Starting phenix.real_space_refine on Fri Jun 13 06:21:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t2t_40987/06_2025/8t2t_40987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2t_40987/06_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_40987/06_2025/8t2t_40987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2t_40987/06_2025/8t2t_40987.map" model { file = "/net/cci-nas-00/data/ceres_data/8t2t_40987/06_2025/8t2t_40987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2t_40987/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.97, per 1000 atoms: 0.67 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: 3.90 Conformation dependent library (CDL) restraints added in 501.7 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: 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: 7.82 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: 7.86 Time building geometry restraints manager: 4.67 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: 3.900 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: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 43.270 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.850 ------------------------------------------------------------------------------- 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 : 0.737 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: 1.3490 time to fit residues: 112.4192 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 : 0.701 ------------------------------------------------------------------------------- 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 = 62)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.129881 restraints weight = 51605.889| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 1.48 r_work: 0.4295 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2206 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 4.63690 ( 1182) covalent geometry : bond 0.00654 (16327) covalent geometry : angle 1.29234 (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 : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6308 (mttp) cc_final: 0.5784 (tttm) REVERT: D 102 TYR cc_start: 0.2585 (OUTLIER) cc_final: 0.1204 (t80) REVERT: D 106 PHE cc_start: 0.1643 (OUTLIER) cc_final: 0.1332 (m-80) REVERT: D 236 MET cc_start: 0.4095 (mtt) cc_final: 0.0926 (ptm) REVERT: D 347 ARG cc_start: 0.3123 (OUTLIER) cc_final: 0.1658 (tpt170) REVERT: D 424 CYS cc_start: -0.2431 (OUTLIER) cc_final: -0.2762 (p) outliers start: 29 outliers final: 3 residues processed: 68 average time/residue: 1.0147 time to fit residues: 77.8374 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 : 0.684 ------------------------------------------------------------------------------- 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: 5.9990 chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 0.1980 chunk 91 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.146550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.132040 restraints weight = 54476.537| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 1.46 r_work: 0.4323 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2667 moved from start: 0.9604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 16327 Z= 0.281 Angle : 1.017 9.656 24756 Z= 0.509 Chirality : 0.052 0.362 3195 Planarity : 0.008 0.080 1089 Dihedral : 26.110 178.340 8809 Min Nonbonded Distance : 0.892 Molprobity Statistics. All-atom Clashscore : 25.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.99 % Favored : 94.75 % Rotamer: Outliers : 8.50 % Allowed : 28.45 % Favored : 63.05 % 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: -1.57 (0.39), residues: 381 helix: -0.31 (0.30), residues: 239 sheet: -0.18 (1.25), residues: 24 loop : -2.64 (0.48), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP D 328 HIS 0.012 0.002 HIS D 284 PHE 0.030 0.005 PHE D 411 TYR 0.019 0.003 TYR D 419 ARG 0.011 0.001 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.12673 ( 599) hydrogen bonds : angle 4.21301 ( 1182) covalent geometry : bond 0.00524 (16327) covalent geometry : angle 1.01672 (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 70 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 41 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: -0.0243 (OUTLIER) cc_final: -0.0557 (tmt) REVERT: D 27 LYS cc_start: 0.6656 (mttp) cc_final: 0.6094 (mtpp) REVERT: D 36 LYS cc_start: 0.6320 (mmtt) cc_final: 0.5890 (tptt) REVERT: D 102 TYR cc_start: 0.2784 (OUTLIER) cc_final: 0.1913 (t80) REVERT: D 253 LEU cc_start: 0.3150 (OUTLIER) cc_final: 0.2441 (tp) outliers start: 29 outliers final: 5 residues processed: 64 average time/residue: 1.0167 time to fit residues: 73.1966 Evaluate side-chains 38 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 102 TYR 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 253 LEU Chi-restraints excluded: chain D residue 395 ASN Chi-restraints excluded: chain D residue 401 VAL 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: 6.