Starting phenix.real_space_refine on Wed Jul 1 21:28:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws9_37802/07_2026/8ws9_37802.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws9_37802/07_2026/8ws9_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ws9_37802/07_2026/8ws9_37802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws9_37802/07_2026/8ws9_37802.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ws9_37802/07_2026/8ws9_37802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws9_37802/07_2026/8ws9_37802.map" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.07, per 1000 atoms: 0.37 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: 0.34 Conformation dependent library (CDL) restraints added in 73.9 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: 0.42 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: 0.40 Time building geometry restraints manager: 0.42 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=" C3' DG D -8 " pdb=" C2' DG D -8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+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=" C1' DC C 7 " pdb=" N1 DC C 7 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.48e+00 bond pdb=" C3' DC C 7 " pdb=" C2' DC C 7 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.69e+00 ... (remaining 3098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 3982 1.15 - 2.31: 343 2.31 - 3.46: 81 3.46 - 4.62: 17 4.62 - 5.77: 5 Bond angle restraints: 4428 Sorted by residual: angle pdb=" N3 DT D -9 " pdb=" C4 DT D -9 " pdb=" O4 DT D -9 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT D -1 " pdb=" C4 DT D -1 " pdb=" O4 DT D -1 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sigma weight residual 117.70 122.56 -4.86 1.20e+00 6.94e-01 1.64e+01 ... (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: 415 0.058 - 0.116: 75 0.116 - 0.174: 16 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: 3.910 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.370 Find NCS groups from input model: 0.010 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 3103 Z= 0.359 Angle : 0.762 5.769 4428 Z= 0.587 Chirality : 0.048 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 : 10.89 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG A 345 TYR 0.006 0.001 TYR A 265 PHE 0.005 0.001 PHE A 352 TRP 0.011 0.002 TRP A 304 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.36 ( 3103) covalent geometry : angle 0.76212 / 0.59 ( 4428) hydrogen bonds : bond 0.21555 / 15.67 ( 82) hydrogen bonds : angle 7.77513 / 5.25 ( 178) *********************** 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 : 0.081 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: 0.1428 time to fit residues: 4.9064 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 : 0.086 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 1 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.0370 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4482 r_free = 0.4482 target = 0.200366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.179145 restraints weight = 4805.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.183239 restraints weight = 2789.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.186227 restraints weight = 1860.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188341 restraints weight = 1358.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.189502 restraints weight = 1065.532| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3103 Z= 0.149 Angle : 0.611 6.430 4428 Z= 0.348 Chirality : 0.042 0.206 508 Planarity : 0.007 0.039 380 Dihedral : 26.649 167.470 958 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.41 % Favored : 91.15 % Rotamer: Outliers : 2.01 % Allowed : 12.56 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.56), residues: 226 helix: -1.22 (0.62), residues: 65 sheet: 0.38 (1.19), residues: 26 loop : -1.31 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 345 TYR 0.007 0.001 TYR A 87 PHE 0.009 0.002 PHE A 350 TRP 0.015 0.002 TRP A 304 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 ( 3103) covalent geometry : angle 0.61067 / 0.35 ( 4428) hydrogen bonds : bond 0.11093 / 7.23 ( 82) hydrogen bonds : angle 6.12437 / 4.44 ( 178) *********************** 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 : 0.082 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7696 (tppt) cc_final: 0.7409 (mmmm) REVERT: A 344 LYS cc_start: 0.8016 (ptmt) cc_final: 0.7769 (ptmt) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 0.1441 time to fit residues: 5.2667 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 : 0.080 ------------------------------------------------------------------------------- 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 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 25 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 135 HIS A 203 GLN ** 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 = 0.4396 r_free = 0.4396 target = 0.193362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.171612 restraints weight = 4671.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.175804 restraints weight = 2611.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.178920 restraints weight = 1701.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.181005 restraints weight = 1232.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.182250 restraints weight = 961.443| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.1663 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= 0.215 Angle : 0.666 6.291 4428 Z= 0.376 Chirality : 0.043 0.212 508 Planarity : 0.006 0.037 380 Dihedral : 26.745 167.955 954 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.18 % Favored : 89.38 % Rotamer: Outliers : 2.51 % Allowed : 14.57 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.56), residues: 226 helix: -1.53 (0.62), residues: 65 sheet: 0.85 (1.21), residues: 24 loop : -1.44 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 276 TYR 0.011 0.002 TYR A 317 PHE 0.007 0.002 PHE A 350 TRP 0.021 0.004 TRP A 304 HIS 0.003 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 ( 3103) covalent geometry : angle 0.66617 / 0.38 ( 4428) hydrogen bonds : bond 0.07630 / 4.59 ( 82) hydrogen bonds : angle 5.80403 / 4.43 ( 178) *********************** 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: 5 poor density : 30 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7818 (tppt) cc_final: 0.7428 (mmmm) REVERT: A 302 LYS cc_start: 0.7909 (ttpp) cc_final: 0.7317 (ttpp) REVERT: A 310 ARG cc_start: 0.6417 (mtm180) cc_final: 0.5943 (mtm180) outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 0.1517 time to fit residues: 5.5194 Evaluate side-chains 33 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.082 ------------------------------------------------------------------------------- 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 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4388 r_free = 0.4388 target = 0.192440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.171059 restraints weight = 4646.