydrogen bonds : angle 4.52937 ( 1182) covalent geometry : bond 0.00590 (16327) covalent geometry : angle 1.13635 (24756) *********************** 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 76 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 47 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6748 (mttp) cc_final: 0.6191 (mtpp) REVERT: D 36 LYS cc_start: 0.6273 (mmtt) cc_final: 0.5948 (tptt) REVERT: D 37 TYR cc_start: 0.4268 (p90) cc_final: 0.4032 (p90) REVERT: D 41 LYS cc_start: 0.4366 (OUTLIER) cc_final: 0.3966 (tptt) REVERT: D 89 PHE cc_start: 0.8700 (t80) cc_final: 0.8422 (t80) REVERT: D 236 MET cc_start: 0.4705 (mtt) cc_final: 0.1253 (ptt) REVERT: D 242 MET cc_start: 0.6118 (mmm) cc_final: 0.5804 (mmp) REVERT: D 310 TRP cc_start: 0.0609 (OUTLIER) cc_final: 0.0353 (m-10) outliers start: 29 outliers final: 7 residues processed: 68 average time/residue: 1.0157 time to fit residues: 77.3521 Evaluate side-chains 45 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 395 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.153499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.140008 restraints weight = 60430.784| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 1.86 r_work: 0.4445 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5035 moved from start: 2.0478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.294 16327 Z= 0.591 Angle : 1.930 18.557 24756 Z= 0.939 Chirality : 0.093 0.714 3195 Planarity : 0.012 0.127 1089 Dihedral : 28.387 173.611 8809 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 55.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.97 % Favored : 89.76 % Rotamer: Outliers : 12.61 % Allowed : 28.45 % Favored : 58.94 % 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: -3.56 (0.36), residues: 381 helix: -1.71 (0.29), residues: 233 sheet: -2.63 (1.73), residues: 10 loop : -3.36 (0.41), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.009 TRP D 328 HIS 0.013 0.006 HIS D 151 PHE 0.068 0.007 PHE D 277 TYR 0.040 0.006 TYR D 316 ARG 0.018 0.002 ARG D 223 Details of bonding type rmsd hydrogen bonds : bond 0.28553 ( 599) hydrogen bonds : angle 6.19153 ( 1182) covalent geometry : bond 0.01113 (16327) covalent geometry : angle 1.93018 (24756) *********************** 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 108 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 65 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: -0.0148 (OUTLIER) cc_final: -0.0493 (tmt) REVERT: D 10 ILE cc_start: 0.6419 (OUTLIER) cc_final: 0.6078 (pp) REVERT: D 94 ILE cc_start: 0.8292 (tt) cc_final: 0.7939 (pp) REVERT: D 206 MET cc_start: 0.6723 (ttm) cc_final: 0.6125 (ttm) REVERT: D 236 MET cc_start: 0.4478 (OUTLIER) cc_final: 0.1223 (ptt) REVERT: D 328 TRP cc_start: 0.5943 (t60) cc_final: 0.5005 (t60) outliers start: 43 outliers final: 8 residues processed: 94 average time/residue: 1.0787 time to fit residues: 112.9955 Evaluate side-chains 53 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 9 GLN Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 268 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 244 ASN D 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.152027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.137760 restraints weight = 59256.666| |-----------------------------------------------------------------------------| r_work (start): 0.4515 rms_B_bonded: 1.70 r_work: 0.4435 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4868 moved from start: 2.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16327 Z= 0.280 Angle : 1.066 10.520 24756 Z= 0.532 Chirality : 0.056 0.512 3195 Planarity : 0.008 0.090 1089 Dihedral : 27.328 178.767 8809 Min Nonbonded Distance : 1.311 Molprobity Statistics. All-atom Clashscore : 27.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.77 % Favored : 93.96 % Rotamer: Outliers : 9.38 % Allowed : 36.66 % Favored : 53.96 % 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: -2.33 (0.38), residues: 381 helix: -0.75 (0.31), residues: 235 sheet: -2.59 (1.50), residues: 10 loop : -2.79 (0.46), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP D 310 HIS 0.008 0.002 HIS D 43 PHE 0.022 0.003 PHE D 277 TYR 0.020 0.003 TYR D 37 ARG 0.007 0.001 ARG D 88 Details of bonding type rmsd hydrogen bonds : bond 0.14759 ( 599) hydrogen bonds : angle 4.40540 ( 1182) covalent geometry : bond 0.00507 (16327) covalent geometry : angle 1.06581 (24756) *********************** 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 85 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 PHE cc_start: 0.8914 (t80) cc_final: 0.8531 (t80) REVERT: D 