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 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 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 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 = 0.4707 r_free = 0.4707 target = 0.153668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.140942 restraints weight = 59250.103| |-----------------------------------------------------------------------------| r_work (start): 0.4534 rms_B_bonded: 1.63 r_work: 0.4455 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4026 moved from start: 1.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 16327 Z= 0.405 Angle : 1.445 12.759 24756 Z= 0.714 Chirality : 0.070 0.465 3195 Planarity : 0.010 0.094 1089 Dihedral : 27.282 176.928 8809 Min Nonbonded Distance : 0.854 Molprobity Statistics. All-atom Clashscore : 44.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.99 % Favored : 94.75 % Rotamer: Outliers : 12.02 % Allowed : 30.21 % Favored : 57.77 % 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: -2.89 (0.37), residues: 381 helix: -1.30 (0.29), residues: 236 sheet: -1.65 (1.44), residues: 14 loop : -2.95 (0.47), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.007 TRP D 328 HIS 0.020 0.004 HIS D 284 PHE 0.042 0.007 PHE D 298 TYR 0.024 0.003 TYR D 102 ARG 0.017 0.002 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.22505 ( 599) hydrogen bonds : angle 5.02763 ( 1182) covalent geometry : bond 0.00757 (16327) covalent geometry : angle 1.44469 (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 95 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 54 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: D 10 ILE cc_start: 0.5863 (OUTLIER) cc_final: 0.5525 (pp) REVERT: D 27 LYS cc_start: 0.6843 (mttp) cc_final: 0.6243 (mtpp) REVERT: D 89 PHE cc_start: 0.9015 (t80) cc_final: 0.8608 (t80) REVERT: D 101 ILE cc_start: 0.7248 (tp) cc_final: 0.6994 (tt) REVERT: D 102 TYR cc_start: 0.3346 (OUTLIER) cc_final: 0.2652 (t80) REVERT: D 236 MET cc_start: 0.3997 (OUTLIER) cc_final: 0.1836 (ptm) REVERT: D 242 MET cc_start: 0.7023 (mmm) cc_final: 0.6565 (mmp) REVERT: D 289 LYS cc_start: 0.7614 (pttt) cc_final: 0.7407 (ptmt) REVERT: D 316 TYR cc_start: 0.5132 (OUTLIER) cc_final: 0.4866 (t80) REVERT: D 347 ARG cc_start: 0.3227 (OUTLIER) cc_final: 0.2482 (tpp-160) REVERT: D 416 MET cc_start: 0.6300 (OUTLIER) cc_final: 0.6083 (mtt) outliers start: 41 outliers final: 9 residues processed: 82 average time/residue: 0.9844 time to fit residues: 90.8975 Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 416 MET 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: 5.9990 chunk 44 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 70 optimal weight: 0.0980 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 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 = 0.4685 r_free = 0.4685 target = 0.151070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.137204 restraints weight = 58711.022| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 1.63 r_work: 0.4423 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4658 moved from start: 1.8929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 16327 Z= 0.339 Angle : 1.242 17.692 24756 Z= 0.608 Chirality : 0.061 0.632 3195 Planarity : 0.009 0.106 1089 Dihedral : 27.223 173.778 8809 Min Nonbonded Distance : 0.905 Molprobity Statistics. All-atom Clashscore : 29.