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.175036 restraints weight = 2597.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.177918 restraints weight = 1707.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.179851 restraints weight = 1245.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.181143 restraints weight = 988.983| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3103 Z= 0.189 Angle : 0.645 6.381 4428 Z= 0.362 Chirality : 0.042 0.209 508 Planarity : 0.006 0.039 380 Dihedral : 26.733 166.798 954 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % Rotamer: Outliers : 3.52 % Allowed : 13.57 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.57), residues: 226 helix: -1.47 (0.62), residues: 65 sheet: 1.31 (1.30), residues: 24 loop : -1.44 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 345 TYR 0.008 0.002 TYR A 199 PHE 0.007 0.002 PHE A 350 TRP 0.022 0.003 TRP A 304 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 ( 3103) covalent geometry : angle 0.64546 / 0.36 ( 4428) hydrogen bonds : bond 0.09125 / 5.65 ( 82) hydrogen bonds : angle 5.50023 / 4.20 ( 178) *********************** 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 32 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.088 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 30 average time/residue: 0.1084 time to fit residues: 3.7369 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 : 0.054 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4402 r_free = 0.4402 target = 0.193638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.172703 restraints weight = 4629.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.176618 restraints weight = 2617.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.179391 restraints weight = 1720.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.181265 restraints weight = 1265.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.182675 restraints weight = 1006.151| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.2159 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= 0.144 Angle : 0.598 6.157 4428 Z= 0.338 Chirality : 0.041 0.211 508 Planarity : 0.006 0.041 380 Dihedral : 26.678 166.729 954 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % Rotamer: Outliers : 2.01 % Allowed : 16.08 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.58), residues: 226 helix: -1.19 (0.61), residues: 65 sheet: 1.35 (1.31), residues: 24 loop : -1.34 (0.56), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 314 TYR 0.005 0.001 TYR A 265 PHE 0.006 0.001 PHE A 352 TRP 0.022 0.003 TRP A 304 HIS 0.001 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 3103) covalent geometry : angle 0.59826 / 0.34 ( 4428) hydrogen bonds : bond 0.08500 / 5.04 ( 82) hydrogen bonds : angle 5.15336 / 3.88 ( 178) *********************** 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 30 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.051 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.0967 time to fit residues: 3.2113 Evaluate side-chains 28 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.081 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.0670 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 21 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4412 r_free = 0.4412 target = 0.194538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.173191 restraints weight = 4651.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.177194 restraints weight = 2646.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.180079 restraints weight = 1743.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.182022 restraints weight = 1275.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.183521 restraints weight = 1007.469| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 0.2298 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 : 0.593 6.080 4428 Z= 0.334 Chirality : 0.041 0.211 508 Planarity : 0.006 0.042 380 Dihedral : 26.653 166.912 954 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.85 % Favored : 90.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.57), residues: 226 helix: -0.95 (0.63), residues: 65 sheet: 1.10 (1.27), residues: 24 loop : -1.30 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 314 TYR 0.004 0.001 TYR A 199 PHE 0.005 0.001 PHE A 352 TRP 0.024 0.003 TRP A 304 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 ( 3103) covalent geometry : angle 0.59256 / 0.33 ( 4428) hydrogen bonds : bond 0.09005 / 5.50 ( 82) hydrogen bonds : angle 4.94071 / 3.70 ( 178) *********************** 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 28 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7522 (mmmm) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.0959 time to fit residues: 2.9662 Evaluate side-chains 27 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.059 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4400 r_free = 0.4400 target = 0.193589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.171869 restraints weight = 4677.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.176059 restraints weight = 2583.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.179008 restraints weight = 1673.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.181097 restraints weight = 1210.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.182311 restraints weight = 951.372| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.2433 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= 0.159 Angle : 0.611 5.947 4428 Z= 0.343 Chirality : 0.041 0.212 508 Planarity : 0.006 0.039 380 Dihedral : 26.657 167.301 954 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % Rotamer: Outliers : 2.51 % Allowed : 19.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.57), residues: 226 helix: -0.93 (0.63), residues: 65 sheet: 0.81 (1.25), residues: 24 loop : -1.33 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 276 TYR 0.006 0.001 TYR A 199 PHE 0.006 0.001 PHE A 350 TRP 0.038 0.004 TRP A 318 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 ( 3103) covalent geometry : angle 0.61105 / 0.34 ( 4428) hydrogen bonds : bond 0.07921 / 4.92 ( 82) hydrogen bonds : angle 4.91429 / 3.73 ( 178) *********************** 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 31 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7508 (mmmm) outliers start: 5 outliers final: 3 residues processed: 28 average time/residue: 0.1020 time to fit residues: 3.3077 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 : 0.081 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.0370 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4414 r_free = 0.4414 target = 0.194777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.173736 restraints weight = 4725.