Starting phenix.real_space_refine on Tue Aug 4 12:38:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws9_37802/08_2026/8ws9_37802.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws9_37802/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ws9_37802/08_2026/8ws9_37802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws9_37802/08_2026/8ws9_37802.map" model { file = "/net/cci-nas-00/data/ceres_data/8ws9_37802/08_2026/8ws9_37802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws9_37802/08_2026/8ws9_37802.cif" } 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-2.2rc3-6140/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: 0.32 Conformation dependent library (CDL) restraints added in 70.0 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: 0.51 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: 0.45 Time building geometry restraints manager: 0.39 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: 3905 1.15 - 2.31: 390 2.31 - 3.46: 111 3.46 - 4.62: 17 4.62 - 5.77: 5 Bond angle restraints: 4428 Sorted by residual: angle pdb=" C3' C B -8 " pdb=" O3' C B -8 " pdb=" P G B -7 " ideal model delta sigma weight residual 119.70 124.88 -5.18 1.20e+00 6.94e-01 1.86e+01 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=" O5' C B -19 " pdb=" C5' C B -19 " pdb=" C4' C B -19 " ideal model delta sigma weight residual 109.40 112.72 -3.32 8.00e-01 1.56e+00 1.72e+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 ... (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: 390 0.058 - 0.116: 81 0.116 - 0.174: 35 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: 5.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.680 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.730 ------------------------------------------------------------------------------- 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= 0.365 Angle : 0.818 5.769 4428 Z= 0.639 Chirality : 0.055 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 0.00465 / 0.36 ( 3103) covalent geometry : angle 0.81794 / 0.64 ( 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 : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7385 (mmmm) REVERT: A 130 ASN cc_start: 0.6527 (m-40) cc_final: 0.6245 (m-40) REVERT: A 135 HIS cc_start: 0.6507 (OUTLIER) cc_final: 0.6167 (m90) REVERT: A 310 ARG cc_start: 0.6445 (mtm180) cc_final: 0.6081 (mtm180) outliers start: 8 outliers final: 3 residues processed: 31 average time/residue: 0.0959 time to fit residues: 3.3105 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 : 0.077 ------------------------------------------------------------------------------- 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 135 HIS 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: 3.9990 chunk 13 optimal weight: 0.4980 chunk 1 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 0.3980 chunk 11 optimal weight: 0.3980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.199532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.178232 restraints weight = 4799.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.182375 restraints weight = 2781.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.185306 restraints weight = 1850.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.186998 restraints weight = 1357.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.188686 restraints weight = 1099.995| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3103 Z= 0.158 Angle : 0.631 6.235 4428 Z= 0.356 Chirality : 0.043 0.226 508 Planarity : 0.007 0.038 380 Dihedral : 26.718 168.079 960 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.85 % Favored : 90.71 % Rotamer: Outliers : 1.51 % Allowed : 12.06 % Favored : 86.43 % 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: -1.69 (0.56), residues: 226 helix: -1.33 (0.61), residues: 65 sheet: 0.34 (1.18), residues: 26 loop : -1.32 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 345 TYR 0.007 0.001 TYR A 87 PHE 0.010 0.002 PHE A 350 TRP 0.015 0.002 TRP A 304 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 ( 3103) covalent geometry : angle 0.63080 / 0.36 ( 4428) hydrogen bonds : bond 0.10907 / 7.05 ( 82) hydrogen bonds : angle 6.17432 / 4.45 ( 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 34 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.048 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7714 (tppt) cc_final: 0.7421 (mmmm) REVERT: A 344 LYS cc_start: 0.8010 (ptmt) cc_final: 0.7775 (ptmt) outliers start: 3 outliers final: 3 residues processed: 33 average time/residue: 0.0907 time to fit residues: 3.3412 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 : 0.076 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN 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 = 0.4393 r_free = 0.4393 target = 0.193349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.171850 restraints weight = 4664.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.175976 restraints weight = 2615.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.178972 restraints weight = 1710.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.181018 restraints weight = 1242.