Starting phenix.real_space_refine on Fri May 9 15:35:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws9_37802/05_2025/8ws9_37802.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws9_37802/05_2025/8ws9_37802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ws9_37802/05_2025/8ws9_37802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws9_37802/05_2025/8ws9_37802.map" model { file = "/net/cci-nas-00/data/ceres_data/8ws9_37802/05_2025/8ws9_37802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws9_37802/05_2025/8ws9_37802.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 51 5.49 5 S 3 5.16 5 C 1696 2.51 5 N 528 2.21 5 O 653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 2931 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1869 Classifications: {'peptide': 234} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 21, 'TRANS': 212} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 545 Classifications: {'RNA': 26} Modifications used: {'rna2p_pyr': 5, 'rna3p_pur': 9, 'rna3p_pyr': 12} Link IDs: {'rna2p': 5, 'rna3p': 20} Chain: "C" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 294 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 223 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 3.48, per 1000 atoms: 1.19 Number of scatterers: 2931 At special positions: 0 Unit cell: (60.72, 76.56, 91.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 P 51 15.00 O 653 8.00 N 528 7.00 C 1696 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: 0.97 Conformation dependent library (CDL) restraints added in 185.2 milliseconds 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 426 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 1 sheets defined 32.1% alpha, 10.3% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 88 removed outlier: 4.636A pdb=" N GLY A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.705A pdb=" N ARG A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.505A pdb=" N THR A 349 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN A 64 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 296 " --> pdb=" O MET A 307 " (cutoff:3.500A) 52 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 677 1.33 - 1.45: 871 1.45 - 1.57: 1452 1.57 - 1.69: 99 1.69 - 1.81: 4 Bond restraints: 3103 Sorted by residual: bond pdb=" CA ARG A 70 " pdb=" C ARG A 70 " ideal model delta sigma weight residual 1.517 1.557 -0.041 1.02e-02 9.61e+03 1.58e+01 bond pdb=" C ARG A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.332 1.373 -0.041 1.33e-02 5.65e+03 9.63e+00 bond pdb=" CA SER A 336 " pdb=" C SER A 336 " ideal model delta sigma weight residual 1.525 1.497 0.028 1.28e-02 6.10e+03 4.70e+00 bond pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 1.469 1.445 0.024 1.28e-02 6.10e+03 3.43e+00 bond pdb=" N ASN A 99 " pdb=" CA ASN A 99 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.29e-02 6.01e+03 2.47e+00 ... (remaining 3098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 4046 1.15 - 2.31: 295 2.31 - 3.46: 63 3.46 - 4.62: 19 4.62 - 5.77: 5 Bond angle restraints: 4428 Sorted by residual: angle pdb=" N LYS A 302 " pdb=" CA LYS A 302 " pdb=" C LYS A 302 " ideal model delta sigma weight residual 114.75 110.65 4.10 1.26e+00 6.30e-01 1.06e+01 angle pdb=" C3' C B -8 " pdb=" O3' C B -8 " pdb=" P G B -7 " ideal model delta sigma weight residual 120.20 124.88 -4.68 1.50e+00 4.44e-01 9.72e+00 angle pdb=" N SER A 105 " pdb=" CA SER A 105 " pdb=" C SER A 105 " ideal model delta sigma weight residual 110.24 114.76 -4.52 1.47e+00 4.63e-01 9.45e+00 angle pdb=" N ASN A 130 " pdb=" CA ASN A 130 " pdb=" C ASN A 130 " ideal model delta sigma weight residual 113.38 109.63 3.75 1.23e+00 6.61e-01 9.31e+00 angle pdb=" CA ARG A 70 " pdb=" C ARG A 70 " pdb=" O ARG A 70 " ideal model delta sigma weight residual 120.94 117.98 2.96 1.01e+00 9.80e-01 8.61e+00 ... (remaining 4423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 1622 34.22 - 68.44: 201 68.44 - 102.66: 13 102.66 - 136.88: 1 136.88 - 171.10: 2 Dihedral angle restraints: 1839 sinusoidal: 1174 harmonic: 665 Sorted by residual: dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual 232.00 72.61 159.39 1 1.70e+01 3.46e-03 6.43e+01 dihedral pdb=" C4' DG D -8 " pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " pdb=" P DG D -7 " ideal model delta sinusoidal sigma weight residual -140.00 31.10 -171.10 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' C B -8 " pdb=" C3' C B -8 " pdb=" O3' C B -8 " pdb=" P G B -7 " ideal model delta sinusoidal sigma weight residual -110.00 15.71 -125.71 1 3.50e+01 8.16e-04 1.24e+01 ... (remaining 1836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 433 0.058 - 0.116: 60 0.116 - 0.174: 13 0.174 - 0.232: 1 0.232 - 0.290: 1 Chirality restraints: 508 Sorted by residual: chirality pdb=" CA ASN A 99 " pdb=" N ASN A 99 " pdb=" C ASN A 99 " pdb=" CB ASN A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ARG A 345 " pdb=" N ARG A 