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.177657 restraints weight = 2651.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.180619 restraints weight = 1732.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.182580 restraints weight = 1252.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.183808 restraints weight = 985.358| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.2565 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= 0.138 Angle : 0.587 6.382 4428 Z= 0.331 Chirality : 0.040 0.211 508 Planarity : 0.006 0.042 380 Dihedral : 26.596 167.123 954 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.57), residues: 226 helix: -0.74 (0.64), residues: 65 sheet: 0.78 (1.26), residues: 24 loop : -1.31 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 314 TYR 0.005 0.001 TYR A 87 PHE 0.005 0.001 PHE A 350 TRP 0.028 0.003 TRP A 318 HIS 0.001 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 3103) covalent geometry : angle 0.58728 / 0.33 ( 4428) hydrogen bonds : bond 0.07667 / 5.04 ( 82) hydrogen bonds : angle 4.69792 / 3.55 ( 178) *********************** 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 31 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7493 (mmmm) outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.0851 time to fit residues: 2.8663 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 : 0.079 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 0.0060 chunk 2 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4385 r_free = 0.4385 target = 0.192417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.170740 restraints weight = 4664.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.174836 restraints weight = 2593.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.177815 restraints weight = 1683.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.179892 restraints weight = 1220.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.180980 restraints weight = 955.648| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.2733 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= 0.174 Angle : 0.626 6.504 4428 Z= 0.351 Chirality : 0.041 0.213 508 Planarity : 0.006 0.038 380 Dihedral : 26.570 167.517 954 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.18 % Favored : 89.38 % Rotamer: Outliers : 2.51 % Allowed : 19.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.56), residues: 226 helix: -0.86 (0.63), residues: 65 sheet: 0.58 (1.23), residues: 24 loop : -1.36 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 276 TYR 0.006 0.001 TYR A 199 PHE 0.007 0.001 PHE A 113 TRP 0.027 0.003 TRP A 304 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 3103) covalent geometry : angle 0.62567 / 0.35 ( 4428) hydrogen bonds : bond 0.07056 / 4.67 ( 82) hydrogen bonds : angle 4.85197 / 3.70 ( 178) *********************** 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 32 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.054 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7482 (mmmm) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.1114 time to fit residues: 3.6521 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 : 0.081 ------------------------------------------------------------------------------- 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 349 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 12 optimal weight: 0.0470 chunk 7 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4393 r_free = 0.4393 target = 0.193061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.172002 restraints weight = 4615.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.175955 restraints weight = 2591.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.178871 restraints weight = 1701.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.180848 restraints weight = 1239.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.182042 restraints weight = 977.491| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.2865 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= 0.156 Angle : 0.604 6.745 4428 Z= 0.339 Chirality : 0.041 0.209 508 Planarity : 0.006 0.041 380 Dihedral : 26.544 166.985 953 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.57), residues: 226 helix: -0.78 (0.63), residues: 65 sheet: 0.79 (1.28), residues: 24 loop : -1.31 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 345 TYR 0.006 0.001 TYR A 199 PHE 0.006 0.001 PHE A 350 TRP 0.030 0.003 TRP A 304 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 ( 3103) covalent geometry : angle 0.60411 / 0.34 ( 4428) hydrogen bonds : bond 0.06922 / 4.66 ( 82) hydrogen bonds : angle 4.69166 / 3.54 ( 178) ********************** 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 : 0.078 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7472 (mmmm) outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.1057 time to fit residues: 3.5364 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 : 0.083 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 4 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 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 = 0.4380 r_free = 0.4380 target = 0.191952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.170672 restraints weight = 4655.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.174685 restraints weight = 2604.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.177667 restraints weight = 1697.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.179422 restraints weight = 1225.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.181053 restraints weight = 977.565| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.3011 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= 0.174 Angle : 0.623 6.565 4428 Z= 0.349 Chirality : 0.041 0.212 508 Planarity : 0.006 0.039 380 Dihedral : 26.519 167.271 953 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.06 % Favored : 88.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.57), residues: 226 helix: -0.83 (0.64), residues: 65 sheet: 0.66 (1.23), residues: 24 loop : -1.27 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 276 TYR 0.006 0.001 TYR A 199 PHE 0.007 0.001 PHE A 113 TRP 0.031 0.004 TRP A 304 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 ( 3103) covalent geometry : angle 0.62256 / 0.35 ( 4428) hydrogen bonds : bond 0.06765 / 4.53 ( 82) hydrogen bonds : angle 4.78633 / 3.64 ( 178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 780.81 seconds wall clock time: 14 minutes 6.09 seconds (846.09 seconds total)