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.182525 restraints weight = 974.258| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3103 Z= 0.208 Angle : 0.679 6.292 4428 Z= 0.380 Chirality : 0.044 0.244 508 Planarity : 0.007 0.039 380 Dihedral : 26.741 168.082 954 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 2.51 % Allowed : 13.57 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.54 (0.61), residues: 65 sheet: 0.90 (1.22), 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 0.010 0.002 TYR A 317 PHE 0.007 0.002 PHE A 350 TRP 0.022 0.004 TRP A 304 HIS 0.003 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 ( 3103) covalent geometry : angle 0.67939 / 0.38 ( 4428) hydrogen bonds : bond 0.07836 / 4.60 ( 82) hydrogen bonds : angle 5.79983 / 4.42 ( 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 : 0.049 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7818 (tppt) cc_final: 0.7430 (mmmm) REVERT: A 135 HIS cc_start: 0.6219 (OUTLIER) cc_final: 0.5832 (m90) outliers start: 5 outliers final: 3 residues processed: 33 average time/residue: 0.1113 time to fit residues: 4.0375 Evaluate side-chains 34 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.047 ------------------------------------------------------------------------------- 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 135 HIS 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: 4.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.0270 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.193755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.172552 restraints weight = 4654.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.176627 restraints weight = 2601.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.179535 restraints weight = 1697.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.181550 restraints weight = 1226.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.182632 restraints weight = 960.027| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3103 Z= 0.164 Angle : 0.626 6.524 4428 Z= 0.351 Chirality : 0.042 0.261 508 Planarity : 0.006 0.045 380 Dihedral : 26.729 167.071 954 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % Rotamer: Outliers : 4.02 % Allowed : 13.57 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.64 (0.57), residues: 226 helix: -1.33 (0.62), residues: 65 sheet: 1.16 (1.27), residues: 24 loop : -1.42 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 314 TYR 0.006 0.001 TYR A 199 PHE 0.006 0.001 PHE A 350 TRP 0.020 0.003 TRP A 304 HIS 0.002 0.000 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 ( 3103) covalent geometry : angle 0.62581 / 0.35 ( 4428) hydrogen bonds : bond 0.09009 / 5.47 ( 82) hydrogen bonds : angle 5.48075 / 4.16 ( 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 34 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.088 Fit side-chains REVERT: A 135 HIS cc_start: 0.6225 (OUTLIER) cc_final: 0.5810 (m90) REVERT: A 277 LYS cc_start: 0.7698 (mmmm) cc_final: 0.7188 (ttmm) outliers start: 8 outliers final: 4 residues processed: 32 average time/residue: 0.0962 time to fit residues: 3.5403 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 : 0.048 ------------------------------------------------------------------------------- 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 135 HIS 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: 4.9990 chunk 17 optimal weight: 0.0470 chunk 12 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 2 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.195242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.174344 restraints weight = 4605.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.178220 restraints weight = 2596.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.181041 restraints weight = 1699.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.183000 restraints weight = 1248.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.184452 restraints weight = 986.907| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.2114 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= 0.142 Angle : 0.608 6.585 4428 Z= 0.342 Chirality : 0.042 0.258 508 Planarity : 0.006 0.045 380 Dihedral : 26.705 166.907 954 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % Rotamer: Outliers : 2.51 % Allowed : 15.58 % 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: -1.46 (0.58), residues: 226 helix: -1.11 (0.62), residues: 65 sheet: 1.25 (1.31), residues: 24 loop : -1.35 (0.55), 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 199 PHE 0.006 0.001 PHE A 352 TRP 0.021 0.003 TRP A 304 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 3103) covalent geometry : angle 0.60811 / 0.34 ( 4428) hydrogen bonds : bond 0.08934 / 5.27 ( 82) hydrogen bonds : angle 5.19489 / 3.91 ( 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 31 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.049 Fit side-chains REVERT: A 135 HIS cc_start: 0.6239 (OUTLIER) cc_final: 0.5826 (m90) outliers start: 5 outliers final: 3 residues processed: 30 average time/residue: 0.0901 time to fit residues: 3.0807 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 : 0.078 ------------------------------------------------------------------------------- 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 135 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.0020 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.193674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.172328 restraints weight = 4662.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.176288 restraints weight = 2626.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.179213 restraints weight = 1729.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.181137 restraints weight = 1261.