Starting phenix.real_space_refine on Sat Apr 26 17:58:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws9_37802/04_2025/8ws9_37802.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws9_37802/04_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_37802/04_2025/8ws9_37802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws9_37802/04_2025/8ws9_37802.map" model { file = "/net/cci-nas-00/data/ceres_data/8ws9_37802/04_2025/8ws9_37802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws9_37802/04_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): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 3.56, per 1000 atoms: 1.21 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: 1.07 Conformation dependent library (CDL) restraints added in 536.4 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: 1.38 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: 0.86 Time building geometry restraints manager: 1.24 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: 3.860 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.740 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.680 ------------------------------------------------------------------------------- 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 : 0.300 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: 0.3531 time to fit residues: 12.1384 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 : 0.218 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.177580 restraints weight = 4733.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.181779 restraints weight = 2745.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.184753 restraints weight = 1827.354| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5725 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 : 0.254 Fit side-chains REVERT: A 62 LYS cc_start: 0.7703 (tppt) cc_final: 0.7445 (mmmm) REVERT: A 344 LYS cc_start: 0.7992 (ptmt) cc_final: 0.7749 (ptmt) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 0.3170 time to fit residues: 11.6735 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 : 0.250 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 0.4980 chunk 4 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.0570 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.3098 ------------------------------------------------------------------------------- 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 = 0.4435 r_free = 0.4435 target = 0.196786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.175600 restraints weight = 4636.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.179665 restraints weight = 2637.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.182540 restraints weight = 1749.052| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5735 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3103 Z= 0.146 Angle : 0.614 5.949 4428 Z= 0.324 Chirality : 0.037 0.137 508 Planarity : 0.006 0.036 380 Dihedral : 26.544 171.067 954 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.73 % Favored : 89.82 % 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: -1.40 (0.57), residues: 226 helix: -0.91 (0.65), residues: 65 sheet: 1.08 (1.22), residues: 24 loop : -1.34 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 304 HIS 0.002 0.001 HIS A 121 PHE 0.005 0.001 PHE A 350 TYR 0.005 0.001 TYR A 87 ARG 0.003 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.09015 ( 82) hydrogen bonds : angle 5.21147 ( 178) covalent geometry : bond 0.00320 ( 3103) covalent geometry : angle 0.61415 ( 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 35 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7774 (tppt) cc_final: 0.7475 (mmmm) REVERT: A 302 LYS cc_start: 0.8062 (ttpp) cc_final: 0.7555 (ttpp) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 0.3125 time to fit residues: 11.5442 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 : 0.233 ------------------------------------------------------------------------------- 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: 0.5980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 chunk 6 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.0770 chunk 8 optimal weight: 1.9990 overall best weight: 0.3352 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.195140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.173832 restraints weight = 4674.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.177854 restraints weight = 2621.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.180723 restraints weight = 1721.998| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3103 Z= 0.147 Angle : 0.611 5.814 4428 Z= 0.322 Chirality : 0.036 0.135 508 Planarity : 0.006 0.040 380 Dihedral : 26.490 171.607 954 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.41 % Favored : 91.15 % Rotamer: Outliers : 3.02 % Allowed : 15.58 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.58), residues: 226 helix: -0.71 (0.64), residues: 65 sheet: 1.49 (1.29), residues: 24 loop : -1.31 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 304 HIS 0.001 0.001 HIS A 121 PHE 0.005 0.001 PHE A 350 TYR 0.005 0.001 TYR A 87 ARG 0.004 0.001 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.08357 ( 82) hydrogen bonds : angle 4.69757 ( 178) covalent geometry : bond 0.00326 ( 3103) covalent geometry : angle 0.61122 ( 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 34 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 ARG cc_start: 0.6290 (mtm180) cc_final: 0.5916 (mtm180) outliers start: 6 outliers final: 2 residues processed: 32 average time/residue: 0.2837 time to fit residues: 10.2228 Evaluate side-chains 29 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0470 chunk 1 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 12 optimal weight: 0.0970 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 overall best weight: 0.1714 ------------------------------------------------------------------------------- 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 = 0.4446 r_free = 0.4446 target = 0.197693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.176974 restraints weight = 4665.