345 " pdb=" C ARG A 345 " pdb=" CB ARG A 345 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA ARG A 70 " pdb=" N ARG A 70 " pdb=" C ARG A 70 " pdb=" CB ARG A 70 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 505 not shown) Planarity restraints: 380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 75 " 0.050 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO A 76 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 71 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C PRO A 71 " 0.047 2.00e-02 2.50e+03 pdb=" O PRO A 71 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 72 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B -1 " -0.024 2.00e-02 2.50e+03 1.21e-02 4.01e+00 pdb=" N9 A B -1 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A B -1 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B -1 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B -1 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A B -1 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B -1 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B -1 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A B -1 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A B -1 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B -1 " -0.001 2.00e-02 2.50e+03 ... (remaining 377 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 577 2.78 - 3.31: 2625 3.31 - 3.84: 5096 3.84 - 4.37: 5917 4.37 - 4.90: 8839 Nonbonded interactions: 23054 Sorted by model distance: nonbonded pdb=" O TYR A 317 " pdb=" N2 G B -20 " model vdw 2.245 3.120 nonbonded pdb=" NH2 ARG A 260 " pdb=" OP2 U B -17 " model vdw 2.307 3.120 nonbonded pdb=" ND2 ASN A 195 " pdb=" O2' C B 4 " model vdw 2.309 3.120 nonbonded pdb=" NZ LYS A 259 " pdb=" OP2 A B -3 " model vdw 2.330 3.120 nonbonded pdb=" ND2 ASN A 138 " pdb=" OP2 DG C -2 " model vdw 2.348 3.120 ... (remaining 23049 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.660 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 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 : 0.004 0.073 3103 Z= 0.223 Angle : 0.718 5.769 4428 Z= 0.437 Chirality : 0.045 0.290 508 Planarity : 0.007 0.075 380 Dihedral : 23.810 171.102 1413 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.18 % Favored : 89.38 % Rotamer: Outliers : 4.02 % Allowed : 2.51 % Favored : 93.47 % 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: -1.96 (0.54), residues: 226 helix: -1.71 (0.59), residues: 62 sheet: -0.15 (1.09), residues: 24 loop : -1.33 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 304 HIS 0.001 0.000 HIS A 121 PHE 0.005 0.001 PHE A 352 TYR 0.006 0.001 TYR A 265 ARG 0.004 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.21555 ( 82) hydrogen bonds : angle 7.77513 ( 178) covalent geometry : bond 0.00395 ( 3103) covalent geometry : angle 0.71790 ( 4428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7382 (mmmm) REVERT: A 130 ASN cc_start: 0.6527 (m-40) cc_final: 0.6259 (m-40) REVERT: A 310 ARG cc_start: 0.6445 (mtm180) cc_final: 0.6082 (mtm180) outliers start: 8 outliers final: 3 residues processed: 31 average time/residue: 0.3407 time to fit residues: 11.7018 Evaluate side-chains 29 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 120 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.0570 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 135 HIS ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.199092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.177604 restraints weight = 4733.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.181795 restraints weight = 2743.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.184703 restraints weight = 1831.193| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5727 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3103 Z= 0.162 Angle : 0.637 6.330 4428 Z= 0.340 Chirality : 0.038 0.144 508 Planarity : 0.006 0.042 380 Dihedral : 26.513 170.657 958 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % Rotamer: Outliers : 2.01 % Allowed : 10.55 % Favored : 87.44 % 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: -1.58 (0.57), residues: 226 helix: -1.17 (0.63), residues: 65 sheet: 0.44 (1.20), residues: 26 loop : -1.30 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 304 HIS 0.002 0.001 HIS A 121 PHE 0.005 0.001 PHE A 335 TYR 0.007 0.001 TYR A 87 ARG 0.003 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.10326 ( 82) hydrogen bonds : angle 5.95891 ( 178) covalent geometry : bond 0.00351 ( 3103) covalent geometry : angle 0.63721 ( 4428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.262 Fit side-chains REVERT: A 62 LYS cc_start: 0.7702 (tppt) cc_final: 0.7444 (mmmm) REVERT: A 344 LYS cc_start: 0.7990 (ptmt) cc_final: 0.7749 (ptmt) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 0.3209 time to fit residues: 11.8014 Evaluate side-chains 34 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 120 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 4 optimal weight: 0.0060 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 203 GLN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.195454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.173915 restraints weight = 4621.