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.182615 restraints weight = 999.228| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.2325 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= 0.170 Angle : 0.638 6.701 4428 Z= 0.354 Chirality : 0.043 0.259 508 Planarity : 0.006 0.043 380 Dihedral : 26.727 167.502 954 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 3.02 % Allowed : 16.08 % 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 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: -1.46 (0.57), residues: 226 helix: -1.08 (0.63), residues: 65 sheet: 1.09 (1.28), residues: 24 loop : -1.32 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 314 TYR 0.006 0.001 TYR A 199 PHE 0.006 0.001 PHE A 350 TRP 0.028 0.003 TRP A 318 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 3103) covalent geometry : angle 0.63751 / 0.35 ( 4428) hydrogen bonds : bond 0.08193 / 5.06 ( 82) hydrogen bonds : angle 5.11499 / 3.87 ( 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 32 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.058 Fit side-chains REVERT: A 62 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7516 (mmmm) REVERT: A 135 HIS cc_start: 0.6233 (OUTLIER) cc_final: 0.5784 (m90) REVERT: A 277 LYS cc_start: 0.7733 (mmmm) cc_final: 0.7173 (ttmm) outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 0.0686 time to fit residues: 2.4194 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 : 0.098 ------------------------------------------------------------------------------- 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 135 HIS Chi-restraints excluded: chain A residue 349 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.0570 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.0670 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** 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 = 0.4419 r_free = 0.4419 target = 0.195107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.173895 restraints weight = 4694.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.177906 restraints weight = 2648.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.180831 restraints weight = 1743.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.182691 restraints weight = 1270.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.184246 restraints weight = 1012.355| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.2456 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= 0.135 Angle : 0.599 6.576 4428 Z= 0.335 Chirality : 0.041 0.262 508 Planarity : 0.006 0.045 380 Dihedral : 26.646 166.902 954 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.85 % Favored : 90.71 % Rotamer: Outliers : 2.51 % Allowed : 17.09 % 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 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: -1.26 (0.58), residues: 226 helix: -0.86 (0.62), residues: 65 sheet: 1.12 (1.30), residues: 24 loop : -1.20 (0.56), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.006 0.001 TYR A 317 PHE 0.006 0.001 PHE A 352 TRP 0.030 0.003 TRP A 318 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 3103) covalent geometry : angle 0.59917 / 0.34 ( 4428) hydrogen bonds : bond 0.08089 / 5.25 ( 82) hydrogen bonds : angle 4.87004 / 3.66 ( 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 29 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.051 Fit side-chains REVERT: A 62 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7430 (mmmm) REVERT: A 135 HIS cc_start: 0.6226 (OUTLIER) cc_final: 0.5790 (m90) REVERT: A 277 LYS cc_start: 0.7734 (mmmm) cc_final: 0.7184 (ttmm) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.0657 time to fit residues: 2.1230 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 : 0.057 ------------------------------------------------------------------------------- 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 135 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.0050 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.0570 overall best weight: 0.3112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.195256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.173742 restraints weight = 4764.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.177848 restraints weight = 2668.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.180824 restraints weight = 1753.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.182867 restraints weight = 1279.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.184298 restraints weight = 1010.150| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.2591 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= 0.137 Angle : 0.591 6.488 4428 Z= 0.331 Chirality : 0.041 0.258 508 Planarity : 0.006 0.044 380 Dihedral : 26.573 167.389 954 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % Rotamer: Outliers : 2.01 % Allowed : 18.09 % 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: -1.15 (0.58), residues: 226 helix: -0.62 (0.64), residues: 65 sheet: 0.92 (1.29), residues: 24 loop : -1.16 (0.56), 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 199 PHE 0.006 0.001 PHE A 350 TRP 0.028 0.003 TRP A 318 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 0.59101 / 0.33 ( 4428) hydrogen bonds : bond 0.07606 / 5.02 ( 82) hydrogen bonds : angle 4.73381 / 3.57 ( 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 27 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.082 Fit side-chains REVERT: A 62 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7517 (mmmm) REVERT: A 135 HIS cc_start: 0.6248 (OUTLIER) cc_final: 0.5800 (m90) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.1008 time to fit residues: 2.9431 Evaluate side-chains 26 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.080 ------------------------------------------------------------------------------- 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 135 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.644 > 50:) chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** 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 = 0.4398 r_free = 0.4398 target = 0.193316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.171452 restraints weight = 4696.