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.77 % Favored : 93.96 % Rotamer: Outliers : 8.50 % Allowed : 37.24 % 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: -2.28 (0.39), residues: 381 helix: -0.72 (0.31), residues: 236 sheet: -1.79 (1.04), residues: 14 loop : -2.87 (0.46), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.007 TRP D 328 HIS 0.004 0.001 HIS D 284 PHE 0.093 0.008 PHE D 221 TYR 0.028 0.005 TYR D 60 ARG 0.015 0.002 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.15427 ( 599) hydrogen bonds : angle 4.56405 ( 1182) covalent geometry : bond 0.00649 (16327) covalent geometry : angle 1.24164 (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 83 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 10 ILE cc_start: 0.6048 (OUTLIER) cc_final: 0.5811 (pp) REVERT: D 89 PHE cc_start: 0.8893 (t80) cc_final: 0.8329 (t80) REVERT: D 94 ILE cc_start: 0.8409 (tt) cc_final: 0.8062 (pp) REVERT: D 236 MET cc_start: 0.4789 (OUTLIER) cc_final: 0.1990 (ptt) REVERT: D 277 PHE cc_start: 0.2340 (OUTLIER) cc_final: 0.1940 (m-80) outliers start: 29 outliers final: 6 residues processed: 74 average time/residue: 0.8488 time to fit residues: 72.2680 Evaluate side-chains 51 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 102 TYR 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 277 PHE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN D 330 ASN D 395 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.149239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.135009 restraints weight = 57151.828| |-----------------------------------------------------------------------------| r_work (start): 0.4469 rms_B_bonded: 1.65 r_work: 0.4383 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5150 moved from start: 2.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 16327 Z= 0.314 Angle : 1.163 13.104 24756 Z= 0.568 Chirality : 0.056 0.368 3195 Planarity : 0.008 0.089 1089 Dihedral : 27.049 177.173 8809 Min Nonbonded Distance : 0.863 Molprobity Statistics. All-atom Clashscore : 30.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 8.21 % Allowed : 38.71 % Favored : 53.08 % Cbeta Deviations : 0.28 % 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: -2.17 (0.39), residues: 381 helix: -0.64 (0.30), residues: 235 sheet: -1.05 (1.06), residues: 24 loop : -2.99 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP D 328 HIS 0.016 0.003 HIS D 43 PHE 0.022 0.005 PHE D 89 TYR 0.041 0.004 TYR D 37 ARG 0.018 0.002 ARG D 301 Details of bonding type rmsd hydrogen bonds : bond 0.16733 ( 599) hydrogen bonds : angle 4.80956 ( 1182) covalent geometry : bond 0.00598 (16327) covalent geometry : angle 1.16329 (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: 28 poor density : 57 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 ILE cc_start: 0.6380 (OUTLIER) cc_final: 0.6081 (pp) REVERT: D 40 LEU cc_start: 0.2410 (tt) cc_final: 0.1538 (mt) REVERT: D 42 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6982 (mp0) REVERT: D 89 PHE cc_start: 0.8904 (t80) cc_final: 0.8695 (t80) REVERT: D 236 MET cc_start: 0.4480 (OUTLIER) cc_final: 0.3042 (ptt) outliers start: 28 outliers final: 12 residues processed: 77 average time/residue: 1.0346 time to fit residues: 89.6530 Evaluate side-chains 56 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 222 VAL 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 415 SER Chi-restraints excluded: chain D residue 417 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.146735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.131323 restraints weight = 57782.146| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 1.64 r_work: 0.4339 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5625 moved from start: 2.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.175 16327 Z= 0.284 Angle : 1.081 14.188 24756 Z= 0.528 Chirality : 0.052 0.444 3195 Planarity : 0.007 0.089 1089 Dihedral : 26.975 176.728 8809 Min Nonbonded Distance : 0.892 Molprobity Statistics. All-atom Clashscore : 25.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 6.16 % Allowed : 39.88 % 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: -2.26 (0.38), residues: 381 helix: -0.82 (0.29), residues: 235 sheet: -1.61 (1.03), residues: 24 loop : -2.64 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.009 TRP D 328 HIS 0.012 0.003 HIS D 43 PHE 0.036 0.005 PHE D 298 TYR 0.030 0.004 TYR D 420 ARG 0.015 0.002 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.13354 ( 599) hydrogen bonds : angle 4.36155 ( 1182) covalent geometry : bond 0.00572 (16327) covalent geometry : angle 1.08070 (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 78 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: 0.0336 (OUTLIER) cc_final: 0.0067 (ttt) REVERT: D 10 ILE cc_start: 0.6457 (OUTLIER) cc_final: 0.6167 (pp) REVERT: D 40 LEU cc_start: 0.2937 (tt) cc_final: 0.2717 (mt) REVERT: D 89 PHE cc_start: 0.9001 (t80) cc_final: 0.8678 (t80) REVERT: D 236 MET cc_start: 0.4167 (OUTLIER) cc_final: 0.3294 (ptt) REVERT: D 328 TRP cc_start: 0.8243 (OUTLIER) cc_final: 0.7812 (t60) REVERT: D 342 LYS