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.180858 restraints weight = 2672.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.183796 restraints weight = 1773.227| |-----------------------------------------------------------------------------| r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5685 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3103 Z= 0.127 Angle : 0.587 5.911 4428 Z= 0.309 Chirality : 0.036 0.136 508 Planarity : 0.006 0.038 380 Dihedral : 26.404 172.658 950 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.52 % Favored : 92.04 % Rotamer: Outliers : 2.01 % Allowed : 17.59 % Favored : 80.40 % 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: -0.92 (0.58), residues: 226 helix: -0.21 (0.66), residues: 65 sheet: 1.51 (1.30), residues: 24 loop : -1.25 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 304 HIS 0.000 0.000 HIS A 121 PHE 0.006 0.001 PHE A 352 TYR 0.010 0.001 TYR A 317 ARG 0.003 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.07922 ( 82) hydrogen bonds : angle 4.38648 ( 178) covalent geometry : bond 0.00289 ( 3103) covalent geometry : angle 0.58669 ( 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 33 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7735 (tppt) cc_final: 0.7405 (mmmm) REVERT: A 113 PHE cc_start: 0.6075 (OUTLIER) cc_final: 0.4853 (t80) REVERT: A 310 ARG cc_start: 0.6146 (mtm180) cc_final: 0.5861 (mtm180) outliers start: 4 outliers final: 1 residues processed: 32 average time/residue: 0.2805 time to fit residues: 10.2202 Evaluate side-chains 31 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 115 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.0060 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 16 optimal weight: 0.0570 overall best weight: 0.1312 ------------------------------------------------------------------------------- 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 = 0.4474 r_free = 0.4474 target = 0.199784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.178764 restraints weight = 4772.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.182815 restraints weight = 2707.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.185494 restraints weight = 1786.462| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3103 Z= 0.123 Angle : 0.565 6.070 4428 Z= 0.297 Chirality : 0.035 0.131 508 Planarity : 0.006 0.038 380 Dihedral : 26.285 173.661 949 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.96 % Favored : 91.59 % Rotamer: Outliers : 2.01 % Allowed : 17.09 % 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: -0.77 (0.58), residues: 226 helix: 0.28 (0.68), residues: 65 sheet: 0.15 (1.15), residues: 31 loop : -1.10 (0.55), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 304 HIS 0.001 0.000 HIS A 121 PHE 0.005 0.001 PHE A 352 TYR 0.009 0.001 TYR A 317 ARG 0.003 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.07371 ( 82) hydrogen bonds : angle 4.08207 ( 178) covalent geometry : bond 0.00281 ( 3103) covalent geometry : angle 0.56479 ( 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 32 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 113 PHE cc_start: 0.6026 (OUTLIER) cc_final: 0.4776 (t80) REVERT: A 272 ARG cc_start: 0.6104 (tpp80) cc_final: 0.5699 (tpp-160) REVERT: A 345 ARG cc_start: 0.7315 (mtp180) cc_final: 0.7084 (ptp-170) outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.2532 time to fit residues: 8.7051 Evaluate side-chains 30 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 0.0070 chunk 2 optimal weight: 0.4980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN 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 = 0.4425 r_free = 0.4425 target = 0.195875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.174473 restraints weight = 4759.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.178539 restraints weight = 2709.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.181407 restraints weight = 1797.992| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5727 moved from start: 0.3073 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= 0.146 Angle : 0.599 6.161 4428 Z= 0.314 Chirality : 0.036 0.136 508 Planarity : 0.006 0.036 380 Dihedral : 26.261 174.564 949 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.73 % Favored : 89.82 % 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: -0.77 (0.57), residues: 226 helix: 0.18 (0.65), residues: 65 sheet: 0.57 (1.23), residues: 26 loop : -1.10 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 304 HIS 0.001 0.000 HIS A 121 PHE 0.006 0.001 PHE A 113 TYR 0.005 0.001 TYR A 199 ARG 0.003 0.000 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.06872 ( 82) hydrogen bonds : angle 4.29609 ( 178) covalent geometry : bond 0.00327 ( 3103) covalent geometry : angle 0.59920 ( 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: 5 poor density : 27 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 PHE cc_start: 0.6446 (OUTLIER) cc_final: 0.5716 (t80) REVERT: A 310 ARG cc_start: 0.6232 (mtm180) cc_final: 0.5840 (mtm180) outliers start: 5 outliers final: 3 residues processed: 30 average time/residue: 0.3284 time to fit residues: 11.0186 Evaluate side-chains 31 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.0670 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.0000 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.3300 ------------------------------------------------------------------------------- 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 = 0.4431 r_free = 0.4431 target = 0.196255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.175152 restraints weight = 4678.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.179079 restraints weight = 2698.