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.175635 restraints weight = 2633.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.178549 restraints weight = 1717.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.180701 restraints weight = 1263.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.182150 restraints weight = 991.776| |-----------------------------------------------------------------------------| r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3103 Z= 0.172 Angle : 0.632 6.461 4428 Z= 0.352 Chirality : 0.042 0.262 508 Planarity : 0.006 0.042 380 Dihedral : 26.573 167.649 953 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.19 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: -1.40 (0.57), residues: 226 helix: -0.81 (0.63), residues: 65 sheet: 0.51 (1.22), residues: 24 loop : -1.28 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 345 TYR 0.006 0.001 TYR A 199 PHE 0.008 0.001 PHE A 113 TRP 0.032 0.004 TRP A 304 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 3103) covalent geometry : angle 0.63207 / 0.35 ( 4428) hydrogen bonds : bond 0.06943 / 4.66 ( 82) hydrogen bonds : angle 4.85984 / 3.72 ( 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 : 0.049 Fit side-chains REVERT: A 62 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7474 (mmmm) REVERT: A 135 HIS cc_start: 0.6253 (OUTLIER) cc_final: 0.5799 (m90) REVERT: A 277 LYS cc_start: 0.7839 (mmmm) cc_final: 0.7448 (ttmm) REVERT: A 310 ARG cc_start: 0.6384 (mtm180) cc_final: 0.5893 (mtm180) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.0733 time to fit residues: 2.4220 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 : 0.048 ------------------------------------------------------------------------------- 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 135 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.0570 chunk 4 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.0870 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.194574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.173036 restraints weight = 4658.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.177139 restraints weight = 2618.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.180129 restraints weight = 1725.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.182207 restraints weight = 1263.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.183416 restraints weight = 991.438| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5924 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3103 Z= 0.146 Angle : 0.602 6.688 4428 Z= 0.337 Chirality : 0.041 0.269 508 Planarity : 0.006 0.044 380 Dihedral : 26.523 167.909 953 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.45 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: -1.25 (0.58), residues: 226 helix: -0.67 (0.64), residues: 65 sheet: 0.64 (1.22), residues: 24 loop : -1.20 (0.56), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 314 TYR 0.005 0.001 TYR A 199 PHE 0.005 0.001 PHE A 350 TRP 0.031 0.003 TRP A 304 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 ( 3103) covalent geometry : angle 0.60202 / 0.34 ( 4428) hydrogen bonds : bond 0.07005 / 4.72 ( 82) hydrogen bonds : angle 4.69000 / 3.57 ( 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 29 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.049 Fit side-chains REVERT: A 62 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7471 (mmmm) REVERT: A 135 HIS cc_start: 0.6267 (OUTLIER) cc_final: 0.5803 (m90) REVERT: A 277 LYS cc_start: 0.7847 (mmmm) cc_final: 0.7469 (ttmm) REVERT: A 310 ARG cc_start: 0.6327 (mtm180) cc_final: 0.5895 (mtm180) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.0664 time to fit residues: 2.0744 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 : 0.048 ------------------------------------------------------------------------------- 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 135 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.0170 chunk 4 optimal weight: 0.3980 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.0070 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** 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 = 0.4435 r_free = 0.4435 target = 0.196368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.174840 restraints weight = 4737.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.178883 restraints weight = 2666.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.181883 restraints weight = 1758.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.183645 restraints weight = 1287.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.185344 restraints weight = 1033.600| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5879 moved from start: 0.3078 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= 0.129 Angle : 0.574 6.745 4428 Z= 0.321 Chirality : 0.041 0.263 508 Planarity : 0.006 0.044 380 Dihedral : 26.434 168.175 953 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.29 % Favored : 90.27 % Rotamer: Outliers : 1.51 % Allowed : 20.10 % 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: -0.97 (0.59), residues: 226 helix: -0.23 (0.66), residues: 65 sheet: 0.87 (1.26), residues: 24 loop : -1.16 (0.56), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.007 0.001 TYR A 317 PHE 0.004 0.001 PHE A 350 TRP 0.028 0.003 TRP A 304 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 ( 3103) covalent geometry : angle 0.57411 / 0.32 ( 4428) hydrogen bonds : bond 0.07214 / 4.82 ( 82) hydrogen bonds : angle 4.44517 / 3.36 ( 178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 677.35 seconds wall clock time: 12 minutes 16.90 seconds (736.90 seconds total)