cc_start: 0.5188 (OUTLIER) cc_final: 0.4970 (mptm) outliers start: 21 outliers final: 7 residues processed: 68 average time/residue: 1.4303 time to fit residues: 108.7139 Evaluate side-chains 55 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 131 ASN 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 285 GLN Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain D residue 418 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 64 optimal weight: 0.0050 chunk 27 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- 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 = 0.4636 r_free = 0.4636 target = 0.146755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.130978 restraints weight = 56961.776| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 1.60 r_work: 0.4338 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5713 moved from start: 2.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16327 Z= 0.201 Angle : 0.877 12.439 24756 Z= 0.430 Chirality : 0.044 0.383 3195 Planarity : 0.006 0.071 1089 Dihedral : 26.547 172.875 8809 Min Nonbonded Distance : 0.939 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.99 % Favored : 94.75 % Rotamer: Outliers : 5.57 % Allowed : 41.94 % Favored : 52.49 % 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: -1.70 (0.40), residues: 381 helix: -0.34 (0.31), residues: 236 sheet: -0.79 (1.11), residues: 24 loop : -2.68 (0.53), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP D 328 HIS 0.005 0.001 HIS D 284 PHE 0.026 0.003 PHE D 277 TYR 0.020 0.003 TYR D 278 ARG 0.013 0.001 ARG D 223 Details of bonding type rmsd hydrogen bonds : bond 0.11631 ( 599) hydrogen bonds : angle 3.98244 ( 1182) covalent geometry : bond 0.00374 (16327) covalent geometry : angle 0.87661 (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 74 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: D 7 MET cc_start: 0.0312 (OUTLIER) cc_final: -0.0034 (ttt) REVERT: D 10 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.6232 (pp) REVERT: D 40 LEU cc_start: 0.2598 (tt) cc_final: 0.2274 (mt) REVERT: D 89 PHE cc_start: 0.8887 (t80) cc_final: 0.8673 (t80) REVERT: D 129 ILE cc_start: 0.8830 (mm) cc_final: 0.8369 (mp) REVERT: D 236 MET cc_start: 0.3537 (OUTLIER) cc_final: 0.3282 (ptt) REVERT: D 242 MET cc_start: 0.7700 (tpt) cc_final: 0.7497 (tpt) REVERT: D 367 GLU cc_start: 0.4703 (tp30) cc_final: 0.4006 (tm-30) outliers start: 19 outliers final: 5 residues processed: 67 average time/residue: 1.2975 time to fit residues: 95.7390 Evaluate side-chains 50 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 37 TYR 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 Chi-restraints excluded: chain D residue 418 ASP 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: 1.9990 chunk 44 optimal weight: 10.0000 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 284 HIS ** 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 = 0.4570 r_free = 0.4570 target = 0.141692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.124784 restraints weight = 54136.037| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 1.69 r_work: 0.4231 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 2.6787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16327 Z= 0.268 Angle : 1.006 13.889 24756 Z= 0.495 Chirality : 0.048 0.397 3195 Planarity : 0.008 0.121 1089 Dihedral : 26.648 178.908 8809 Min Nonbonded Distance : 0.884 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.77 % Favored : 93.70 % Rotamer: Outliers : 5.87 % Allowed : 42.52 % Favored : 51.61 % 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: -2.11 (0.41), residues: 381 helix: -0.81 (0.32), residues: 236 sheet: -0.48 (1.34), residues: 14 loop : -2.47 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.007 TRP D 328 HIS 0.014 0.003 HIS D 284 PHE 0.047 0.005 PHE D 298 TYR 0.041 0.004 TYR D 420 ARG 0.014 0.002 ARG D 282 Details of bonding type rmsd hydrogen bonds : bond 0.12403 ( 599) hydrogen bonds : angle 4.59397 ( 1182) covalent geometry : bond 0.00499 (16327) covalent geometry : angle 1.00633 (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 78 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: 0.0582 (OUTLIER) cc_final: 0.0075 (ttt) REVERT: D 10 ILE cc_start: 0.6510 (OUTLIER) cc_final: 0.6217 (pp) REVERT: D 40 LEU cc_start: 0.3772 (OUTLIER) cc_final: 0.3360 (mp) REVERT: D 89 PHE cc_start: 0.8927 (t80) cc_final: 0.8563 (t80) REVERT: D 235 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6908 (mm-30) REVERT: D 