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.178019 restraints weight = 2592.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.180949 restraints weight = 1710.711| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5767 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3103 Z= 0.159 Angle : 0.628 6.006 4428 Z= 0.332 Chirality : 0.037 0.139 508 Planarity : 0.006 0.043 380 Dihedral : 26.571 171.010 954 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.18 % Favored : 89.38 % Rotamer: Outliers : 2.01 % Allowed : 13.07 % Favored : 84.92 % 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: -1.47 (0.57), residues: 226 helix: -1.04 (0.64), residues: 65 sheet: 1.13 (1.23), residues: 24 loop : -1.37 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 304 HIS 0.002 0.001 HIS A 121 PHE 0.006 0.001 PHE A 350 TYR 0.006 0.001 TYR A 87 ARG 0.003 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.08851 ( 82) hydrogen bonds : angle 5.31797 ( 178) covalent geometry : bond 0.00349 ( 3103) covalent geometry : angle 0.62847 ( 4428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7782 (tppt) cc_final: 0.7474 (mmmm) REVERT: A 302 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7480 (ttpp) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 0.3004 time to fit residues: 10.7338 Evaluate side-chains 31 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 120 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.0470 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 HIS ** A 258 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 = 0.4395 r_free = 0.4395 target = 0.193368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.172422 restraints weight = 4682.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.176362 restraints weight = 2646.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.179111 restraints weight = 1750.289| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3103 Z= 0.164 Angle : 0.639 6.041 4428 Z= 0.336 Chirality : 0.037 0.137 508 Planarity : 0.006 0.041 380 Dihedral : 26.517 171.351 954 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % Rotamer: Outliers : 3.52 % Allowed : 15.58 % Favored : 80.90 % 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: -1.36 (0.57), residues: 226 helix: -0.93 (0.63), residues: 65 sheet: 1.36 (1.28), residues: 24 loop : -1.35 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 304 HIS 0.002 0.001 HIS A 121 PHE 0.007 0.001 PHE A 350 TYR 0.006 0.001 TYR A 199 ARG 0.004 0.001 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.08321 ( 82) hydrogen bonds : angle 4.89746 ( 178) covalent geometry : bond 0.00359 ( 3103) covalent geometry : angle 0.63906 ( 4428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 310 ARG cc_start: 0.6351 (mtm180) cc_final: 0.5950 (mtm180) outliers start: 7 outliers final: 3 residues processed: 34 average time/residue: 0.2696 time to fit residues: 10.3440 Evaluate side-chains 32 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 120 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.0170 chunk 16 optimal weight: 0.5980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 258 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 = 0.4415 r_free = 0.4415 target = 0.194986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.174185 restraints weight = 4606.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.178131 restraints weight = 2627.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.180968 restraints weight = 1735.866| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3103 Z= 0.143 Angle : 0.617 5.842 4428 Z= 0.326 Chirality : 0.037 0.149 508 Planarity : 0.006 0.037 380 Dihedral : 26.446 172.106 954 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.41 % Favored : 91.15 % Rotamer: Outliers : 2.51 % Allowed : 17.59 % Favored : 79.90 % 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: -1.18 (0.58), residues: 226 helix: -0.63 (0.64), residues: 65 sheet: 1.35 (1.29), residues: 24 loop : -1.29 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 304 HIS 0.001 0.000 HIS A 121 PHE 0.005 0.001 PHE A 352 TYR 0.006 0.001 TYR A 317 ARG 0.005 0.001 ARG A 70 Details of bonding type rmsd hydrogen bonds : bond 0.07796 ( 82) hydrogen bonds : angle 4.62159 ( 178) covalent geometry : bond 0.00320 ( 3103) covalent geometry : angle 0.61747 ( 4428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 310 ARG cc_start: 0.6286 (mtm180) cc_final: 0.5967 (mtm180) outliers start: 5 outliers final: 3 residues processed: 30 average time/residue: 0.2372 time to fit residues: 8.1335 Evaluate side-chains 29 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 349 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 16 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 135 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.190098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.168843 restraints weight = 4635.