223 ARG cc_start: 0.7277 (ttp80) cc_final: 0.6887 (ttp80) REVERT: D 236 MET cc_start: 0.4144 (OUTLIER) cc_final: 0.2520 (ptt) outliers start: 32 outliers final: 8 residues processed: 74 average time/residue: 1.0214 time to fit residues: 85.1863 Evaluate side-chains 49 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 319 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 27 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 244 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 = 0.4609 r_free = 0.4609 target = 0.145476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.129310 restraints weight = 57634.246| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 1.88 r_work: 0.4296 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5825 moved from start: 2.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 16327 Z= 0.404 Angle : 1.407 13.963 24756 Z= 0.681 Chirality : 0.068 0.475 3195 Planarity : 0.010 0.111 1089 Dihedral : 27.719 178.218 8809 Min Nonbonded Distance : 0.863 Molprobity Statistics. All-atom Clashscore : 39.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 7.62 % Allowed : 37.24 % Favored : 55.13 % 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: -2.99 (0.38), residues: 381 helix: -1.33 (0.29), residues: 233 sheet: -2.21 (1.11), residues: 24 loop : -2.99 (0.51), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.007 TRP D 328 HIS 0.010 0.003 HIS D 284 PHE 0.032 0.004 PHE D 275 TYR 0.050 0.005 TYR D 272 ARG 0.040 0.002 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.19917 ( 599) hydrogen bonds : angle 5.13618 ( 1182) covalent geometry : bond 0.00755 (16327) covalent geometry : angle 1.40673 (24756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 PHE cc_start: 0.8987 (t80) cc_final: 0.8523 (t80) REVERT: D 102 TYR cc_start: 0.4075 (OUTLIER) cc_final: 0.3589 (t80) REVERT: D 157 LEU cc_start: 0.7915 (mt) cc_final: 0.7682 (pp) REVERT: D 160 ARG cc_start: 0.4226 (tmm-80) cc_final: 0.4004 (ptm-80) REVERT: D 236 MET cc_start: 0.4576 (OUTLIER) cc_final: 0.3035 (ptt) outliers start: 26 outliers final: 7 residues processed: 76 average time/residue: 1.1121 time to fit residues: 94.3177 Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 319 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.150588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.135298 restraints weight = 58649.253| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 1.64 r_work: 0.4396 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 2.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16327 Z= 0.181 Angle : 0.877 12.188 24756 Z= 0.430 Chirality : 0.045 0.403 3195 Planarity : 0.006 0.092 1089 Dihedral : 26.776 175.092 8809 Min Nonbonded Distance : 1.364 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.11 % Allowed : 41.64 % Favored : 54.25 % 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: -2.02 (0.39), residues: 381 helix: -0.66 (0.31), residues: 234 sheet: -2.33 (1.73), residues: 10 loop : -2.35 (0.49), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 328 HIS 0.002 0.001 HIS D 284 PHE 0.024 0.003 PHE D 277 TYR 0.022 0.002 TYR D 272 ARG 0.010 0.001 ARG D 326 Details of bonding type rmsd hydrogen bonds : bond 0.11601 ( 599) hydrogen bonds : angle 4.08786 ( 1182) covalent geometry : bond 0.00345 (16327) covalent geometry : angle 0.87735 (24756) *********************** 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 65 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: D 89 PHE cc_start: 0.8911 (t80) cc_final: 0.8499 (t80) REVERT: D 157 LEU cc_start: 0.7427 (mt) cc_final: 0.7121 (pp) REVERT: D 236 MET cc_start: 0.4108 (OUTLIER) cc_final: 0.3447 (ptt) outliers start: 14 outliers final: 6 residues processed: 59 average time/residue: 1.3311 time to fit residues: 86.3227 Evaluate side-chains 47 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 325 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 30 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.140660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.122841 restraints weight = 54473.999| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 1.91 r_work: 0.4210 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 2.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 16327 Z= 0.342 Angle : 1.157 16.007 24756 Z= 0.562 Chirality : 0.056 0.431 3195 Planarity : 0.008 0.102 1089 Dihedral : 27.198 179.134 8809 Min Nonbonded Distance : 0.923 Molprobity Statistics. All-atom Clashscore : 32.