236 MET cc_start: 0.4313 (OUTLIER) cc_final: 0.3375 (ptt) REVERT: D 242 MET cc_start: 0.7913 (tpt) cc_final: 0.7680 (tpt) REVERT: D 297 LYS cc_start: 0.6762 (pptt) cc_final: 0.6488 (pttt) REVERT: D 354 MET cc_start: 0.5927 (tmt) cc_final: 0.5682 (tmt) REVERT: D 388 LYS cc_start: 0.4272 (mptt) cc_final: 0.3666 (tptt) REVERT: D 389 ARG cc_start: 0.5719 (mtp180) cc_final: 0.5508 (mtp180) outliers start: 20 outliers final: 3 residues processed: 67 average time/residue: 1.3142 time to fit residues: 97.0719 Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 236 MET 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: 5.9990 chunk 17 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 314 ASN ** D 366 GLN ** 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 = 0.4432 r_free = 0.4432 target = 0.131312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.110895 restraints weight = 53112.812| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.82 r_work: 0.4009 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 2.9674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 16327 Z= 0.427 Angle : 1.276 17.482 24756 Z= 0.621 Chirality : 0.061 0.392 3195 Planarity : 0.010 0.138 1089 Dihedral : 27.085 174.224 8809 Min Nonbonded Distance : 1.234 Molprobity Statistics. All-atom Clashscore : 32.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 4.40 % Allowed : 44.57 % Favored : 51.03 % 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: -2.81 (0.39), residues: 381 helix: -1.21 (0.30), residues: 236 sheet: -1.09 (1.04), residues: 24 loop : -3.17 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.114 0.009 TRP D 328 HIS 0.012 0.003 HIS D 284 PHE 0.040 0.006 PHE D 298 TYR 0.046 0.005 TYR D 392 ARG 0.035 0.003 ARG D 282 Details of bonding type rmsd hydrogen bonds : bond 0.16199 ( 599) hydrogen bonds : angle 5.04193 ( 1182) covalent geometry : bond 0.00804 (16327) covalent geometry : angle 1.27590 (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 70 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.750 Fit side-chains REVERT: D 7 MET cc_start: 0.0991 (OUTLIER) cc_final: 0.0180 (ttt) REVERT: D 10 ILE cc_start: 0.6522 (OUTLIER) cc_final: 0.6245 (pt) REVERT: D 40 LEU cc_start: 0.4513 (OUTLIER) cc_final: 0.4110 (mt) REVERT: D 42 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6512 (mp0) REVERT: D 83 PRO cc_start: 0.3613 (Cg_endo) cc_final: 0.3198 (Cg_exo) REVERT: D 174 TYR cc_start: 0.2897 (OUTLIER) cc_final: 0.2164 (m-80) REVERT: D 202 LEU cc_start: 0.8724 (mt) cc_final: 0.8218 (pp) REVERT: D 206 MET cc_start: 0.8662 (ttm) cc_final: 0.8399 (tpp) REVERT: D 263 LYS cc_start: 0.7304 (mmpt) cc_final: 0.7018 (mmpt) REVERT: D 354 MET cc_start: 0.6936 (tmt) cc_final: 0.6672 (tmt) REVERT: D 389 ARG cc_start: 0.6515 (mtp180) cc_final: 0.6304 (mtp180) outliers start: 15 outliers final: 2 residues processed: 62 average time/residue: 1.5263 time to fit residues: 105.2764 Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 174 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 10 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 131 ASN ** D 405 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 = 0.4458 r_free = 0.4458 target = 0.132858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.112663 restraints weight = 52761.054| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 1.64 r_work: 0.4041 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 3.0206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16327 Z= 0.265 Angle : 0.957 13.730 24756 Z= 0.467 Chirality : 0.047 0.451 3195 Planarity : 0.007 0.077 1089 Dihedral : 26.475 171.017 8809 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 24.39 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.82 % Favored : 92.65 % Rotamer: Outliers : 4.11 % Allowed : 46.63 % Favored : 49.27 % 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: -2.10 (0.40), residues: 381 helix: -0.80 (0.31), residues: 236 sheet: -0.27 (1.11), residues: 24 loop : -2.65 (0.52), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.006 TRP D 328 HIS 0.004 0.001 HIS D 151 PHE 0.019 0.004 PHE D 106 TYR 0.032 0.004 TYR D 392 ARG 0.017 0.002 ARG D 223 Details of bonding type rmsd hydrogen bonds : bond 0.11254 ( 599) hydrogen bonds : angle 4.29071 ( 1182) covalent geometry : bond 0.00506 (16327) covalent geometry : angle 0.95679 (24756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10366.87 seconds wall clock time: 185 minutes 7.07 seconds (11107.07 seconds total)