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.172814 restraints weight = 2592.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.175809 restraints weight = 1698.212| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3103 Z= 0.214 Angle : 0.705 6.514 4428 Z= 0.367 Chirality : 0.039 0.159 508 Planarity : 0.006 0.039 380 Dihedral : 26.492 172.571 950 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.62 % Favored : 88.94 % Rotamer: Outliers : 2.51 % Allowed : 17.59 % Favored : 79.90 % 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: -1.52 (0.56), residues: 226 helix: -1.04 (0.63), residues: 65 sheet: 0.90 (1.25), residues: 24 loop : -1.38 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 318 HIS 0.002 0.001 HIS A 121 PHE 0.010 0.002 PHE A 113 TYR 0.008 0.001 TYR A 199 ARG 0.005 0.001 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.07259 ( 82) hydrogen bonds : angle 4.90286 ( 178) covalent geometry : bond 0.00464 ( 3103) covalent geometry : angle 0.70515 ( 4428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7765 (tppt) cc_final: 0.7486 (mmmm) REVERT: A 310 ARG cc_start: 0.6452 (mtm180) cc_final: 0.5935 (mtm180) outliers start: 5 outliers final: 4 residues processed: 30 average time/residue: 0.2836 time to fit residues: 9.5847 Evaluate side-chains 30 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 349 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 135 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.192613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.171495 restraints weight = 4743.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.175582 restraints weight = 2644.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.178476 restraints weight = 1724.860| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3103 Z= 0.164 Angle : 0.635 6.142 4428 Z= 0.333 Chirality : 0.037 0.146 508 Planarity : 0.006 0.037 380 Dihedral : 26.345 173.397 950 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.41 % Favored : 91.15 % Rotamer: Outliers : 3.02 % Allowed : 17.59 % Favored : 79.40 % 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: -1.26 (0.57), residues: 226 helix: -0.66 (0.65), residues: 65 sheet: 0.86 (1.25), residues: 24 loop : -1.26 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 304 HIS 0.001 0.000 HIS A 121 PHE 0.005 0.001 PHE A 350 TYR 0.007 0.001 TYR A 87 ARG 0.004 0.001 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.06984 ( 82) hydrogen bonds : angle 4.55845 ( 178) covalent geometry : bond 0.00362 ( 3103) covalent geometry : angle 0.63460 ( 4428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7740 (tppt) cc_final: 0.7474 (mmmm) REVERT: A 113 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.5849 (t80) REVERT: A 310 ARG cc_start: 0.6380 (mtm180) cc_final: 0.6017 (mtm180) outliers start: 6 outliers final: 3 residues processed: 31 average time/residue: 0.2917 time to fit residues: 10.1566 Evaluate side-chains 30 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 349 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 99 ASN A 135 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.189054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.167918 restraints weight = 4611.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.172104 restraints weight = 2566.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.174934 restraints weight = 1662.389| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3103 Z= 0.223 Angle : 0.706 6.758 4428 Z= 0.369 Chirality : 0.040 0.140 508 Planarity : 0.006 0.037 380 Dihedral : 26.419 173.474 949 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.50 % Favored : 88.05 % Rotamer: Outliers : 3.02 % Allowed : 18.59 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.57), residues: 226 helix: -1.10 (0.63), residues: 65 sheet: 0.48 (1.21), residues: 24 loop : -1.32 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP A 304 HIS 0.002 0.001 HIS A 121 PHE 0.008 0.001 PHE A 113 TYR 0.008 0.001 TYR A 199 ARG 0.004 0.001 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.07120 ( 82) hydrogen bonds : angle 4.82524 ( 178) covalent geometry : bond 0.00484 ( 3103) covalent geometry : angle 0.70600 ( 4428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7765 (tppt) cc_final: 0.7495 (mmmm) REVERT: A 113 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.5565 (t80) REVERT: A 302 LYS cc_start: 0.8037 (ttpp) cc_final: 0.7399 (ttpp) REVERT: A 310 ARG cc_start: 0.6463 (mtm180) cc_final: 0.6141 (mtm180) outliers start: 6 outliers final: 3 residues processed: 34 average time/residue: 0.3132 time to fit residues: 11.8385 Evaluate side-chains 35 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 349 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 130 ASN A 135 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.191263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.170121 restraints weight = 4615.