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.87 % Allowed : 41.94 % Favored : 52.20 % 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: -2.30 (0.39), residues: 381 helix: -1.00 (0.29), residues: 234 sheet: -0.56 (1.17), residues: 24 loop : -2.57 (0.53), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 328 HIS 0.007 0.002 HIS D 151 PHE 0.014 0.003 PHE D 248 TYR 0.028 0.004 TYR D 272 ARG 0.015 0.002 ARG D 217 Details of bonding type rmsd hydrogen bonds : bond 0.14190 ( 599) hydrogen bonds : angle 4.63098 ( 1182) covalent geometry : bond 0.00644 (16327) covalent geometry : angle 1.15661 (24756) *********************** 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 69 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: D 42 GLU cc_start: 0.6271 (mt-10) cc_final: 0.5762 (mp0) REVERT: D 89 PHE cc_start: 0.8933 (t80) cc_final: 0.8391 (t80) REVERT: D 101 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7467 (mp) REVERT: D 213 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7686 (tp30) REVERT: D 236 MET cc_start: 0.4686 (OUTLIER) cc_final: 0.3523 (ptt) REVERT: D 280 ASP cc_start: 0.6585 (OUTLIER) cc_final: 0.6229 (t0) outliers start: 20 outliers final: 7 residues processed: 59 average time/residue: 1.1498 time to fit residues: 75.3427 Evaluate side-chains 47 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 319 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 GLN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.135653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.116236 restraints weight = 53051.581| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 1.87 r_work: 0.4098 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 2.9431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.181 16327 Z= 0.345 Angle : 1.168 22.102 24756 Z= 0.559 Chirality : 0.054 0.429 3195 Planarity : 0.009 0.097 1089 Dihedral : 27.128 174.923 8809 Min Nonbonded Distance : 0.895 Molprobity Statistics. All-atom Clashscore : 26.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.52 % Allowed : 45.45 % Favored : 51.03 % 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: -2.59 (0.39), residues: 381 helix: -1.27 (0.30), residues: 234 sheet: -0.88 (1.07), residues: 24 loop : -2.52 (0.54), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP D 328 HIS 0.004 0.001 HIS D 284 PHE 0.048 0.005 PHE D 298 TYR 0.042 0.004 TYR D 392 ARG 0.020 0.002 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.14105 ( 599) hydrogen bonds : angle 5.05694 ( 1182) covalent geometry : bond 0.00670 (16327) covalent geometry : angle 1.16816 (24756) ********************** 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 64 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.732 Fit side-chains REVERT: D 42 GLU cc_start: 0.6284 (mt-10) cc_final: 0.5893 (mp0) REVERT: D 89 PHE cc_start: 0.8884 (t80) cc_final: 0.8256 (t80) REVERT: D 135 ASP cc_start: 0.7124 (p0) cc_final: 0.6274 (p0) REVERT: D 280 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6536 (t0) REVERT: D 381 ARG cc_start: 0.6755 (mtm110) cc_final: 0.5994 (ptt180) REVERT: D 389 ARG cc_start: 0.6155 (mtp180) cc_final: 0.5706 (mtp180) outliers start: 12 outliers final: 3 residues processed: 59 average time/residue: 1.1983 time to fit residues: 78.4078 Evaluate side-chains 47 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 280 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 HIS ** D 131 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 = 0.4418 r_free = 0.4418 target = 0.130141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.109447 restraints weight = 52060.691| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.73 r_work: 0.3992 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 3.0414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 16327 Z= 0.352 Angle : 1.147 16.522 24756 Z= 0.555 Chirality : 0.054 0.442 3195 Planarity : 0.010 0.125 1089 Dihedral : 26.988 179.889 8809 Min Nonbonded Distance : 0.924 Molprobity Statistics. All-atom Clashscore : 28.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.52 % Allowed : 46.63 % Favored : 49.85 % 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: -2.46 (0.39), residues: 381 helix: -1.09 (0.30), residues: 231 sheet: -0.22 (1.15), residues: 24 loop : -2.77 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP D 328 HIS 0.006 0.002 HIS D 284 PHE 0.019 0.003 PHE D 248 TYR 0.025 0.003 TYR D 272 ARG 0.018 0.002 ARG D 389 Details of bonding type rmsd hydrogen bonds : bond 0.13397 ( 599) hydrogen bonds : angle 4.91223 ( 1182) covalent geometry : bond 0.00663 (16327) covalent geometry : angle 1.14745 (24756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9315.12 seconds wall clock time: 161 minutes 26.92 seconds (9686.92 seconds total)