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.181965 restraints weight = 1801.210| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5715 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3103 Z= 0.141 Angle : 0.586 6.512 4428 Z= 0.308 Chirality : 0.035 0.133 508 Planarity : 0.005 0.036 380 Dihedral : 26.233 174.437 949 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % Rotamer: Outliers : 2.51 % Allowed : 18.09 % 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: -0.59 (0.59), residues: 226 helix: 0.46 (0.67), residues: 65 sheet: 0.66 (1.27), residues: 26 loop : -1.07 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 304 HIS 0.001 0.000 HIS A 121 PHE 0.004 0.001 PHE A 113 TYR 0.005 0.001 TYR A 87 ARG 0.002 0.000 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.06526 ( 82) hydrogen bonds : angle 4.23354 ( 178) covalent geometry : bond 0.00319 ( 3103) covalent geometry : angle 0.58603 ( 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 29 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 113 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.5666 (t80) REVERT: A 272 ARG cc_start: 0.6248 (tpp80) cc_final: 0.5721 (tpp-160) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.2874 time to fit residues: 8.7857 Evaluate side-chains 28 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 120 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: 2.9990 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.0020 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.190402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.168917 restraints weight = 4613.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.172997 restraints weight = 2625.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.175896 restraints weight = 1741.669| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.3459 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 : 0.698 6.828 4428 Z= 0.363 Chirality : 0.039 0.138 508 Planarity : 0.006 0.034 380 Dihedral : 26.318 174.764 949 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 2.51 % Allowed : 18.09 % 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: -1.02 (0.58), residues: 226 helix: -0.26 (0.65), residues: 65 sheet: 0.88 (1.28), residues: 24 loop : -1.20 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 318 HIS 0.002 0.001 HIS A 121 PHE 0.008 0.002 PHE A 113 TYR 0.008 0.002 TYR A 199 ARG 0.006 0.001 ARG A 276 Details of bonding type rmsd hydrogen bonds : bond 0.06829 ( 82) hydrogen bonds : angle 4.64713 ( 178) covalent geometry : bond 0.00484 ( 3103) covalent geometry : angle 0.69785 ( 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 31 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 113 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.5587 (t80) outliers start: 5 outliers final: 3 residues processed: 30 average time/residue: 0.2824 time to fit residues: 9.5377 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 : 0.216 ------------------------------------------------------------------------------- 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 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.0040 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.192519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.171129 restraints weight = 4715.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.175065 restraints weight = 2706.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.177989 restraints weight = 1799.225| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5801 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3103 Z= 0.169 Angle : 0.645 6.850 4428 Z= 0.336 Chirality : 0.037 0.139 508 Planarity : 0.006 0.034 380 Dihedral : 26.210 174.956 949 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.18 % Favored : 89.38 % Rotamer: Outliers : 2.51 % Allowed : 18.09 % 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: -0.90 (0.58), residues: 226 helix: -0.08 (0.65), residues: 65 sheet: 0.85 (1.28), residues: 24 loop : -1.15 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 304 HIS 0.001 0.000 HIS A 121 PHE 0.006 0.001 PHE A 113 TYR 0.007 0.001 TYR A 87 ARG 0.009 0.001 ARG A 70 Details of bonding type rmsd hydrogen bonds : bond 0.06204 ( 82) hydrogen bonds : angle 4.46171 ( 178) covalent geometry : bond 0.00377 ( 3103) covalent geometry : angle 0.64465 ( 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 30 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 113 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.5983 (t80) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.2659 time to fit residues: 8.7586 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 : 0.227 ------------------------------------------------------------------------------- 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 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.2980 chunk 9 optimal weight: 0.0370 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.0270 chunk 15 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.2516 ------------------------------------------------------------------------------- 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 = 0.4424 r_free = 0.4424 target = 0.195671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.174245 restraints weight = 4695.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.178251 restraints weight = 2692.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.181171 restraints weight = 1792.229| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5735 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3103 Z= 0.136 Angle : 0.594 6.921 4428 Z= 0.311 Chirality : 0.036 0.137 508 Planarity : 0.005 0.033 380 Dihedral : 26.160 175.378 949 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.85 % Favored : 90.71 % 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: -0.70 (0.58), residues: 226 helix: 0.42 (0.67), residues: 65 sheet: 0.71 (1.25), residues: 24 loop : -1.16 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 304 HIS 0.000 0.000 HIS A 121 PHE 0.004 0.001 PHE A 350 TYR 0.006 0.001 TYR A 87 ARG 0.002 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.05847 ( 82) hydrogen bonds : angle 4.21456 ( 178) covalent geometry : bond 0.00308 ( 3103) covalent geometry : angle 0.59352 ( 4428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1556.14 seconds wall clock time: 27 minutes 27.20 seconds (1647.20 seconds total)