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.174290 restraints weight = 2560.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.177128 restraints weight = 1659.992| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5825 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3103 Z= 0.177 Angle : 0.655 6.656 4428 Z= 0.344 Chirality : 0.038 0.140 508 Planarity : 0.006 0.039 380 Dihedral : 26.338 173.849 949 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.62 % Favored : 88.94 % Rotamer: Outliers : 3.52 % Allowed : 18.09 % Favored : 78.39 % 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: -1.31 (0.58), residues: 226 helix: -0.86 (0.64), residues: 65 sheet: 0.79 (1.28), residues: 24 loop : -1.20 (0.56), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP A 304 HIS 0.002 0.000 HIS A 121 PHE 0.006 0.001 PHE A 350 TYR 0.008 0.001 TYR A 87 ARG 0.004 0.001 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.06763 ( 82) hydrogen bonds : angle 4.61844 ( 178) covalent geometry : bond 0.00389 ( 3103) covalent geometry : angle 0.65455 ( 4428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.234 Fit side-chains REVERT: A 62 LYS cc_start: 0.7731 (tppt) cc_final: 0.7477 (mmmm) REVERT: A 113 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6021 (t80) REVERT: A 310 ARG cc_start: 0.6424 (mtm180) cc_final: 0.6165 (mtm180) outliers start: 7 outliers final: 4 residues processed: 32 average time/residue: 0.2665 time to fit residues: 9.6231 Evaluate side-chains 33 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 349 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 130 ASN A 135 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.191019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.169831 restraints weight = 4704.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.174082 restraints weight = 2632.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.176895 restraints weight = 1713.759| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3103 Z= 0.181 Angle : 0.658 6.792 4428 Z= 0.345 Chirality : 0.038 0.139 508 Planarity : 0.006 0.039 380 Dihedral : 26.339 174.019 949 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.62 % Favored : 88.94 % Rotamer: Outliers : 3.02 % Allowed : 18.09 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.30 (0.59), residues: 226 helix: -0.81 (0.63), residues: 65 sheet: 0.71 (1.28), residues: 24 loop : -1.20 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP A 304 HIS 0.002 0.000 HIS A 121 PHE 0.006 0.001 PHE A 350 TYR 0.008 0.001 TYR A 87 ARG 0.004 0.001 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.06710 ( 82) hydrogen bonds : angle 4.57266 ( 178) covalent geometry : bond 0.00400 ( 3103) covalent geometry : angle 0.65821 ( 4428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 452 Ramachandran restraints generated. 226 Oldfield, 0 Emsley, 226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.244 Fit side-chains REVERT: A 62 LYS cc_start: 0.7736 (tppt) cc_final: 0.7481 (mmmm) REVERT: A 113 PHE cc_start: 0.6826 (OUTLIER) cc_final: 0.5995 (t80) REVERT: A 310 ARG cc_start: 0.6440 (mtm180) cc_final: 0.6208 (mtm180) outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.2838 time to fit residues: 9.3049 Evaluate side-chains 30 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 349 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.0000 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 135 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.191416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.170474 restraints weight = 4641.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.174490 restraints weight = 2616.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.177367 restraints weight = 1715.682| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5820 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3103 Z= 0.174 Angle : 0.651 6.822 4428 Z= 0.341 Chirality : 0.038 0.144 508 Planarity : 0.006 0.039 380 Dihedral : 26.330 174.205 949 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.62 % Favored : 88.94 % Rotamer: Outliers : 3.52 % Allowed : 17.09 % Favored : 79.40 % 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: -1.28 (0.58), residues: 226 helix: -0.74 (0.63), residues: 65 sheet: 0.64 (1.26), residues: 24 loop : -1.20 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 304 HIS 0.002 0.000 HIS A 121 PHE 0.006 0.001 PHE A 350 TYR 0.008 0.001 TYR A 87 ARG 0.004 0.001 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.06542 ( 82) hydrogen bonds : angle 4.51191 ( 178) covalent geometry : bond 0.00384 ( 3103) covalent geometry : angle 0.65143 ( 4428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.65 seconds wall clock time: 26 minutes 9.28 seconds (1569.28 seconds total)